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Master-Thesis-Analyses/Cortisol_ASQ_Total.R
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| #ITU_Thesis_Cort_ASQ | |
| ### Results of cortisol and ASQ total | |
| #30.06.2021 | |
| ### Data preparation #### | |
| #setwd("C:/Users/User/Desktop/Internship/RScripts/Cortisol/Master_Thesis") | |
| setwd("C:/Users/alici/Desktop/Git_Folder/ITU_cortisol_analyses/Master_Thesis") | |
| ##libraries | |
| library(dplyr) | |
| library(gtsummary) | |
| library(gdata) | |
| library(VGAM) | |
| library(rcompanion) | |
| library(tidyverse) | |
| library(broom) | |
| library(apaTables) | |
| library(tidyr) | |
| library(data.table) | |
| library(APAstyler) | |
| ## 1. cortisol data #### | |
| load("Rdata/ITU_combined_cortisol_dates_times_wide_format.Rdata") | |
| comments_to_be_excluded <- c(88,6,12,3,15,9999,7,16,45,5,34,17,57,67,99) | |
| wide_cort <- wide_cort[!(wide_cort$notes %in% comments_to_be_excluded),] | |
| cort_IDs <- unique(wide_cort$participantID) | |
| wide_cort <- subset(wide_cort, CAR_time_interval < 0.75) | |
| final_cort <- wide_cort %>% | |
| tidyr::pivot_wider( | |
| id_cols = c(participantID), | |
| names_from = c(pregstage), # Can accommodate more variables, if needed. | |
| values_from = c(9,21:23) | |
| ) | |
| wide_cort <- wide_cort %>% | |
| group_by(participantID) %>% | |
| mutate(Diur_Slope = mean(S1_slp_no_CAR, na.rm=T)) | |
| cors_CAR <- apa.cor.table(final_cort[,c("d_AUC_CAR_only_I","d_AUC_CAR_only_II","d_AUC_CAR_only_III")]) | |
| cors_DIUR <- apa.cor.table(final_cort[,c("cort_d_AUC_noCAR_I","cort_d_AUC_noCAR_II","cort_d_AUC_noCAR_III")]) | |
| cors_combined <- apa.cor.table(final_cort[,c("cort_d_AUC_I","cort_d_AUC_II","cort_d_AUC_III")]) | |
| load("Rdata/CAR_parameters.Rdata") | |
| CAR_parameters <- setDT(CAR_parameters, keep.rownames = "participantID_old") | |
| CAR_parameters <- separate(CAR_parameters, | |
| col = "participantID_old", | |
| into = c("participantID", NA), | |
| sep = "/I", | |
| extra = "drop") | |
| CAR_parameters <- CAR_parameters[,c("participantID", "hours_since_waking")] | |
| names(CAR_parameters)[2] <- "Morning_Slope" | |
| CAR_parameters <- subset(CAR_parameters, !(duplicated(CAR_parameters))) | |
| load("Rdata/Diurnal_parameters.Rdata") | |
| DIUR_parameters <- setDT(DIUR_parameters, keep.rownames = "participantID_old") | |
| DIUR_parameters <- separate(DIUR_parameters, | |
| col = "participantID_old", | |
| into = c("participantID", NA), | |
| sep = "/I", | |
| extra = "drop") | |
| DIUR_parameters <- DIUR_parameters[,c("participantID", "hours_since_waking")] | |
| names(DIUR_parameters)[2] <- "Diurnal_Slope" | |
| DIUR_parameters <- subset(DIUR_parameters, !(duplicated(DIUR_parameters))) | |
| ## add to cortisol dataframe | |
| final_cort <- left_join(final_cort, | |
| CAR_parameters) | |
| final_cort <- left_join(final_cort, | |
| DIUR_parameters) | |
| wide_cort_sub <- wide_cort[,c("participantID", "Diur_Slope")] | |
| wide_cort_sub <- subset(wide_cort_sub, !duplicated(wide_cort_sub)) | |
| final_cort <- left_join(final_cort, | |
| wide_cort_sub) | |
| ## 2. maternal well-being during pregnancy #### | |
| load("Rdata/processed_wellbeingduringpreg_completevars.Rdata") | |
| #for now only sleep, anxiety and CESD are included | |
| cols <- c("1", "2",grep("gestage", names(q_data_complete)), | |
| grep("GWdiff_cort_qclosest", names(q_data_complete)), | |
| grep("Cesd", names(q_data_complete)), | |
| #grep("puqe", names(q_data_complete)), | |
| grep("PSQI", names(q_data_complete)), | |
| #grep("ESS", names(q_data_complete)), | |
| grep("BAI",names(q_data_complete))) | |
| q_data_sub <- q_data_complete[,c(as.numeric(cols))] | |
| q_data_sub <- subset(q_data_sub, abs(GWdiff_cort_qclosest_to_cortGW) < 2) | |
| ## Depressive Symptoms Severity | |
| q_data_sub$Depressive_Symptom_Severity <- NA | |
| q_data_sub$Depressive_Symptom_Severity_num <- NA | |
| for(i in 1:nrow(q_data_sub)){ | |
| m <- q_data_sub$Cesd_qclosest_to_cortGW_pregMean[[i]] | |
| if(!is.na(m)){ | |
| if(m<16){ | |
| q_data_sub$Depressive_Symptom_Severity[[i]] <- "Below_Clinical (CES-D < 16)" | |
| q_data_sub$Depressive_Symptom_Severity_num[[i]] <- 0 | |
| } | |
| if(m>=16){ | |
| q_data_sub$Depressive_Symptom_Severity[[i]] <- "Clinical (CES-D >= 16)" | |
| q_data_sub$Depressive_Symptom_Severity_num[[i]] <- 1 | |
| } | |
| } | |
| } | |
| q_data_sub$Depressive_Symptom_Severity <- factor(q_data_sub$Depressive_Symptom_Severity) | |
| #Anxiety Symptom Severity | |
| q_data_sub$Anxiety_Symptom_Severity <- NA | |
| q_data_sub$Anxiety_Symptom_Severity_num <- NA | |
| for(i in 1:nrow(q_data_sub)){ | |
| m <- q_data_sub$BAI_qclosest_to_cortGW_pregMean[[i]] | |
| if(!is.na(m)){ | |
| if(m>21){ | |
| q_data_sub$Anxiety_Symptom_Severity[[i]] <- "Moderate/Severe" | |
| q_data_sub$Anxiety_Symptom_Severity_num[[i]] <- 1 | |
| } | |
| if(m<=21){ | |
| q_data_sub$Anxiety_Symptom_Severity[[i]] <- "Low/Normal" | |
| q_data_sub$Anxiety_Symptom_Severity_num[[i]] <- 0 | |
| } | |
| } | |
| } | |
| q_data_sub$psych_distress <- rowSums(q_data_sub[,c("Depressive_Symptom_Severity_num", | |
| "Anxiety_Symptom_Severity_num")], | |
| na.rm=F) | |
| ### compute additive depression score | |
| q_data_sub$clinD <- NA | |
| for(i in 1:nrow(q_data_sub)){ | |
| cesd <- q_data_sub$Cesd_qclosest_to_cortGW[[i]] | |
| if(!is.na(cesd)){ | |
| if(cesd >= 16){ | |
| q_data_sub$clinD[[i]] <- 1 | |
| } | |
| if(cesd < 16){ | |
| q_data_sub$clinD[[i]] <- 0 | |
| } | |
| } | |
| } | |
| ##sum occasions of clinical depression together | |
| q_data_sub <- q_data_sub %>% | |
| group_by(participantID) %>% | |
| mutate(additive_clinD = sum(clinD, na.rm = T)) | |
| ## data selection | |
| q_data_subx <- q_data_sub[,c("participantID", | |
| "pregstage", | |
| "Cesd_qclosest_to_cortGW_pregMean", | |
| "Depressive_Symptom_Severity", | |
| "Depressive_Symptom_Severity_num", | |
| "BAI_qclosest_to_cortGW_pregMean", | |
| "PSQI_qclosest_to_cortGW_pregMean", | |
| "qclosest_based_clin_Cesd", | |
| "Cesd_qclosest_to_cortGW", | |
| "BAI_qclosest_to_cortGW", | |
| "PSQI_qclosest_to_cortGW", | |
| "additive_clinD")] | |
| ## Sample stratification | |
| ## those with multiple assessments | |
| at_least_two_assessments <- c() | |
| q_data_subx <- as.data.frame(q_data_subx) | |
| IDs <- unique(q_data_subx$participantID[!is.na(q_data_subx$Cesd_qclosest_to_cortGW)]) | |
| for(i in 1:length(IDs)){ | |
| ID <- IDs[[i]] | |
| #print(ID) | |
| trims <- unique(q_data_subx[q_data_subx$participantID == ID, c("pregstage")]) | |
| #print(length(trims)) | |
| if(length(trims) >= 2){ | |
| at_least_two_assessments <- append(at_least_two_assessments, ID) | |
| } | |
| } | |
| ### Data in wide format | |
| q_data_sub_final <- q_data_subx %>% | |
| tidyr::pivot_wider( | |
| id_cols = c(participantID, | |
| pregstage, | |
| Cesd_qclosest_to_cortGW_pregMean, | |
| Depressive_Symptom_Severity, | |
| Depressive_Symptom_Severity_num, | |
| BAI_qclosest_to_cortGW_pregMean, | |
| PSQI_qclosest_to_cortGW_pregMean, | |
| additive_clinD), | |
| names_from = c(pregstage), # Can accommodate more variables, if needed. | |
| values_from = c(8:11) | |
| ) | |
| # Qs transformations #### | |
| q_data_sub_final$Cesd_qclosest_to_cortGW_pregMean_cent <- c(scale(sqrt(q_data_sub_final$Cesd_qclosest_to_cortGW_pregMean), scale = TRUE)) | |
| q_data_sub_final$BAI_qclosest_to_cortGW_pregMean_cent <- c(scale(sqrt(q_data_sub_final$BAI_qclosest_to_cortGW_pregMean), scale = TRUE)) | |
| q_data_sub_final$PSQI_qclosest_to_cortGW_pregMean_cent <- c(scale(sqrt(q_data_sub_final$PSQI_qclosest_to_cortGW_pregMean), scale = TRUE)) | |
| #add categorical anxiety severity | |
| q_data_sub_final$Anxiety_Severity_greateroneSD_num <- ifelse(q_data_sub_final$BAI_qclosest_to_cortGW_pregMean_cent > 1, 1, 0) | |
| q_data_sub_final$Anxiety_Severity_greateroneSD <- factor(ifelse(q_data_sub_final$BAI_qclosest_to_cortGW_pregMean_cent > 1, "yes", "no")) | |
| q_data_sub_final$Anxiety_Severity_greateroneSD <- factor(q_data_sub_final$Anxiety_Severity_greateroneSD) | |
| #add psych distress score | |
| q_data_sub_final$psych_distress <- rowSums(q_data_sub_final[,c("Depressive_Symptom_Severity_num", | |
| "Anxiety_Severity_greateroneSD_num")], | |
| na.rm=F) | |
| q_data_sub_final$psych_distress <- factor(q_data_sub_final$psych_distress) | |
| q_data_sub_final$PSQI_severity <- NA | |
| for(i in 1:nrow(q_data_sub_final)){ | |
| psqi <- q_data_sub_final$PSQI_qclosest_to_cortGW_pregMean_cent[[i]] | |
| if(!is.na(psqi)){ | |
| q_data_sub_final$PSQI_severity[[i]] <- "mean" | |
| if(psqi <= -1){ | |
| q_data_sub_final$PSQI_severity[[i]] <- "-1SD" | |
| } | |
| if(psqi >= 1){ | |
| q_data_sub_final$PSQI_severity[[i]] <- "+1SD" | |
| } | |
| } | |
| } | |
| q_data_sub_final$PSQI_severity <- factor(q_data_sub_final$PSQI_severity) | |
| ## 3. maternal follow-up data #### | |
| followUp <- read.delim("Rdata/ITU_1to2YearsFollowup_MaternalandChildQuestionnaires.dat") | |
| names(followUp)[1] <- "participantID" | |
| relevant_followUp <- c("1", | |
| grep("CESD", names(followUp)), | |
| grep("BAI", names(followUp))) | |
| postpartum_followUp <- followUp[,c(as.numeric(relevant_followUp))] | |
| postpartum_followUp$ITU_1.7y_mother_CESD_sum_nomis <- as.numeric(gsub(",", ".", postpartum_followUp$ITU_1.7y_mother_CESD_sum_nomis)) | |
| postpartum_followUp$ITU_1.7y_mother_BAI_sum_no_missing <- as.numeric(gsub(",", ".", postpartum_followUp$ITU_1.7y_mother_BAI_sum_no_missing)) | |
| postpartum_df <- postpartum_followUp[,c("participantID", | |
| "ITU_1.7y_mother_CESD_sum_nomis", | |
| "ITU_1.7y_mother_BAI_sum_no_missing")] | |
| names(postpartum_df)[2] <- "postpartum_Cesd" | |
| names(postpartum_df)[3] <- "postpartum_BAI" | |
| ## Depressive Symptoms Severity | |
| postpartum_df$postpartum_Depressive_Symptom_Severity <- NA | |
| postpartum_df$postpartum_Depressive_Symptom_Severity_num <- NA | |
| for(i in 1:nrow(postpartum_df)){ | |
| m <- postpartum_df$postpartum_Cesd[[i]] | |
| if(!is.na(m)){ | |
| if(m<16){ | |
| postpartum_df$postpartum_Depressive_Symptom_Severity[[i]] <- "Non-Clinical (CES-D < 16)" | |
| postpartum_df$postpartum_Depressive_Symptom_Severity_num[[i]] <- 0 | |
| } | |
| if(m>=16){ | |
| postpartum_df$postpartum_Depressive_Symptom_Severity[[i]] <- "Clinical (CES-D >= 16)" | |
| postpartum_df$postpartum_Depressive_Symptom_Severity_num[[i]] <- 1 | |
| } | |
| } | |
| } | |
| postpartum_df$postpartum_Depressive_Symptom_Severity <- factor(postpartum_df$postpartum_Depressive_Symptom_Severity) | |
| #view(postpartum_df[,c("postpartum_Cesd","postpartum_Depressive_Symptom_Severity_num")]) | |
| #Anxiety Symptom Severity | |
| postpartum_df$postpartum_Anxiety_Symptom_Severity <- NA | |
| postpartum_df$postpartum_Anxiety_Symptom_Severity_num <- NA | |
| for(i in 1:nrow(postpartum_df)){ | |
| m <- postpartum_df$postpartum_BAI[[i]] | |
| if(!is.na(m)){ | |
| if(m>21){ | |
| postpartum_df$postpartum_Anxiety_Symptom_Severity[[i]] <- "Moderate/Severe" | |
| postpartum_df$postpartum_Anxiety_Symptom_Severity_num[[i]] <- 1 | |
| } | |
| if(m<=21){ | |
| postpartum_df$postpartum_Anxiety_Symptom_Severity[[i]] <- "Low/Normal" | |
| postpartum_df$postpartum_Anxiety_Symptom_Severity_num[[i]] <- 0 | |
| } | |
| } | |
| } | |
| #summary(factor(postpartum_df$postpartum_Anxiety_Symptom_Severity)) n = 5 | |
| #summary(factor(postpartum_df$postpartum_Depressive_Symptom_Severity)) n = 102 | |
| ### transformations | |
| postpartum_df$postpartum_BAI_cent <- c(scale(sqrt(postpartum_df$postpartum_BAI), scale = TRUE)) | |
| postpartum_df$postpartum_Cesd_cent <- c(scale(sqrt(postpartum_df$postpartum_Cesd), scale = TRUE)) | |
| ### anxiety severity by SD above the sample mean | |
| postpartum_df$postpartum_Anxiety_Severity_greateroneSD_num <- ifelse(postpartum_df$postpartum_BAI_cent > 1, 1, 0) | |
| postpartum_df$postpartum_Anxiety_Severity_greateroneSD <- factor(ifelse(postpartum_df$postpartum_BAI_cent > 1, "yes", "no")) | |
| postpartum_df$postpartum_psych_distress <- rowSums(postpartum_df[,c("postpartum_Depressive_Symptom_Severity_num", | |
| "postpartum_Anxiety_Severity_greateroneSD_num")], | |
| na.rm=F) | |
| postpartum_df$postpartum_psych_distress <- factor(postpartum_df$postpartum_psych_distress) | |
| postpartum_df_final <- postpartum_df[,c("participantID", | |
| "postpartum_BAI_cent", | |
| "postpartum_Cesd_cent", | |
| "postpartum_Depressive_Symptom_Severity", | |
| "postpartum_Anxiety_Severity_greateroneSD", | |
| "postpartum_psych_distress", | |
| "postpartum_Depressive_Symptom_Severity_num")] | |
| # 3.1 Maternal Education #### | |
| maternal_edu <- read.delim("Rdata/ITU maternal education.dat") | |
| names(maternal_edu)[1] <- "participantID" | |
| names(maternal_edu)[3] <- "Maternal_Education" | |
| maternal_edu <- maternal_edu[,c("participantID", | |
| "Maternal_Education")] | |
| library(naniar) | |
| maternal_edu <- maternal_edu %>% replace_with_na(replace = list(Maternal_Education = -9)) | |
| maternal_edu$Maternal_Education <- factor(maternal_edu$Maternal_Education, | |
| levels = c(1,2,3), | |
| labels = c("primary", "applied university", "university")) | |
| ## 4. Register data during pregnancy #### | |
| load("Rdata/processed_register_data.Rdata") | |
| register_data$Maternal_Smoking_During_Pregnancy <- factor(register_data$Maternal_Smoking_During_Pregnancy, | |
| levels = c("no", "quit_T1", "yes"), | |
| labels = c("no", "no", "yes")) | |
| register_data$Maternal_Hypertensive_Disorders_anyVSnone <- factor(register_data$Maternal_Hypertensive_Disorders_anyVSnone, | |
| levels = c(-999,0,1), | |
| labels = c("no", "no", "yes")) | |
| register_data$Maternal_Diabetes_Disorders_anyVSnone <- factor(register_data$Maternal_Diabetes_Disorders_anyVSnone, | |
| levels = c(-999,0,1), | |
| labels = c("no", "no", "yes")) | |
| register_data$Maternal_Body_Mass_Index_in_Early_Pregnancy_cent <- c(scale(register_data$Maternal_Body_Mass_Index_in_Early_Pregnancy, scale = F)) | |
| register_data$Weight_Gain_cent <- c(scale(register_data$Weight_Gain, scale = F)) | |
| register_data$Gestational_Age_Weeks_cent <- c(scale(register_data$Gestational_Age_Weeks, scale = F)) | |
| register_data$Child_Birth_Weight_cent <- c(scale(register_data$Child_Birth_Weight, scale = F)) | |
| register_data$Maternal_Age_Years_cent <- c(scale(register_data$Maternal_Age_Years, scale = F)) | |
| regis_final <- register_data[,c("participantID", | |
| "caseVScontrol", | |
| "Parity", | |
| "Maternal_Smoking_During_Pregnancy", | |
| "Maternal_Corticosteroid_Treatment_during_Pregnancy", | |
| "Maternal_Body_Mass_Index_in_Early_Pregnancy_cent", | |
| "Child_Sex" , | |
| "Gestational_Age_Weeks_cent", | |
| "Child_Birth_Weight_cent", | |
| "Weight_Gain_cent", | |
| "Maternal_Hypertensive_Disorders_anyVSnone", | |
| "Maternal_Diabetes_Disorders_anyVSnone", | |
| "Maternal_Age_Years_cent" | |
| )] | |
| ## 5. medication data #### | |
| medication <- read.delim("Rdata/ITU_psychotrophicmedication05July21_Maternal_CurrentPregnancy.dat") | |
| names(medication)[1] <- "participantID" | |
| ## 6. ASQ data #### | |
| ASQ <- read.csv2("Rdata/ASQ_dataset_ITU_01122020r_shorter.csv") | |
| names(ASQ)[1] <- "participantID" | |
| #extract only participants who have cortisol data and finalagerange scores | |
| #ASQ_final <- ASQ[ASQ$participantID %in% cort_IDs,c(1,3, 18:23)] | |
| ASQ_final <- ASQ[ASQ$participantID %in% cort_IDs,c(1,3, 18:23)] | |
| ASQ_final_samplesizes <- left_join(ASQ_final, wide_cort) | |
| ASQ_final$Child_ASQ_grossmotor_development_infancy_sum_finalagerange <- | |
| as.numeric(ASQ_final$Child_ASQ_grossmotor_development_infancy_sum_finalagerange) | |
| #normalized rank scores | |
| for(col in 3:ncol(ASQ_final)){ | |
| column <- ASQ_final[col] | |
| name <- paste0(names(ASQ_final[col]), "_norm") | |
| ASQ_final[name] <- blom(column, method = "rankit") | |
| } | |
| #dichotomize normalized rank scores | |
| for(col in 9:ncol(ASQ_final)){ | |
| column <- ASQ_final[col] | |
| old_name <- names(ASQ_final[col]) | |
| new_name <- paste0(names(ASQ_final[col]), "_dichom") | |
| ASQ_final[new_name] <- NA | |
| for(i in 1:nrow(ASQ_final)){ | |
| ASQ_score <- ASQ_final[[i, c(old_name)]] | |
| if(!is.na(ASQ_score)){ | |
| if(ASQ_score <= -1){ | |
| ASQ_final[[i,c(new_name)]] <- 1 | |
| } | |
| if(ASQ_score > -1){ | |
| ASQ_final[[i,c(new_name)]] <- 0 | |
| } | |
| } | |
| } | |
| } | |
| ASQ_final$ChildAge_ASQ_months_allchildren_cent <- | |
| c(scale(ASQ_final$ChildAge_ASQ_months_allchildren, scale = F)) | |
| #select subset of relevant variables | |
| ASQ_final <- ASQ_final[,c("participantID", | |
| "ChildAge_ASQ_months_allchildren_cent", | |
| "ChildAge_ASQ_months_allchildren", | |
| "Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom", | |
| "Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange")] | |
| ## 7. On Pregnancy Averages: merge all data #### | |
| #use all the ASQ data | |
| ASQ_df1 <- left_join(ASQ_final, q_data_sub_final) | |
| ASQ_df2 <- left_join(ASQ_df1, maternal_edu) | |
| ASQ_df3 <- left_join(ASQ_df2, postpartum_df_final) | |
| ASQ_df_final <- left_join(ASQ_df3, regis_final) | |
| ASQ_df_final <- left_join(ASQ_df_final, medication[,c("participantID", | |
| "ITUbroadpsychiatricmedication_18_KELA", | |
| "antidepressants_18_KELA")], | |
| copy=TRUE) | |
| ASQ_df_final$ITUbroadpsychiatricmedication_18_KELA <- factor(ASQ_df_final$ITUbroadpsychiatricmedication_18_KELA, | |
| levels = c(0,1), | |
| labels = c("no", "yes")) | |
| ASQ_df_final <- left_join(ASQ_df_final, final_cort) | |
| #exclude violattions against cortisol collection protocol | |
| ASQ_df_final <- ASQ_df_final[!(ASQ_df_final$Maternal_Corticosteroid_Treatment_during_Pregnancy == "yes"),] | |
| # length(unique(ASQ_df1$participantID[!is.na(ASQ_df_final$Cesd_qclosest_to_cortGW_pregMean)])) | |
| # length(unique(ASQ_df1$participantID[!is.na(ASQ_df_final$Cesd_qclosest_to_cortGW_I)])) | |
| # length(unique(ASQ_df1$participantID[!is.na(ASQ_df_final$Cesd_qclosest_to_cortGW_II)])) | |
| # length(unique(ASQ_df1$participantID[!is.na(ASQ_df_final$Cesd_qclosest_to_cortGW_III)])) | |
| ## 8. Apply Exclusion Criteria #### | |
| ASQ_df_final <- subset(ASQ_df_final, !(Maternal_Corticosteroid_Treatment_during_Pregnancy == "yes")) | |
| rm(list= ls()[!(ls() %in% c("ASQ_df_final", "at_least_two_assessments"))]) | |
| #for sensitivity analyses | |
| ASQ_df_final_sub <- subset(ASQ_df_final, !(ITUbroadpsychiatricmedication_18_KELA == "yes") & participantID %in% at_least_two_assessments) | |
| ################################################################################ | |
| ## Set up results table #### | |
| ## morning concentrations #### | |
| ASQ_total_results_morning_cort <- setNames(data.frame(matrix(ncol = 13, nrow = 15)), | |
| c("Cortisol Concentration by pregnancy stage", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| ASQ_total_results_morning_cort[,1] <- c("Model 1", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 2", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 3", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean") | |
| ## Sensitivity analyses | |
| AppenC_ASQ_total_results_morning_cort <- setNames(data.frame(matrix(ncol = 13, nrow = 15)), | |
| c("Cortisol Concentration by pregnancy stage", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| AppenC_ASQ_total_results_morning_cort[,1] <- c("Model 1", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 2", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 3", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean") | |
| ## diurnal concentrations #### | |
| ASQ_total_results_diurnal_cort <- setNames(data.frame(matrix(ncol = 13, nrow = 15)), | |
| c("Cortisol Concentration by pregnancy stage", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| ASQ_total_results_diurnal_cort[,1] <- c("Model 1", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 2", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 3", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean") | |
| ##sensitivity analyses | |
| AppenC_ASQ_total_results_diurnal_cort <- setNames(data.frame(matrix(ncol = 13, nrow = 15)), | |
| c("Cortisol Concentration by pregnancy stage", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| AppenC_ASQ_total_results_diurnal_cort[,1] <- c("Model 1", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 2", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean", | |
| "Model 3", | |
| "Early Pregnancy", | |
| "Mid Pregnancy", | |
| "Late Pregnancy", | |
| "Pregnancy Mean") | |
| ## diurnal Cortisol Rythm #### | |
| ASQ_total_results_diurnalRhythm <- setNames(data.frame(matrix(ncol = 13, nrow = 9)), | |
| c("Cortisol Concentration by pregnancy stage", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| ASQ_total_results_diurnalRhythm[,1] <- c("Model 1", | |
| "Mean Morning_Slope", | |
| "Mean Diurnal_Slope", | |
| "Model 2", | |
| "Mean Morning_Slope", | |
| "Mean Diurnal_Slope", | |
| "Model 3", | |
| "Mean Morning_Slope", | |
| "Mean Diurnal_Slope") | |
| ## Sensitivity Analysis | |
| AppenC_ASQ_total_results_diurnalRhythm <- setNames(data.frame(matrix(ncol = 13, nrow = 9)), | |
| c("Cortisol Concentration by pregnancy stage", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| AppenC_ASQ_total_results_diurnalRhythm[,1] <- c("Model 1", | |
| "Mean Morning_Slope", | |
| "Mean Diurnal_Slope", | |
| "Model 2", | |
| "Mean Morning_Slope", | |
| "Mean Diurnal_Slope", | |
| "Model 3", | |
| "Mean Morning_Slope", | |
| "Mean Diurnal_Slope") | |
| ## Set up functions to report statistics in APA #### | |
| tobit_apa <- function(m,x){ #m=tobit model, x=predictor as displayed in model summary table | |
| #document results | |
| estimate <- format(round(coef(summary(m))[x,1],2)) | |
| SE <- format(round(coef(summary(m))[x,2],2)) | |
| CI <- c(confint(m,x)) | |
| LL <- format(round(CI[1],2)) | |
| UL <- format(round(CI[2],2)) | |
| z <- format(round(coef(summary(m))[x,3],2)) | |
| p <- snip(as.numeric(format(round(coef(summary(m))[x,4],3))),lead = 1) | |
| output <- list(estimate,SE,LL,UL,z,p) | |
| names(output) <- c("estimate","SE","LL","UL","z","p") | |
| return(output) #output = list object of any parameters that may be interesting to report | |
| } | |
| logit_apa <- function(m,x){ #m=lobit model, x=predictor as displayed in model summary table | |
| #document results | |
| estimate <- format(round(exp(coef(summary(m))[x,1]),2)) | |
| SE <- format(round(exp(coef(summary(m))[x,2]),2)) | |
| CI <- as.numeric(exp(c(confint(m,x)))) | |
| LL <- format(round(CI[1],2)) | |
| UL <- format(round(CI[2],2)) | |
| z <- format(round(coef(summary(m))[x,3],2)) | |
| p <- format(round(coef(summary(m))[x,4],3)) | |
| if(as.numeric(p) < 1){ | |
| p <- snip(as.numeric(p), lead=1) | |
| } | |
| output <- list(estimate,SE,LL,UL,z,p) | |
| names(output) <- c("estimate","SE","LL","UL","z","p") | |
| return(output) #output = list object of any parameters (of OR) that may be interesting to report | |
| } | |
| ########################## Tobit Regression ###################################### | |
| ############ Morning Cortisol Concentrations and Slope #### | |
| #### Tobit analyses on Pregnancy CAR concentrations per pregnancy stage #### | |
| ## I #### | |
| #Model 1 | |
| M.CAR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.CAR_con) | |
| res <- tobit_apa(M.CAR_con, "d_AUC_CAR_only_I") | |
| ASQ_total_results_morning_cort[2,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final$yhat <- fitted(M.CAR_con)[,1] | |
| # ASQ_df_final$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.CAR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov1, "d_AUC_CAR_only_I") | |
| ASQ_total_results_morning_cort[7,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_CARcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| d_AUC_CAR_only_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov2, "d_AUC_CAR_only_I") | |
| ASQ_total_results_morning_cort[12,2:7] <- res | |
| #Sex-specific effects | |
| M.CARcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.CARcon_INT_ChS) | |
| #document results | |
| Tobit_res.CAR_conxChSI <- tobit_apa(M.CARcon_INT_ChS, "Child_Sexgirl:d_AUC_CAR_only_I") | |
| #ASQ_total_results_INT[2,2:7] <- Tobit_res.CAR_conxChSI | |
| #caseVScontrol | |
| M.CAR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.CAR_con_CaCo) | |
| #document results | |
| Tobit_res.CAR_conxCaCoI <- tobit_apa(M.CAR_con_CaCo, "caseVScontrolcontrol:d_AUC_CAR_only_I") | |
| #ASQ_total_results_INT[13,2:7] <- Tobit_res.CAR_conxCaCoI | |
| ## II #### | |
| #Model 1 | |
| M.CAR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.CAR_con) | |
| res <- tobit_apa(M.CAR_con, "d_AUC_CAR_only_II") | |
| ASQ_total_results_morning_cort[3,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final$yhat <- fitted(M.CAR_con)[,1] | |
| # ASQ_df_final$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.CAR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov1, "d_AUC_CAR_only_II") | |
| ASQ_total_results_morning_cort[8,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_CARcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| d_AUC_CAR_only_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov2, "d_AUC_CAR_only_II") | |
| ASQ_total_results_morning_cort[13,2:7] <- res | |
| #Sex-specific effects | |
| M.CARcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.CARcon_INT_ChS) | |
| #document results | |
| Tobit_res.CAR_conxChSII <- tobit_apa(M.CARcon_INT_ChS, "Child_Sexgirl:d_AUC_CAR_only_II") | |
| #ASQ_total_results_INT[3,2:7] <- Tobit_res.CAR_conxChSII | |
| #caseVScontrol | |
| M.CAR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.CAR_con_CaCo) | |
| #document results | |
| Tobit_res.CAR_conxCaCoII <- tobit_apa(M.CAR_con_CaCo, "caseVScontrolcontrol:d_AUC_CAR_only_II") | |
| #ASQ_total_results_INT[14,2:7] <- Tobit_res.CAR_conxCaCoII | |
| ## III #### | |
| #Model 1 | |
| M.CAR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.CAR_con) | |
| res <- tobit_apa(M.CAR_con, "d_AUC_CAR_only_III") | |
| ASQ_total_results_morning_cort[4,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final$yhat <- fitted(M.CAR_con)[,1] | |
| # ASQ_df_final$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.CAR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov1, "d_AUC_CAR_only_III") | |
| ASQ_total_results_morning_cort[9,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_CARcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| d_AUC_CAR_only_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov2, "d_AUC_CAR_only_III") | |
| ASQ_total_results_morning_cort[14,2:7] <- res | |
| #Sex-specific effects | |
| M.CARcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.CARcon_INT_ChS) | |
| #document results | |
| Tobit_res.CAR_conxChSIII <- tobit_apa(M.CARcon_INT_ChS, "Child_Sexgirl:d_AUC_CAR_only_III") | |
| #ASQ_total_results_INT[4,2:7] <- Tobit_res.CAR_conxChSIII | |
| #caseVScontrol | |
| M.CAR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.CAR_con_CaCo) | |
| #document results | |
| Tobit_res.CAR_conxCaCoIII <- tobit_apa(M.CAR_con_CaCo, "caseVScontrolcontrol:d_AUC_CAR_only_III") | |
| #ASQ_total_results_INT[15,2:7] <- Tobit_res.CAR_conxCaCoIII | |
| #### Tobit analyses on Pregnancy CAR mean concentrations #### | |
| ASQ_df_final$mean_d_AUC_CAR_only <- rowMeans(ASQ_df_final[,c("d_AUC_CAR_only_I", | |
| "d_AUC_CAR_only_II", | |
| "d_AUC_CAR_only_III")], | |
| na.rm=T) | |
| #Model 1 | |
| M.CAR_Meancon <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.CAR_Meancon) | |
| res <- tobit_apa(M.CAR_Meancon, "mean_d_AUC_CAR_only") | |
| ASQ_total_results_morning_cort[5,2:7] <- res | |
| #Sex-specific effects | |
| M.CAR_Meancon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.CAR_Meancon_INT_ChS) | |
| #document results | |
| Tobit_res.CAR_MeanconxChS <- tobit_apa(M.CAR_Meancon_INT_ChS, "Child_Sexgirl:mean_d_AUC_CAR_only") | |
| #ASQ_total_results_INT[5,2:7] <- Tobit_res.CAR_MeanconxChS | |
| #caseVScontrol | |
| M.CAR_Meancon_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.CAR_Meancon_CaCo) | |
| #document results | |
| Tobit_res.CAR_MeanconxCaCo <- tobit_apa(M.CAR_Meancon_CaCo, "caseVScontrolcontrol:mean_d_AUC_CAR_only") | |
| #ASQ_total_results_INT[16,2:7] <- Tobit_res.CAR_MeanconxCaCo | |
| ### M2 adding prenatal covariates | |
| M.CAR_Meancon.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_CAR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_Meancon.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_Meancon.cov1, "mean_d_AUC_CAR_only") | |
| ASQ_total_results_morning_cort[10,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_Meancon.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_Mean_con <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_Meancon.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| mean_d_AUC_CAR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_Meancon.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_Meancon.cov2, "mean_d_AUC_CAR_only") | |
| ASQ_total_results_morning_cort[15,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_Meancon.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_Meancon <- r^2 | |
| #### Tobit analyses on Morning Decline #### | |
| #Model 1 | |
| M.CAR_MornSlope <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.CAR_MornSlope) | |
| res <- tobit_apa(M.CAR_MornSlope, "Morning_Slope") | |
| ASQ_total_results_diurnalRhythm[2,2:7] <- res | |
| #Sex-specific effects | |
| M.CAR_MornSlope_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope + | |
| Morning_Slope:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.CAR_MornSlope_INT_ChS) | |
| #document results | |
| Tobit_res.CAR_MornSlopexChS <- tobit_apa(M.CAR_MornSlope_INT_ChS, "Child_Sexgirl:Morning_Slope") | |
| #caseVScontrol | |
| M.CAR_MornSlope_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Morning_Slope + | |
| Morning_Slope:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.CAR_MornSlope_CaCo) | |
| #document results | |
| Tobit_res.CAR_MornSlopexCaCo <- tobit_apa(M.CAR_MornSlope_CaCo, "caseVScontrolcontrol:Morning_Slope") | |
| ### M2 adding prenatal covariates | |
| M.CAR_MornSlope.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Morning_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_MornSlope.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_MornSlope.cov1, "Morning_Slope") | |
| ASQ_total_results_diurnalRhythm[5,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_MornSlope.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_MornSlope <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_MornSlope.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| Morning_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.CAR_MornSlope.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_MornSlope.cov2, "Morning_Slope") | |
| ASQ_total_results_diurnalRhythm[8,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.CAR_MornSlope.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_Morn_Slope <- r^2 | |
| ###### Sensitivity analyses in participants taking no psychotropic medication and being tested at least twice #### | |
| ## I #### | |
| #Model 1 | |
| M.CAR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.CAR_con) | |
| res <- tobit_apa(M.CAR_con, "d_AUC_CAR_only_I") | |
| AppenC_ASQ_total_results_morning_cort[2,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final_sub$yhat <- fitted(M.CAR_con)[,1] | |
| # ASQ_df_final_sub$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final_sub$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final_sub, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.CAR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov1, "d_AUC_CAR_only_I") | |
| AppenC_ASQ_total_results_morning_cort[7,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_CARcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| d_AUC_CAR_only_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov2, "d_AUC_CAR_only_I") | |
| AppenC_ASQ_total_results_morning_cort[12,2:7] <- res | |
| #Sex-specific effects | |
| M.CARcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CARcon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.CAR_conxChSI <- tobit_apa(M.CARcon_INT_ChS, "Child_Sexgirl:d_AUC_CAR_only_I") | |
| #AppenC_ASQ_total_results_INT[2,2:7] <- AppenC_Tobit_res.CAR_conxChSI | |
| #caseVScontrol | |
| M.CAR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con_CaCo) | |
| #document results | |
| AppenC_Tobit_res.CAR_conxCaCoI <- tobit_apa(M.CAR_con_CaCo, "caseVScontrolcontrol:d_AUC_CAR_only_I") | |
| #AppenC_ASQ_total_results_INT[13,2:7] <- AppenC_Tobit_res.CAR_conxCaCoI | |
| ## II #### | |
| #Model 1 | |
| M.CAR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.CAR_con) | |
| res <- tobit_apa(M.CAR_con, "d_AUC_CAR_only_II") | |
| AppenC_ASQ_total_results_morning_cort[3,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final_sub$yhat <- fitted(M.CAR_con)[,1] | |
| # ASQ_df_final_sub$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final_sub$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final_sub, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.CAR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov1, "d_AUC_CAR_only_II") | |
| AppenC_ASQ_total_results_morning_cort[8,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_CARcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| d_AUC_CAR_only_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov2, "d_AUC_CAR_only_II") | |
| AppenC_ASQ_total_results_morning_cort[13,2:7] <- res | |
| #Sex-specific effects | |
| M.CARcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.CARcon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.CAR_conxChSII <- tobit_apa(M.CARcon_INT_ChS, "Child_Sexgirl:d_AUC_CAR_only_II") | |
| #AppenC_ASQ_total_results_INT[3,2:7] <- AppenC_Tobit_res.CAR_conxChSII | |
| #caseVScontrol | |
| M.CAR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con_CaCo) | |
| #document results | |
| AppenC_Tobit_res.CAR_conxCaCoII <- tobit_apa(M.CAR_con_CaCo, "caseVScontrolcontrol:d_AUC_CAR_only_II") | |
| #AppenC_ASQ_total_results_INT[14,2:7] <- AppenC_Tobit_res.CAR_conxCaCoII | |
| ## III #### | |
| #Model 1 | |
| M.CAR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.CAR_con) | |
| res <- tobit_apa(M.CAR_con, "d_AUC_CAR_only_III") | |
| AppenC_ASQ_total_results_morning_cort[4,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final_sub$yhat <- fitted(M.CAR_con)[,1] | |
| # ASQ_df_final_sub$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final_sub$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final_sub, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.CAR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov1, "d_AUC_CAR_only_III") | |
| AppenC_ASQ_total_results_morning_cort[9,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_CARcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| d_AUC_CAR_only_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_con.cov2, "d_AUC_CAR_only_III") | |
| AppenC_ASQ_total_results_morning_cort[14,2:7] <- res | |
| #Sex-specific effects | |
| M.CARcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CARcon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.CAR_conxChSIII <- tobit_apa(M.CARcon_INT_ChS, "Child_Sexgirl:d_AUC_CAR_only_III") | |
| #AppenC_ASQ_total_results_INT[4,2:7] <- AppenC_Tobit_res.CAR_conxChSIII | |
| #caseVScontrol | |
| M.CAR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_con_CaCo) | |
| #document results | |
| AppenC_Tobit_res.CAR_conxCaCoIII <- tobit_apa(M.CAR_con_CaCo, "caseVScontrolcontrol:d_AUC_CAR_only_III") | |
| #AppenC_ASQ_total_results_INT[15,2:7] <- AppenC_Tobit_res.CAR_conxCaCoIII | |
| ## CAR mean concentrations #### | |
| ASQ_df_final_sub$mean_d_AUC_CAR_only <- rowMeans(ASQ_df_final_sub[,c("d_AUC_CAR_only_I", | |
| "d_AUC_CAR_only_II", | |
| "d_AUC_CAR_only_III")], | |
| na.rm=T) | |
| #Model 1 | |
| M.CAR_Meancon <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.CAR_Meancon) | |
| res <- tobit_apa(M.CAR_Meancon, "mean_d_AUC_CAR_only") | |
| AppenC_ASQ_total_results_morning_cort[5,2:7] <- res | |
| #Sex-specific effects | |
| M.CAR_Meancon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final_sub) | |
| summary(M.CAR_Meancon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.CAR_MeanconxChS <- tobit_apa(M.CAR_Meancon_INT_ChS, "Child_Sexgirl:mean_d_AUC_CAR_only") | |
| #ASQ_total_results_INT[5,2:7] <- AppenC_Tobit_res.CAR_MeanconxChS | |
| #caseVScontrol | |
| M.CAR_Meancon_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_Meancon_CaCo) | |
| #document results | |
| AppenC_Tobit_res.CAR_MeanconxCaCo <- tobit_apa(M.CAR_Meancon_CaCo, "caseVScontrolcontrol:mean_d_AUC_CAR_only") | |
| #AppenC_ASQ_total_results_INT[16,2:7] <- AppenC_Tobit_res.CAR_MeanconxCaCo | |
| ### M2 adding prenatal covariates | |
| M.CAR_Meancon.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_CAR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_Meancon.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_Meancon.cov1, "mean_d_AUC_CAR_only") | |
| AppenC_ASQ_total_results_morning_cort[10,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_Meancon.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_Mean_con <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_Meancon.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| mean_d_AUC_CAR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_Meancon.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_Meancon.cov2, "mean_d_AUC_CAR_only") | |
| AppenC_ASQ_total_results_morning_cort[15,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_Meancon.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_Meancon <- r^2 | |
| ## Morning Decline #### | |
| #Model 1 | |
| M.CAR_MornSlope <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.CAR_MornSlope) | |
| res <- tobit_apa(M.CAR_MornSlope, "Morning_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[2,2:7] <- res | |
| #Sex-specific effects | |
| M.CAR_MornSlope_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope + | |
| Morning_Slope:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_MornSlope_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.CAR_MornSlopexChS <- tobit_apa(M.CAR_MornSlope_INT_ChS, "Child_Sexgirl:Morning_Slope") | |
| #caseVScontrol | |
| M.CAR_MornSlope_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Morning_Slope + | |
| Morning_Slope:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_MornSlope_CaCo) | |
| #document results | |
| AppenC_Tobit_res.CAR_MornSlopexCaCo <- tobit_apa(M.CAR_MornSlope_CaCo, "caseVScontrolcontrol:Morning_Slope") | |
| ### M2 adding prenatal covariates | |
| M.CAR_MornSlope.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Morning_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_MornSlope.cov1) | |
| #document results | |
| res <- tobit_apa(M.CAR_MornSlope.cov1, "Morning_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[5,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_MornSlope.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_MornSlope <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.CAR_MornSlope.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| Morning_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.CAR_MornSlope.cov2) | |
| #document results | |
| res <- tobit_apa(M.CAR_MornSlope.cov2, "Morning_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[8,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.CAR_MornSlope.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_Morn_Slope <- r^2 | |
| ############ Diurnal Concentrations and Slope ##### | |
| #### Tobit analyses on Pregnancy Diurnal concentrations per pregnancy stage #### | |
| ## I #### | |
| #Model 1 | |
| M.DIUR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_con) | |
| res <- tobit_apa(M.DIUR_con, "cort_d_AUC_noCAR_I") | |
| ASQ_total_results_diurnal_cort[2,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final$yhat <- fitted(M.DIUR_con)[,1] | |
| # ASQ_df_final$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.DIUR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov1, "cort_d_AUC_noCAR_I") | |
| ASQ_total_results_diurnal_cort[7,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_diurnalcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| cort_d_AUC_noCAR_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov2, "cort_d_AUC_noCAR_I") | |
| ASQ_total_results_diurnal_cort[12,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_con.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_DIURcon <- r^2 | |
| #Sex-specific effects | |
| M.DIURcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.DIURcon_INT_ChS) | |
| #document results | |
| Tobit_res.DIUR_conxChSI <- tobit_apa(M.DIURcon_INT_ChS, "Child_Sexgirl:cort_d_AUC_noCAR_I") | |
| #ASQ_total_results_INT[7,2:7] <- Tobit_res.DIUR_conxChSI | |
| #caseVScontrol | |
| M.DIUR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con_CaCo) | |
| #document results | |
| Tobit_res.DIUR_conxCaCoI <- tobit_apa(M.DIUR_con_CaCo, "caseVScontrolcontrol:cort_d_AUC_noCAR_I") | |
| #ASQ_total_results_INT[18,2:7] <- Tobit_res.DIUR_conxCaCoI | |
| ## II #### | |
| #Model 1 | |
| M.DIUR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_con) | |
| res <- tobit_apa(M.DIUR_con, "cort_d_AUC_noCAR_II") | |
| ASQ_total_results_diurnal_cort[3,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final$yhat <- fitted(M.DIUR_con)[,1] | |
| # ASQ_df_final$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.DIUR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov1, "cort_d_AUC_noCAR_II") | |
| ASQ_total_results_diurnal_cort[8,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_diurnalcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| cort_d_AUC_noCAR_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov2, "cort_d_AUC_noCAR_II") | |
| ASQ_total_results_diurnal_cort[13,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_con.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_DIURcon <- r^2 | |
| #Sex-specific effects | |
| M.DIURcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.DIURcon_INT_ChS) | |
| #document results | |
| Tobit_res.DIUR_conxChSII <- tobit_apa(M.DIURcon_INT_ChS, "Child_Sexgirl:cort_d_AUC_noCAR_II") | |
| #ASQ_total_results_INT[8,2:7] <- Tobit_res.DIUR_conxChSII | |
| #caseVScontrol | |
| M.DIUR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con_CaCo) | |
| #document results | |
| Tobit_res.DIUR_conxCaCoII <- tobit_apa(M.DIUR_con_CaCo, "caseVScontrolcontrol:cort_d_AUC_noCAR_II") | |
| #ASQ_total_results_INT[19,2:7] <- Tobit_res.DIUR_conxCaCoII | |
| ## III #### | |
| #Model 1 | |
| M.DIUR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_con) | |
| res <- tobit_apa(M.DIUR_con, "cort_d_AUC_noCAR_III") | |
| ASQ_total_results_diurnal_cort[4,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final$yhat <- fitted(M.DIUR_con)[,1] | |
| # ASQ_df_final$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.DIUR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov1, "cort_d_AUC_noCAR_III") | |
| ASQ_total_results_diurnal_cort[9,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_diurnalcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| cort_d_AUC_noCAR_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov2, "cort_d_AUC_noCAR_III") | |
| ASQ_total_results_diurnal_cort[14,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_con.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_DIURcon <- r^2 | |
| #Sex-specific effects | |
| M.DIURcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.DIURcon_INT_ChS) | |
| #document results | |
| Tobit_res.DIUR_conxChSIII <- tobit_apa(M.DIURcon_INT_ChS, "Child_Sexgirl:cort_d_AUC_noCAR_III") | |
| #ASQ_total_results_INT[9,2:7] <- Tobit_res.DIUR_conxChSIII | |
| #caseVScontrol | |
| M.DIUR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.DIUR_con_CaCo) | |
| #document results | |
| Tobit_res.DIUR_conxCaCoIII <- tobit_apa(M.DIUR_con_CaCo, "caseVScontrolcontrol:cort_d_AUC_noCAR_III") | |
| #ASQ_total_results_INT[20,2:7] <- Tobit_res.DIUR_conxCaCoIII | |
| #### Tobit analyses on Pregnancy Diurnal mean concentrations #### | |
| ASQ_df_final$mean_d_AUC_DIUR_only <- rowMeans(ASQ_df_final[,c("cort_d_AUC_noCAR_I", | |
| "cort_d_AUC_noCAR_II", | |
| "cort_d_AUC_noCAR_III")], | |
| na.rm=T) | |
| #Model 1 | |
| M.DIUR_Meancon <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_Meancon) | |
| res <- tobit_apa(M.DIUR_Meancon, "mean_d_AUC_DIUR_only") | |
| ASQ_total_results_diurnal_cort[5,2:7] <- res | |
| #Sex-specific effects | |
| M.DIUR_Meancon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.DIUR_Meancon_INT_ChS) | |
| #document results | |
| Tobit_res.DIUR_MeanconxChS <- tobit_apa(M.DIUR_Meancon_INT_ChS, "Child_Sexgirl:mean_d_AUC_DIUR_only") | |
| #ASQ_total_results_INT[10,2:7] <- Tobit_res.DIUR_MeanconxChS | |
| #caseVScontrol | |
| M.DIUR_Meancon_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.DIUR_Meancon_CaCo) | |
| #document results | |
| Tobit_res.DIUR_MeanconxCaCo <- tobit_apa(M.DIUR_Meancon_CaCo, "caseVScontrolcontrol:mean_d_AUC_DIUR_only") | |
| #ASQ_total_results_INT[21,2:7] <- Tobit_res.DIUR_MeanconxCaCo | |
| ### M2 adding prenatal covariates | |
| M.DIUR_Meancon.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_DIUR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_Meancon.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Meancon.cov1, "mean_d_AUC_DIUR_only") | |
| ASQ_total_results_diurnal_cort[10,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_Meancon.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_DMean_con <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_Meancon.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| mean_d_AUC_DIUR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_Meancon.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Meancon.cov2, "mean_d_AUC_DIUR_only") | |
| ASQ_total_results_diurnal_cort[15,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_Meancon.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_DMeancon <- r^2 | |
| #### Tobit analyses on diurnal Decline #### | |
| #Model 1 | |
| M.DIUR_Slope <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_Slope) | |
| res <- tobit_apa(M.DIUR_Slope, "Diurnal_Slope") | |
| ASQ_total_results_diurnalRhythm[3,2:7] <- res | |
| #Sex-specific effects | |
| M.DIUR_Slope_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope + | |
| Diurnal_Slope:Child_Sex, | |
| tobit(Upper = 300), data = ASQ_df_final) | |
| summary(M.DIUR_Slope_INT_ChS) | |
| #document results | |
| Tobit_res.DIUR_SlopexChS <- tobit_apa(M.DIUR_Slope_INT_ChS, "Child_Sexgirl:Diurnal_Slope") | |
| #ASQ_total_results_INT[11,2:7] <- Tobit_res.CAR_MornSlopexChS | |
| #caseVScontrol | |
| M.DIUR_Slope_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Diurnal_Slope + | |
| Diurnal_Slope:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final) | |
| summary(M.DIUR_Slope_CaCo) | |
| #document results | |
| Tobit_res.DIUR_SlopexCaCo <- tobit_apa(M.DIUR_Slope_CaCo, "caseVScontrolcontrol:Diurnal_Slope") | |
| #ASQ_total_results_INT[22,2:7] <- Tobit_res.DIUR_SlopexCaCo | |
| ### M2 adding prenatal covariates | |
| M.DIUR_Slope.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Diurnal_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_Slope.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Slope.cov1, "Diurnal_Slope") | |
| ASQ_total_results_diurnalRhythm[6,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_Slope.cov1)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained.prenat_DIURSlope <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_Slope.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| Diurnal_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final) | |
| summary(M.DIUR_Slope.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Slope.cov2, "Diurnal_Slope") | |
| ASQ_total_results_diurnalRhythm[9,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final$yhat <- fitted(M.DIUR_Slope.cov2)[,1] | |
| r <- cor(ASQ_df_final$yhat, | |
| ASQ_df_final$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| Tobit_var.explained_post_DIUR_Slope <- r^2 | |
| ### Sensitivity Analyses #### | |
| ## I #### | |
| #Model 1 | |
| M.DIUR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_con) | |
| res <- tobit_apa(M.DIUR_con, "cort_d_AUC_noCAR_I") | |
| AppenC_ASQ_total_results_diurnal_cort[2,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final_sub$yhat <- fitted(M.DIUR_con)[,1] | |
| # ASQ_df_final_sub$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final_sub$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final_sub, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.DIUR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov1, "cort_d_AUC_noCAR_I") | |
| AppenC_ASQ_total_results_diurnal_cort[7,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_diurnalcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| cort_d_AUC_noCAR_I, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov2, "cort_d_AUC_noCAR_I") | |
| AppenC_ASQ_total_results_diurnal_cort[12,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_con.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_DIURcon <- r^2 | |
| #Sex-specific effects | |
| M.DIURcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIURcon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.DIUR_conxChSI <- tobit_apa(M.DIURcon_INT_ChS, "Child_Sexgirl:cort_d_AUC_noCAR_I") | |
| #AppenC_ASQ_total_results_INT[7,2:7] <- AppenC_Tobit_res.DIUR_conxChSI | |
| #caseVScontrol | |
| M.DIUR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con_CaCo) | |
| #document results | |
| AppenC_Tobit_res.DIUR_conxCaCoI <- tobit_apa(M.DIUR_con_CaCo, "caseVScontrolcontrol:cort_d_AUC_noCAR_I") | |
| #AppenC_ASQ_total_results_INT[18,2:7] <- AppenC_Tobit_res.DIUR_conxCaCoI | |
| ## II #### | |
| #Model 1 | |
| M.DIUR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_con) | |
| res <- tobit_apa(M.DIUR_con, "cort_d_AUC_noCAR_II") | |
| AppenC_ASQ_total_results_diurnal_cort[3,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final_sub$yhat <- fitted(M.DIUR_con)[,1] | |
| # ASQ_df_final_sub$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final_sub$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final_sub, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.DIUR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov1, "cort_d_AUC_noCAR_II") | |
| AppenC_ASQ_total_results_diurnal_cort[8,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_diurnalcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| cort_d_AUC_noCAR_II, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov2, "cort_d_AUC_noCAR_II") | |
| AppenC_ASQ_total_results_diurnal_cort[13,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_con.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_DIURcon <- r^2 | |
| #Sex-specific effects | |
| M.DIURcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIURcon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.DIUR_conxChSII <- tobit_apa(M.DIURcon_INT_ChS, "Child_Sexgirl:cort_d_AUC_noCAR_II") | |
| #AppenC_ASQ_total_results_INT[8,2:7] <- AppenC_Tobit_res.DIUR_conxChSII | |
| #caseVScontrol | |
| M.DIUR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con_CaCo) | |
| #document results | |
| AppenC_Tobit_res.DIUR_conxCaCoII <- tobit_apa(M.DIUR_con_CaCo, "caseVScontrolcontrol:cort_d_AUC_noCAR_II") | |
| #AppenC_ASQ_total_results_INT[19,2:7] <- AppenC_Tobit_res.DIUR_conxCaCoII | |
| ## III #### | |
| #Model 1 | |
| M.DIUR_con <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_con) | |
| res <- tobit_apa(M.DIUR_con, "cort_d_AUC_noCAR_III") | |
| AppenC_ASQ_total_results_diurnal_cort[4,2:7] <- res | |
| ##test assumptions | |
| # ASQ_df_final_sub$yhat <- fitted(M.DIUR_con)[,1] | |
| # ASQ_df_final_sub$rr <- resid(M.CAR_con, type = "response") | |
| # ASQ_df_final_sub$rp <- resid(M.CAR_con, type = "pearson")[,1] | |
| # par(mfcol = c(2, 3)) | |
| # | |
| # with(ASQ_df_final_sub, { | |
| # plot(yhat, rr, main = "Fitted vs Residuals") | |
| # qqnorm(rr) | |
| # plot(yhat, rp, main = "Fitted vs Pearson Residuals") | |
| # qqnorm(rp) | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # rp, main = "Actual vs Pearson Residuals") | |
| # plot(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| # yhat, main = "Actual vs Fitted") | |
| # }) | |
| ### M2 adding prenatal covariates | |
| M.DIUR_con.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov1, "cort_d_AUC_noCAR_III") | |
| AppenC_ASQ_total_results_diurnal_cort[9,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_con.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_diurnalcon <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_con.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| cort_d_AUC_noCAR_III, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_con.cov2, "cort_d_AUC_noCAR_III") | |
| AppenC_ASQ_total_results_diurnal_cort[14,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_con.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_DIURcon <- r^2 | |
| #Sex-specific effects | |
| M.DIURcon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIURcon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.DIUR_conxChSIII <- tobit_apa(M.DIURcon_INT_ChS, "Child_Sexgirl:cort_d_AUC_noCAR_III") | |
| #AppenC_ASQ_total_results_INT[9,2:7] <- AppenC_Tobit_res.DIUR_conxChSIII | |
| #caseVScontrol | |
| M.DIUR_con_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_con_CaCo) | |
| #document results | |
| AppenC_Tobit_res.DIUR_conxCaCoIII <- tobit_apa(M.DIUR_con_CaCo, "caseVScontrolcontrol:cort_d_AUC_noCAR_III") | |
| #AppenC_ASQ_total_results_INT[20,2:7] <- AppenC_Tobit_res.DIUR_conxCaCoIII | |
| ## DIUR mean concentration ##### | |
| ASQ_df_final_sub$mean_d_AUC_DIUR_only <- rowMeans(ASQ_df_final_sub[,c("cort_d_AUC_noCAR_I", | |
| "cort_d_AUC_noCAR_II", | |
| "cort_d_AUC_noCAR_III")], | |
| na.rm=T) | |
| #Model 1 | |
| M.DIUR_Meancon <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_Meancon) | |
| res <- tobit_apa(M.DIUR_Meancon, "mean_d_AUC_DIUR_only") | |
| AppenC_ASQ_total_results_diurnal_cort[5,2:7] <- res | |
| #Sex-specific effects | |
| M.DIUR_Meancon_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Meancon_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.DIUR_MeanconxChS <- tobit_apa(M.DIUR_Meancon_INT_ChS, "Child_Sexgirl:mean_d_AUC_DIUR_only") | |
| #AppenC_ASQ_total_results_INT[10,2:7] <- AppenC_Tobit_res.DIUR_MeanconxChS | |
| #caseVScontrol | |
| M.DIUR_Meancon_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Meancon_CaCo) | |
| #document results | |
| AppenC_Tobit_res.DIUR_MeanconxCaCo <- tobit_apa(M.DIUR_Meancon_CaCo, "caseVScontrolcontrol:mean_d_AUC_DIUR_only") | |
| #AppenC_ASQ_total_results_INT[21,2:7] <- AppenC_Tobit_res.DIUR_MeanconxCaCo | |
| ### M2 adding prenatal covariates | |
| M.DIUR_Meancon.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_DIUR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Meancon.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Meancon.cov1, "mean_d_AUC_DIUR_only") | |
| AppenC_ASQ_total_results_diurnal_cort[10,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_Meancon.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_DMean_con <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_Meancon.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| mean_d_AUC_DIUR_only, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Meancon.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Meancon.cov2, "mean_d_AUC_DIUR_only") | |
| AppenC_ASQ_total_results_diurnal_cort[15,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_Meancon.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_DMeancon <- r^2 | |
| ## DIUR Slope #### | |
| #Model 1 | |
| M.DIUR_Slope <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub, | |
| na.action = "na.exclude") | |
| summary(M.DIUR_Slope) | |
| res <- tobit_apa(M.DIUR_Slope, "Diurnal_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[3,2:7] <- res | |
| #Sex-specific effects | |
| M.DIUR_Slope_INT_ChS <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope + | |
| Diurnal_Slope:Child_Sex, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Slope_INT_ChS) | |
| #document results | |
| AppenC_Tobit_res.DIUR_SlopexChS <- tobit_apa(M.DIUR_Slope_INT_ChS, "Child_Sexgirl:Diurnal_Slope") | |
| #AppenC_ASQ_total_results_INT[11,2:7] <- AppenC_Tobit_res.CAR_MornSlopexChS | |
| #caseVScontrol | |
| M.DIUR_Slope_CaCo <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Diurnal_Slope + | |
| Diurnal_Slope:caseVScontrol, | |
| tobit(Upper = 300), | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Slope_CaCo) | |
| #document results | |
| AppenC_Tobit_res.DIUR_SlopexCaCo <- tobit_apa(M.DIUR_Slope_CaCo, "caseVScontrolcontrol:Diurnal_Slope") | |
| #AppenC_ASQ_total_results_INT[22,2:7] <- AppenC_Tobit_res.DIUR_SlopexCaCo | |
| ### M2 adding prenatal covariates | |
| M.DIUR_Slope.cov1 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Diurnal_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Slope.cov1) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Slope.cov1, "Diurnal_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[6,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_Slope.cov1)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained.prenat_DIURSlope <- format(round(r^2,2)) | |
| ## M3 adding the postnatal factors | |
| M.DIUR_Slope.cov2 <- vglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_Cesd_cent + | |
| postpartum_BAI_cent + | |
| Diurnal_Slope, | |
| tobit(Upper = 300), | |
| na.action = "na.exclude", | |
| data = ASQ_df_final_sub) | |
| summary(M.DIUR_Slope.cov2) | |
| #document results | |
| res <- tobit_apa(M.DIUR_Slope.cov2, "Diurnal_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[9,2:7] <- res | |
| #total variance explained by tobit model | |
| ASQ_df_final_sub$yhat <- fitted(M.DIUR_Slope.cov2)[,1] | |
| r <- cor(ASQ_df_final_sub$yhat, | |
| ASQ_df_final_sub$Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange, | |
| use = "pairwise.complete.obs") | |
| AppenC_Tobit_var.explained_post_DIUR_Slope <- r^2 | |
| ############################# Logistic Regression ################################## | |
| ######### Morning Cortisol Concentrations and Slope #### | |
| # assumptions ### | |
| # new_ASQ.total <- na.omit(ASQ_df_final[,-c(4, 7:18,22)]) #first exclude the pregnancy-stage specific predictors | |
| # # # Fit the logistic regression model | |
| # model <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| # ChildAge_ASQ_months_allchildren_cent + | |
| # Child_Sex + | |
| # caseVScontrol + | |
| # Maternal_Age_Years_cent + | |
| # Maternal_Education + | |
| # Parity + | |
| # Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| # Weight_Gain_cent + | |
| # Maternal_Hypertensive_Disorders_anyVSnone + | |
| # Maternal_Diabetes_Disorders_anyVSnone + | |
| # Maternal_Smoking_During_Pregnancy + | |
| # Gestational_Age_Weeks_cent + | |
| # Child_Birth_Weight_cent + | |
| # postpartum_Cesd_cent + | |
| # postpartum_BAI_cent, | |
| # data = new_ASQ.total, | |
| # family = binomial, | |
| # na.action = "na.exclude") | |
| # | |
| # # Predict the probability (p) of diabete positivity | |
| # probabilities <- predict(model, type = "response") | |
| # # predicted.classes <- ifelse(probabilities > 0.3, "pos", "neg") | |
| # # head(predicted.classes) | |
| # # Select only numeric predictors | |
| # mydata <- new_ASQ.total %>% | |
| # dplyr::select_if(is.numeric) | |
| # #mydata <- mydata[,-c(5:10)] | |
| # predictors <- colnames(mydata) | |
| # # Bind the logit and tidying the data for plot | |
| # mydata <- mydata %>% | |
| # mutate(logit = log(probabilities/(1-probabilities))) %>% | |
| # gather(key = "predictors", value = "predictor.value", -logit) | |
| # | |
| # #create scatterplots | |
| # ggplot(mydata, aes(logit, predictor.value))+ | |
| # geom_point(size = 0.5, alpha = 0.5) + | |
| # geom_smooth(method = "loess") + | |
| # theme_bw() + | |
| # facet_wrap(~predictors, scales = "free_y") | |
| # | |
| # ## Cook's distance | |
| # plot(model, which = 4, id.n = 3) | |
| # | |
| # #influential cases | |
| # # Extract model results | |
| # #new_ASQ <- ASQ_df_final[,-c(10:14)] #first exclude the other outcome variables | |
| # model.data <- augment(model, data = new_ASQ.total) %>% mutate(index = 1:n()) | |
| # outliers <- model.data %>% top_n(3, .cooksd) #with with neurodevelopmental delay, high depression and anxiety (two controls, one case) | |
| # | |
| # #plot standardize residuals | |
| # ggplot(model.data, aes(index, .std.resid)) + | |
| # geom_point(aes(color = Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom), alpha = .5) + | |
| # theme_bw() | |
| # model.data %>% | |
| # filter(abs(.std.resid) > 3) #no influential cases | |
| # | |
| # #multicollinearity | |
| # car::vif(model) | |
| #### Logistic Regression on Pregnancy CAR concentrations per pregnancy stage#### | |
| ## I #### | |
| #M1 | |
| M1_total_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_CARcon) | |
| #document results | |
| res <- logit_apa(M1_total_CARcon,"d_AUC_CAR_only_I") | |
| ASQ_total_results_morning_cort[2,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_I, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_CARcon,"d_AUC_CAR_only_I") | |
| ASQ_total_results_morning_cort[7,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| d_AUC_CAR_only_I, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_CARcon,"d_AUC_CAR_only_I") | |
| ASQ_total_results_morning_cort[12,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_CARcon) | |
| logit.res_CARconxChSI <- logit_apa(M1_total.INT1_CARcon,"Child_Sexgirl:d_AUC_CAR_only_I") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_CARcon) | |
| logit.res__CARconxCaCoI <- logit_apa(M1_total.INT2_CARcon,"caseVScontrolcontrol:d_AUC_CAR_only_I") | |
| ## II #### | |
| #M1 | |
| M1_total_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_CARcon) | |
| #document results | |
| res <- logit_apa(M1_total_CARcon,"d_AUC_CAR_only_II") | |
| ASQ_total_results_morning_cort[3,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_II, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_CARcon,"d_AUC_CAR_only_II") | |
| ASQ_total_results_morning_cort[8,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| d_AUC_CAR_only_II, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_CARcon,"d_AUC_CAR_only_II") | |
| ASQ_total_results_morning_cort[13,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_CARcon) | |
| logit.res_CARconxChSII <- logit_apa(M1_total.INT1_CARcon,"Child_Sexgirl:d_AUC_CAR_only_II") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_CARcon) | |
| logit.res__CARconxCaCoII <- logit_apa(M1_total.INT2_CARcon,"caseVScontrolcontrol:d_AUC_CAR_only_II") | |
| ## III #### | |
| #M1 | |
| M1_total_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_CARcon) | |
| #document results | |
| res <- logit_apa(M1_total_CARcon,"d_AUC_CAR_only_III") | |
| ASQ_total_results_morning_cort[4,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_III, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_CARcon,"d_AUC_CAR_only_III") | |
| ASQ_total_results_morning_cort[9,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| d_AUC_CAR_only_III, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_CARcon,"d_AUC_CAR_only_III") | |
| ASQ_total_results_morning_cort[14,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_CARcon) | |
| logit.res_CARconxChSIII <- logit_apa(M1_total.INT1_CARcon,"Child_Sexgirl:d_AUC_CAR_only_III") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_CARcon) | |
| logit.res__CARconxCaCoIII <- logit_apa(M1_total.INT2_CARcon,"caseVScontrolcontrol:d_AUC_CAR_only_III") | |
| #### Logistic Regression CAR mean concentrations #### | |
| #M1 | |
| M1_total_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_Meancon) | |
| #document results | |
| res <- logit_apa(M1_total_Meancon,"mean_d_AUC_CAR_only") | |
| ASQ_total_results_morning_cort[5,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_Meancon) | |
| logit.res_MeanconxChS <- logit_apa(M1_total.INT1_Meancon,"Child_Sexgirl:mean_d_AUC_CAR_only") | |
| #ASQ and prenatal Cesd*caseVScontrol | |
| M1_total.INT2_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_Meancon) | |
| logit.res_MeanconxCaCo <- logit_apa(M1_total.INT2_Meancon,"caseVScontrolcontrol:mean_d_AUC_CAR_only") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_CAR_only, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_Meancon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_Meancon,"mean_d_AUC_CAR_only") | |
| ASQ_total_results_morning_cort[10,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| mean_d_AUC_CAR_only, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_Meancon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_Meancon,"mean_d_AUC_CAR_only") | |
| ASQ_total_results_morning_cort[15,8:13] <- res | |
| #### Logistic Regression on morning slope #### | |
| #M1 | |
| M1_total_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_mornSlope) | |
| #document results | |
| res <- logit_apa(M1_total_mornSlope,"Morning_Slope") | |
| ASQ_total_results_diurnalRhythm[2,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope + | |
| Morning_Slope:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_mornSlope) | |
| logit.res_mornSlopexChS <- logit_apa(M1_total.INT1_mornSlope,"Child_Sexgirl:Morning_Slope") | |
| #ASQ and prenatal cort*caseVScontrol | |
| M1_total.INT2_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Morning_Slope + | |
| Morning_Slope:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_mornSlope) | |
| logit.res_mornSlopexCaCo <- logit_apa(M1_total.INT2_mornSlope,"caseVScontrolcontrol:Morning_Slope") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Morning_Slope, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_mornSlope) | |
| #document results | |
| res <- logit_apa(M2_total.cov_mornSlope,"Morning_Slope") | |
| ASQ_total_results_diurnalRhythm[5,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| Morning_Slope, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_mornSlope) | |
| #document results | |
| res <- logit_apa(M3_total.cov_mornSlope,"Morning_Slope") | |
| ASQ_total_results_diurnalRhythm[8,8:13] <- res | |
| ###### Sensitivity Analyses ##### | |
| ## I #### | |
| #M1 | |
| M1_total_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_CARcon) | |
| #document results | |
| res <- logit_apa(M1_total_CARcon,"d_AUC_CAR_only_I") | |
| AppenC_ASQ_total_results_morning_cort[2,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_I, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_CARcon,"d_AUC_CAR_only_I") | |
| AppenC_ASQ_total_results_morning_cort[7,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| d_AUC_CAR_only_I, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_CARcon,"d_AUC_CAR_only_I") | |
| AppenC_ASQ_total_results_morning_cort[12,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_CARcon) | |
| AppenC_logit.res_CARconxChSI <- logit_apa(M1_total.INT1_CARcon,"Child_Sexgirl:d_AUC_CAR_only_I") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_I + | |
| d_AUC_CAR_only_I:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_CARcon) | |
| AppenC_logit.res__CARconxCaCoI <- logit_apa(M1_total.INT2_CARcon,"caseVScontrolcontrol:d_AUC_CAR_only_I") | |
| ## II #### | |
| #M1 | |
| M1_total_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_CARcon) | |
| #document results | |
| res <- logit_apa(M1_total_CARcon,"d_AUC_CAR_only_II") | |
| AppenC_ASQ_total_results_morning_cort[3,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_II, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_CARcon,"d_AUC_CAR_only_II") | |
| AppenC_ASQ_total_results_morning_cort[8,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| d_AUC_CAR_only_II, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_CARcon,"d_AUC_CAR_only_II") | |
| AppenC_ASQ_total_results_morning_cort[13,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_CARcon) | |
| AppenC_logit.res_CARconxChSII <- logit_apa(M1_total.INT1_CARcon,"Child_Sexgirl:d_AUC_CAR_only_II") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_II + | |
| d_AUC_CAR_only_II:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_CARcon) | |
| AppenC_logit.res__CARconxCaCoII <- logit_apa(M1_total.INT2_CARcon,"caseVScontrolcontrol:d_AUC_CAR_only_II") | |
| ## III #### | |
| #M1 | |
| M1_total_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_CARcon) | |
| #document results | |
| res <- logit_apa(M1_total_CARcon,"d_AUC_CAR_only_III") | |
| AppenC_ASQ_total_results_morning_cort[4,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| d_AUC_CAR_only_III, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_CARcon,"d_AUC_CAR_only_III") | |
| AppenC_ASQ_total_results_morning_cort[9,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| d_AUC_CAR_only_III, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_CARcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_CARcon,"d_AUC_CAR_only_III") | |
| AppenC_ASQ_total_results_morning_cort[14,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_CARcon) | |
| AppenC_logit.res_CARconxChSIII <- logit_apa(M1_total.INT1_CARcon,"Child_Sexgirl:d_AUC_CAR_only_III") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_CARcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| d_AUC_CAR_only_III + | |
| d_AUC_CAR_only_III:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_CARcon) | |
| AppenC_logit.res__CARconxCaCoIII <- logit_apa(M1_total.INT2_CARcon,"caseVScontrolcontrol:d_AUC_CAR_only_III") | |
| #### Logistic Regression CAR mean concentrations #### | |
| #M1 | |
| M1_total_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_Meancon) | |
| #document results | |
| res <- logit_apa(M1_total_Meancon,"mean_d_AUC_CAR_only") | |
| AppenC_ASQ_total_results_morning_cort[5,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_Meancon) | |
| AppenC_logit.res_MeanconxChS <- logit_apa(M1_total.INT1_Meancon,"Child_Sexgirl:mean_d_AUC_CAR_only") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_CAR_only + | |
| mean_d_AUC_CAR_only:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_Meancon) | |
| AppenC_logit.res_MeanconxCaCo <- logit_apa(M1_total.INT2_Meancon,"caseVScontrolcontrol:mean_d_AUC_CAR_only") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_CAR_only, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_Meancon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_Meancon,"mean_d_AUC_CAR_only") | |
| AppenC_ASQ_total_results_morning_cort[10,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_Meancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| mean_d_AUC_CAR_only, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_Meancon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_Meancon,"mean_d_AUC_CAR_only") | |
| AppenC_ASQ_total_results_morning_cort[15,8:13] <- res | |
| #### Logistic Regression on morning slope #### | |
| #M1 | |
| M1_total_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_mornSlope) | |
| #document results | |
| res <- logit_apa(M1_total_mornSlope,"Morning_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[2,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Morning_Slope + | |
| Morning_Slope:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_mornSlope) | |
| AppenC_logit.res_mornSlopexChS <- logit_apa(M1_total.INT1_mornSlope,"Child_Sexgirl:Morning_Slope") | |
| #ASQ and prenatal cort*caseVScontrol | |
| M1_total.INT2_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Morning_Slope + | |
| Morning_Slope:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_mornSlope) | |
| AppenC_logit.res_mornSlopexCaCo <- logit_apa(M1_total.INT2_mornSlope,"caseVScontrolcontrol:Morning_Slope") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Morning_Slope, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_mornSlope) | |
| #document results | |
| res <- logit_apa(M2_total.cov_mornSlope,"Morning_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[5,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_mornSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| Morning_Slope, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_mornSlope) | |
| #document results | |
| res <- logit_apa(M3_total.cov_mornSlope,"Morning_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[8,8:13] <- res | |
| ######### Diurnal Cortisol Concentrations and Slope ####### | |
| #### Logistic Regression on Pregnancy diurnal concentrations per pregnancy stage#### | |
| # I #### | |
| #M1 | |
| M1_total_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_DIURcon) | |
| #document results | |
| res <- logit_apa(M1_total_DIURcon,"cort_d_AUC_noCAR_I") | |
| ASQ_total_results_diurnal_cort[2,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_I, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURcon,"cort_d_AUC_noCAR_I") | |
| ASQ_total_results_diurnal_cort[7,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| cort_d_AUC_noCAR_I, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURcon,"cort_d_AUC_noCAR_I") | |
| ASQ_total_results_diurnal_cort[12,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURcon) | |
| logit.res_DIURconxChSI <- logit_apa(M1_total.INT1_DIURcon,"Child_Sexgirl:cort_d_AUC_noCAR_I") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURcon) | |
| logit.res_DIURconxCaCoI <- logit_apa(M1_total.INT2_DIURcon,"caseVScontrolcontrol:cort_d_AUC_noCAR_I") | |
| # II #### | |
| #M1 | |
| M1_total_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_DIURcon) | |
| #document results | |
| res <- logit_apa(M1_total_DIURcon,"cort_d_AUC_noCAR_II") | |
| ASQ_total_results_diurnal_cort[3,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_II, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURcon,"cort_d_AUC_noCAR_II") | |
| ASQ_total_results_diurnal_cort[8,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| cort_d_AUC_noCAR_II, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURcon,"cort_d_AUC_noCAR_II") | |
| ASQ_total_results_diurnal_cort[13,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURcon) | |
| logit.res_DIURconxChSII <- logit_apa(M1_total.INT1_DIURcon,"Child_Sexgirl:cort_d_AUC_noCAR_II") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURcon) | |
| logit.res_DIURconxCaCoII <- logit_apa(M1_total.INT2_DIURcon,"caseVScontrolcontrol:cort_d_AUC_noCAR_II") | |
| # III #### | |
| #M1 | |
| M1_total_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_DIURcon) | |
| #document results | |
| res <- logit_apa(M1_total_DIURcon,"cort_d_AUC_noCAR_III") | |
| ASQ_total_results_diurnal_cort[4,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_III, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURcon,"cort_d_AUC_noCAR_III") | |
| ASQ_total_results_diurnal_cort[9,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| cort_d_AUC_noCAR_III, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURcon,"cort_d_AUC_noCAR_III") | |
| ASQ_total_results_diurnal_cort[14,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURcon) | |
| logit.res_DIURconxChSIII <- logit_apa(M1_total.INT1_DIURcon,"Child_Sexgirl:cort_d_AUC_noCAR_III") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURcon) | |
| logit.res_DIURconxCaCoIII <- logit_apa(M1_total.INT2_DIURcon,"caseVScontrolcontrol:cort_d_AUC_noCAR_III") | |
| #### Logistic Regression diurnal mean concentrations #### | |
| #M1 | |
| M1_total_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_DMeancon) | |
| #document results | |
| res <- logit_apa(M1_total_DMeancon,"mean_d_AUC_DIUR_only") | |
| ASQ_total_results_diurnal_cort[5,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_DMeancon) | |
| logit.res_DMeanconxChS <- logit_apa(M1_total.INT1_DMeancon,"Child_Sexgirl:mean_d_AUC_DIUR_only") | |
| #ASQ and prenatal Cesd*caseVScontrol | |
| M1_total.INT2_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_DMeancon) | |
| logit.res_DMeanconxCaCo <- logit_apa(M1_total.INT2_DMeancon,"caseVScontrolcontrol:mean_d_AUC_DIUR_only") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_DIUR_only, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_DMeancon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DMeancon,"mean_d_AUC_DIUR_only") | |
| ASQ_total_results_diurnal_cort[10,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| mean_d_AUC_DIUR_only, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_DMeancon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DMeancon,"mean_d_AUC_DIUR_only") | |
| ASQ_total_results_diurnal_cort[15,8:13] <- res | |
| #### Logistic Regression on diurnal slope #### | |
| #M1 | |
| M1_total_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total_DIURSlope) | |
| #document results | |
| res <- logit_apa(M1_total_DIURSlope,"Diurnal_Slope") | |
| ASQ_total_results_diurnalRhythm[3,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope + | |
| Diurnal_Slope:Child_Sex, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURSlope) | |
| logit.res_DIURSlopexChS <- logit_apa(M1_total.INT1_DIURSlope,"Child_Sexgirl:Diurnal_Slope") | |
| #ASQ and prenatal cort*caseVScontrol | |
| M1_total.INT2_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Diurnal_Slope + | |
| Diurnal_Slope:caseVScontrol, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURSlope) | |
| logit.res_DIURSlopexCaCo <- logit_apa(M1_total.INT2_DIURSlope,"caseVScontrolcontrol:Diurnal_Slope") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Diurnal_Slope, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURSlope) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURSlope,"Diurnal_Slope") | |
| ASQ_total_results_diurnalRhythm[6,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| Diurnal_Slope, | |
| data = ASQ_df_final, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURSlope) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURSlope,"Diurnal_Slope") | |
| ASQ_total_results_diurnalRhythm[9,8:13] <- res | |
| # ## Effects look very fishy: use of bayesian version instead ##### | |
| # library(arm) | |
| # M1_total_DIURSlope <- bayesglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| # ChildAge_ASQ_months_allchildren_cent + | |
| # Child_Sex + | |
| # Diurnal_Slope, | |
| # data = ASQ_df_final, | |
| # family = "binomial") | |
| # summary(M1_total_DIURSlope) | |
| # | |
| # #document results | |
| # res <- logit_apa(M1_total_DIURSlope,"Diurnal_Slope") | |
| # ASQ_total_results_diurnalRhythm[3,8:13] <- res | |
| # | |
| # #ASQ and prenatal Cesd*child sex | |
| # M1_total.INT1_DIURSlope <- bayesglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| # ChildAge_ASQ_months_allchildren_cent + | |
| # Child_Sex + | |
| # Diurnal_Slope + | |
| # Diurnal_Slope:Child_Sex, | |
| # data = ASQ_df_final, | |
| # family = "binomial") | |
| # summary(M1_total.INT1_DIURSlope) | |
| # logit.res_DIURSlopexChS <- logit_apa(M1_total.INT1_DIURSlope,"Child_Sexgirl:Diurnal_Slope") | |
| # | |
| # #ASQ and prenatal cort*caseVScontrol | |
| # M1_total.INT2_DIURSlope <- bayesglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| # ChildAge_ASQ_months_allchildren_cent + | |
| # Child_Sex + | |
| # caseVScontrol + | |
| # Diurnal_Slope + | |
| # Diurnal_Slope:caseVScontrol, | |
| # data = ASQ_df_final, | |
| # family = "binomial") | |
| # summary(M1_total.INT2_DIURSlope) | |
| # logit.res_DIURSlopexCaCo <- logit_apa(M1_total.INT2_DIURSlope,"caseVScontrolcontrol:Diurnal_Slope") | |
| # | |
| # #M2 ASQ and cortisol concentration + prenatal covariates | |
| # M2_total.cov_DIURSlope <- bayesglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| # ChildAge_ASQ_months_allchildren_cent + | |
| # Child_Sex + | |
| # caseVScontrol + | |
| # Maternal_Age_Years_cent + | |
| # Maternal_Education + | |
| # Parity + | |
| # Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| # Weight_Gain_cent + | |
| # Maternal_Hypertensive_Disorders_anyVSnone + | |
| # Maternal_Diabetes_Disorders_anyVSnone + | |
| # Maternal_Smoking_During_Pregnancy + | |
| # Gestational_Age_Weeks_cent + | |
| # Child_Birth_Weight_cent + | |
| # Diurnal_Slope, | |
| # data = ASQ_df_final, | |
| # family = "binomial") | |
| # summary(M2_total.cov_DIURSlope) | |
| # #document results | |
| # res <- logit_apa(M2_total.cov_DIURSlope,"Diurnal_Slope") | |
| # ASQ_total_results_diurnalRhythm[6,8:13] <- res | |
| # | |
| # #ASQ and prenatal Cesd + postnatal covariates | |
| # M3_total.cov_DIURSlope <- bayesglm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| # ChildAge_ASQ_months_allchildren_cent + | |
| # Child_Sex + | |
| # caseVScontrol + | |
| # Maternal_Age_Years_cent + | |
| # Maternal_Education + | |
| # Parity + | |
| # Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| # Weight_Gain_cent + | |
| # Maternal_Hypertensive_Disorders_anyVSnone + | |
| # Maternal_Diabetes_Disorders_anyVSnone + | |
| # Maternal_Smoking_During_Pregnancy + | |
| # Gestational_Age_Weeks_cent + | |
| # Child_Birth_Weight_cent + | |
| # postpartum_BAI_cent + | |
| # postpartum_Cesd_cent + | |
| # Diurnal_Slope, | |
| # data = ASQ_df_final, | |
| # family = "binomial") | |
| # summary(M3_total.cov_DIURSlope) | |
| # #document results | |
| # res <- logit_apa(M3_total.cov_DIURSlope,"Diurnal_Slope") | |
| # ASQ_total_results_diurnalRhythm[9,8:13] <- res | |
| ##### Sensitivity Analysis ##### | |
| # I #### | |
| #M1 | |
| M1_total_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_DIURcon) | |
| #document results | |
| res <- logit_apa(M1_total_DIURcon,"cort_d_AUC_noCAR_I") | |
| AppenC_ASQ_total_results_diurnal_cort[2,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_I, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURcon,"cort_d_AUC_noCAR_I") | |
| AppenC_ASQ_total_results_diurnal_cort[7,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| cort_d_AUC_noCAR_I, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURcon,"cort_d_AUC_noCAR_I") | |
| AppenC_ASQ_total_results_diurnal_cort[12,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURcon) | |
| AppenC_logit.res_DIURconxChSI <- logit_apa(M1_total.INT1_DIURcon,"Child_Sexgirl:cort_d_AUC_noCAR_I") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_I + | |
| cort_d_AUC_noCAR_I:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURcon) | |
| AppenC_logit.res_DIURconxCaCoI <- logit_apa(M1_total.INT2_DIURcon,"caseVScontrolcontrol:cort_d_AUC_noCAR_I") | |
| # II #### | |
| #M1 | |
| M1_total_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_DIURcon) | |
| #document results | |
| res <- logit_apa(M1_total_DIURcon,"cort_d_AUC_noCAR_II") | |
| AppenC_ASQ_total_results_diurnal_cort[3,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_II, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURcon,"cort_d_AUC_noCAR_II") | |
| AppenC_ASQ_total_results_diurnal_cort[8,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| cort_d_AUC_noCAR_II, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURcon,"cort_d_AUC_noCAR_II") | |
| AppenC_ASQ_total_results_diurnal_cort[13,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURcon) | |
| AppenC_logit.res_DIURconxChSII <- logit_apa(M1_total.INT1_DIURcon,"Child_Sexgirl:cort_d_AUC_noCAR_II") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_II + | |
| cort_d_AUC_noCAR_II:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURcon) | |
| AppenC_logit.res_DIURconxCaCoII <- logit_apa(M1_total.INT2_DIURcon,"caseVScontrolcontrol:cort_d_AUC_noCAR_II") | |
| # III #### | |
| #M1 | |
| M1_total_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_DIURcon) | |
| #document results | |
| res <- logit_apa(M1_total_DIURcon,"cort_d_AUC_noCAR_III") | |
| AppenC_ASQ_total_results_diurnal_cort[4,8:13] <- res | |
| #ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| cort_d_AUC_noCAR_III, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURcon,"cort_d_AUC_noCAR_III") | |
| AppenC_ASQ_total_results_diurnal_cort[9,8:13] <- res | |
| #ASQ and prenatal Cort + postnatal covariates | |
| M3_total.cov_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| cort_d_AUC_noCAR_III, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURcon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURcon,"cort_d_AUC_noCAR_III") | |
| AppenC_ASQ_total_results_diurnal_cort[14,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURcon) | |
| AppenC_logit.res_DIURconxChSIII <- logit_apa(M1_total.INT1_DIURcon,"Child_Sexgirl:cort_d_AUC_noCAR_III") | |
| #ASQ and prenatal Cort*caseVScontrol | |
| M1_total.INT2_DIURcon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| cort_d_AUC_noCAR_III + | |
| cort_d_AUC_noCAR_III:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURcon) | |
| AppenC_logit.res_DIURconxCaCoIII <- logit_apa(M1_total.INT2_DIURcon,"caseVScontrolcontrol:cort_d_AUC_noCAR_III") | |
| #### Logistic Regression diurnal mean concentrations #### | |
| #M1 | |
| M1_total_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_DMeancon) | |
| #document results | |
| res <- logit_apa(M1_total_DMeancon,"mean_d_AUC_DIUR_only") | |
| AppenC_ASQ_total_results_diurnal_cort[5,8:13] <- res | |
| #ASQ and prenatal Cesd*child sex | |
| M1_total.INT1_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_DMeancon) | |
| AppenC_logit.res_DMeanconxChS <- logit_apa(M1_total.INT1_DMeancon,"Child_Sexgirl:mean_d_AUC_DIUR_only") | |
| #ASQ and prenatal Cesd*caseVScontrol | |
| M1_total.INT2_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| mean_d_AUC_DIUR_only + | |
| mean_d_AUC_DIUR_only:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_DMeancon) | |
| AppenC_logit.res_DMeanconxCaCo <- logit_apa(M1_total.INT2_DMeancon,"caseVScontrolcontrol:mean_d_AUC_DIUR_only") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| mean_d_AUC_DIUR_only, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_DMeancon) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DMeancon,"mean_d_AUC_DIUR_only") | |
| AppenC_ASQ_total_results_diurnal_cort[10,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_DMeancon <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| mean_d_AUC_DIUR_only, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_DMeancon) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DMeancon,"mean_d_AUC_DIUR_only") | |
| AppenC_ASQ_total_results_diurnal_cort[15,8:13] <- res | |
| #### Logistic Regression on diurnal slope #### | |
| #M1 | |
| M1_total_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total_DIURSlope) | |
| #document results | |
| res <- logit_apa(M1_total_DIURSlope,"Diurnal_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[3,8:13] <- res | |
| #ASQ and prenatal Cort*child sex | |
| M1_total.INT1_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| Diurnal_Slope + | |
| Diurnal_Slope:Child_Sex, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT1_DIURSlope) | |
| AppenC_logit.res_DIURSlopexChS <- logit_apa(M1_total.INT1_DIURSlope,"Child_Sexgirl:Diurnal_Slope") | |
| #ASQ and prenatal cort*caseVScontrol | |
| M1_total.INT2_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Diurnal_Slope + | |
| Diurnal_Slope:caseVScontrol, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M1_total.INT2_DIURSlope) | |
| AppenC_logit.res_DIURSlopexCaCo <- logit_apa(M1_total.INT2_DIURSlope,"caseVScontrolcontrol:Diurnal_Slope") | |
| #M2 ASQ and cortisol concentration + prenatal covariates | |
| M2_total.cov_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| Diurnal_Slope, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M2_total.cov_DIURSlope) | |
| #document results | |
| res <- logit_apa(M2_total.cov_DIURSlope,"Diurnal_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[6,8:13] <- res | |
| #ASQ and prenatal Cesd + postnatal covariates | |
| M3_total.cov_DIURSlope <- glm(Child_ASQ_totaldevelopmentalmilestones_Infancy_Sum_finalagerange_norm_dichom ~ | |
| ChildAge_ASQ_months_allchildren_cent + | |
| Child_Sex + | |
| caseVScontrol + | |
| Maternal_Age_Years_cent + | |
| Maternal_Education + | |
| Parity + | |
| Maternal_Body_Mass_Index_in_Early_Pregnancy_cent + | |
| Weight_Gain_cent + | |
| Maternal_Hypertensive_Disorders_anyVSnone + | |
| Maternal_Diabetes_Disorders_anyVSnone + | |
| Maternal_Smoking_During_Pregnancy + | |
| Gestational_Age_Weeks_cent + | |
| Child_Birth_Weight_cent + | |
| postpartum_BAI_cent + | |
| postpartum_Cesd_cent + | |
| Diurnal_Slope, | |
| data = ASQ_df_final_sub, | |
| family = "binomial") | |
| summary(M3_total.cov_DIURSlope) | |
| #document results | |
| res <- logit_apa(M3_total.cov_DIURSlope,"Diurnal_Slope") | |
| AppenC_ASQ_total_results_diurnalRhythm[9,8:13] <- res | |
| #### Repeat using bayesian approach ##### | |
| #### Interaction Table #### | |
| ### interaction effects #### | |
| ASQ_total_results_INT <- setNames(data.frame(matrix(ncol = 13, nrow = 22)), | |
| c("Cortisol Index", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| ASQ_total_results_INT[,1] <- c("By Child Sex", | |
| "Morning Early Pregnancy", | |
| "Morning Mid Pregnancy", | |
| "Morning Late Pregnancy", | |
| "Morning Pregnancy Mean", | |
| "Mean Morning_Slope", | |
| "Diurnal Early Pregnancy", | |
| "Diurnal Mid Pregnancy", | |
| "Diurnal Late Pregnancy", | |
| "Diurnal Pregnancy Mean", | |
| "Mean Diurnal_Slope", | |
| "By Case VS Control", | |
| "Morning Early Pregnancy", | |
| "Morning Mid Pregnancy", | |
| "Morning Late Pregnancy", | |
| "Morning Pregnancy Mean", | |
| "Mean Morning_Slope", | |
| "Diurnal Early Pregnancy", | |
| "Diurnal Mid Pregnancy", | |
| "Diurnal Late Pregnancy", | |
| "Diurnal Pregnancy Mean", | |
| "Mean Diurnal_Slope") | |
| ## sensitivity analysis | |
| AppenC_ASQ_total_results_INT <- setNames(data.frame(matrix(ncol = 13, nrow = 22)), | |
| c("Cortisol Parameter", | |
| "B", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p", | |
| "OR", | |
| "SE", | |
| "LL", | |
| "UL", | |
| "z", | |
| "p")) | |
| AppenC_ASQ_total_results_INT[,1] <- c("By Child Sex", | |
| "Morning Early Pregnancy", | |
| "Morning Mid Pregnancy", | |
| "Morning Late Pregnancy", | |
| "Morning Pregnancy Mean", | |
| "Mean Morning_Slope", | |
| "Diurnal Early Pregnancy", | |
| "Diurnal Mid Pregnancy", | |
| "Diurnal Late Pregnancy", | |
| "Diurnal Pregnancy Mean", | |
| "Mean Diurnal_Slope", | |
| "By Case VS Control", | |
| "Morning Early Pregnancy", | |
| "Morning Mid Pregnancy", | |
| "Morning Late Pregnancy", | |
| "Morning Pregnancy Mean", | |
| "Mean Morning_Slope", | |
| "Diurnal Early Pregnancy", | |
| "Diurnal Mid Pregnancy", | |
| "Diurnal Late Pregnancy", | |
| "Diurnal Pregnancy Mean", | |
| "Mean Diurnal_Slope") | |
| #add interaction effects | |
| ASQ_total_results_INT[2,2:7] <- Tobit_res.CAR_conxChSI #[c("z","p")] | |
| ASQ_total_results_INT[3,2:7] <- Tobit_res.CAR_conxChSII #[c("z","p")] | |
| ASQ_total_results_INT[4,2:7] <- Tobit_res.CAR_conxChSIII #[c("z","p")] | |
| ASQ_total_results_INT[5,2:7] <- Tobit_res.CAR_MeanconxChS #[c("z","p")] | |
| ASQ_total_results_INT[6,2:7] <- Tobit_res.CAR_MornSlopexChS #[c("z","p")] | |
| ASQ_total_results_INT[7,2:7] <- Tobit_res.DIUR_conxChSI #[c("z","p")] | |
| ASQ_total_results_INT[8,2:7] <- Tobit_res.DIUR_conxChSII #[c("z","p")] | |
| ASQ_total_results_INT[9,2:7] <- Tobit_res.DIUR_conxChSIII # [c("z","p")] | |
| ASQ_total_results_INT[10,2:7] <- Tobit_res.DIUR_MeanconxChS #[c("z","p")] | |
| ASQ_total_results_INT[11,2:7] <- Tobit_res.DIUR_SlopexChS #[c("z","p")] | |
| #neurodevelopemntal delay | |
| ASQ_total_results_INT[2,8:13] <- logit.res_CARconxChSI #[c("z","p")] | |
| ASQ_total_results_INT[3,8:13] <- logit.res_CARconxChSII #[c("z","p")] | |
| ASQ_total_results_INT[4,8:13] <- logit.res_CARconxChSIII #[c("z","p")] | |
| ASQ_total_results_INT[5,8:13] <- logit.res_MeanconxChS #[c("z","p")] | |
| ASQ_total_results_INT[6,8:13] <- logit.res_mornSlopexChS #[c("z","p")] | |
| ASQ_total_results_INT[7,8:13] <- logit.res_DIURconxChSI #[c("z","p")] | |
| ASQ_total_results_INT[8,8:13] <- logit.res_DIURconxChSII #[c("z","p")] | |
| ASQ_total_results_INT[9,8:13] <- logit.res_DIURconxChSIII #[c("z","p")] | |
| ASQ_total_results_INT[10,8:13] <- logit.res_DMeanconxChS #[c("z","p")] | |
| ASQ_total_results_INT[11,8:13] <- logit.res_DIURSlopexChS #[c("z","p")] | |
| #caseVScontrol | |
| ASQ_total_results_INT[13,2:7] <- Tobit_res.CAR_conxCaCoI #[c("z","p")] | |
| ASQ_total_results_INT[14,2:7] <- Tobit_res.CAR_conxCaCoII #[c("z","p")] | |
| ASQ_total_results_INT[15,2:7] <- Tobit_res.CAR_conxCaCoIII #[c("z","p")] | |
| ASQ_total_results_INT[16,2:7] <- Tobit_res.CAR_MeanconxCaCo #[c("z","p")] | |
| ASQ_total_results_INT[17,2:7] <- Tobit_res.CAR_MornSlopexCaCo #[c("z","p")] | |
| ASQ_total_results_INT[18,2:7] <- Tobit_res.DIUR_conxCaCoI #[c("z","p")] | |
| ASQ_total_results_INT[19,2:7] <- Tobit_res.DIUR_conxCaCoII #[c("z","p")] | |
| ASQ_total_results_INT[20,2:7] <- Tobit_res.DIUR_conxCaCoIII #[c("z","p")] | |
| ASQ_total_results_INT[21,2:7] <- Tobit_res.DIUR_MeanconxCaCo #[c("z","p")] | |
| ASQ_total_results_INT[22,2:7] <- Tobit_res.DIUR_SlopexCaCo #[c("z","p")] | |
| #for neurodevelopemtnal delay | |
| ASQ_total_results_INT[13,8:13] <- logit.res__CARconxCaCoI #[c("z","p")] | |
| ASQ_total_results_INT[14,8:13] <- logit.res__CARconxCaCoII #[c("z","p")] | |
| ASQ_total_results_INT[15,8:13] <- logit.res__CARconxCaCoIII #[c("z","p")] | |
| ASQ_total_results_INT[16,8:13] <- logit.res_MeanconxCaCo #[c("z","p")] | |
| ASQ_total_results_INT[17,8:13] <- logit.res_mornSlopexCaCo #[c("z","p")] | |
| ASQ_total_results_INT[18,8:13] <- logit.res_DIURconxCaCoI #[c("z","p")] | |
| ASQ_total_results_INT[19,8:13] <- logit.res_DIURconxCaCoII #[c("z","p")] | |
| ASQ_total_results_INT[20,8:13] <- logit.res_DIURconxCaCoIII #[c("z","p")] | |
| ASQ_total_results_INT[21,8:13] <- logit.res_DMeanconxCaCo #[c("z","p")] | |
| ASQ_total_results_INT[22,8:13] <- logit.res_DIURSlopexCaCo #[c("z","p")] | |
| # ##sensitivity analysis | |
| # #add interaction effects | |
| AppenC_ASQ_total_results_INT[2,2:3] <- AppenC_Tobit_res.CAR_conxChSI #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[3,2:3] <- AppenC_Tobit_res.CAR_conxChSII #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[4,2:3] <- AppenC_Tobit_res.CAR_conxChSIII #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[5,2:3] <- AppenC_Tobit_res.CAR_MeanconxChS #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[6,2:3] <- AppenC_Tobit_res.CAR_MornSlopexChS #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[7,2:3] <- AppenC_Tobit_res.DIUR_conxChSI #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[8,2:3] <- AppenC_Tobit_res.DIUR_conxChSII #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[9,2:3] <- AppenC_Tobit_res.DIUR_conxChSIII #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[10,2:3] <- AppenC_Tobit_res.DIUR_MeanconxChS #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[11,2:3] <- AppenC_Tobit_res.DIUR_SlopexChS #[c("z","p")] | |
| #neurodevelopemntal delay | |
| AppenC_ASQ_total_results_INT[2,4:5] <- AppenC_logit.res_CARconxChSI #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[3,4:5] <- AppenC_logit.res_CARconxChSII #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[4,4:5] <- AppenC_logit.res_CARconxChSIII #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[5,4:5] <- AppenC_logit.res_MeanconxChS #[c("z","p")] | |
| AppenC_ASQ_total_results_INT[6,4:5] <- AppenC_logit.res_mornSlopexChS#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[7,4:5] <- AppenC_logit.res_DIURconxChSI#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[8,4:5] <- AppenC_logit.res_DIURconxChSII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[9,4:5] <- AppenC_logit.res_DIURconxChSIII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[10,4:5] <- AppenC_logit.res_DMeanconxChS#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[11,4:5] <- AppenC_logit.res_DIURSlopexChS#[c("z","p")] | |
| #caseVScontrol | |
| AppenC_ASQ_total_results_INT[13,2:3] <- AppenC_Tobit_res.CAR_conxCaCoI#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[14,2:3] <- AppenC_Tobit_res.CAR_conxCaCoII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[15,2:3] <- AppenC_Tobit_res.CAR_conxCaCoIII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[16,2:3] <- AppenC_Tobit_res.CAR_MeanconxCaCo#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[17,2:3] <- AppenC_Tobit_res.CAR_MornSlopexCaCo#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[18,2:3] <- AppenC_Tobit_res.DIUR_conxCaCoI#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[19,2:3] <- AppenC_Tobit_res.DIUR_conxCaCoII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[20,2:3] <- AppenC_Tobit_res.DIUR_conxCaCoIII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[21,2:3] <- AppenC_Tobit_res.DIUR_MeanconxCaCo#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[22,2:3] <- AppenC_Tobit_res.DIUR_SlopexCaCo#[c("z","p")] | |
| #for neurodevelopemtnal delay | |
| AppenC_ASQ_total_results_INT[13,4:5] <- AppenC_logit.res__CARconxCaCoI#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[14,4:5] <- AppenC_logit.res__CARconxCaCoII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[15,4:5] <- AppenC_logit.res__CARconxCaCoIII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[16,4:5] <- AppenC_logit.res_MeanconxCaCo#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[17,4:5] <- AppenC_logit.res_mornSlopexCaCo#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[18,4:5] <- AppenC_logit.res_DIURconxCaCoI#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[19,4:5] <- AppenC_logit.res_DIURconxCaCoII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[20,4:5] <- AppenC_logit.res_DIURconxCaCoIII#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[21,4:5] <- AppenC_logit.res_DMeanconxCaCo#[c("z","p")] | |
| AppenC_ASQ_total_results_INT[22,4:5] <- AppenC_logit.res_DIURSlopexCaCo#[c("z","p")] | |