improved documentation

replace x by object if possible

R/AllGeneric.R

@@ -1,33 +1,33 @@
 # Rainer Walke, MPIDR Rostock
 
-setGeneric("header", function(x) standardGeneric("header"))
+setGeneric("header", function(object) standardGeneric("header"))
 
-setGeneric("footer", function(x) standardGeneric("footer"))
+setGeneric("footer", function(object) standardGeneric("footer"))
 
-setGeneric("lt1", function(x) standardGeneric("lt1"))
+setGeneric("lt1", function(object) standardGeneric("lt1"))
 
-setGeneric("content", function(x) standardGeneric("content"))
+setGeneric("content", function(object) standardGeneric("content"))
 
-setGeneric("country", function(x) standardGeneric("country"))
+setGeneric("country", function(object) standardGeneric("country"))
 
-setGeneric("protocol", function(x) standardGeneric("protocol"))
+setGeneric("protocol", function(object) standardGeneric("protocol"))
 
-setGeneric("lt1<-", function(x, value) standardGeneric("lt1<-"))
+setGeneric("lt1<-", function(object, value) standardGeneric("lt1<-"))
 
-setGeneric("selectYears", function(x, selectYears) standardGeneric("selectYears"))
+setGeneric("selectYears", function(object, selectYears) standardGeneric("selectYears"))
 
-setGeneric("ex1", function(x) standardGeneric("ex1"))
+setGeneric("ex1", function(object) standardGeneric("ex1"))
 
-setGeneric("ex1<-", function(x, value) standardGeneric("ex1<-"))
+setGeneric("ex1<-", function(object, value) standardGeneric("ex1<-"))
 
 
-setGeneric("rd1", function(x) standardGeneric("rd1"))
+setGeneric("rd1", function(object) standardGeneric("rd1"))
 
-setGeneric("rd1<-", function(x, value) standardGeneric("rd1<-"))
+setGeneric("rd1<-", function(object, value) standardGeneric("rd1<-"))
 
-setGeneric("selectRegion", function(x, selectRegion) standardGeneric("selectRegion"))
+setGeneric("selectRegion", function(object, selectRegion) standardGeneric("selectRegion"))
 
-setGeneric("re1", function(x) standardGeneric("re1"))
+setGeneric("re1", function(object) standardGeneric("re1"))
 
-setGeneric("re1<-", function(x, value) standardGeneric("re1<-"))
+setGeneric("re1<-", function(object, value) standardGeneric("re1<-"))
 

R/GENESISClasses.R

@@ -22,22 +22,22 @@ setClass("RD1",
 
 # slot getters
 #' @export
-setMethod("header", "RD1", function(x) x@header)
+setMethod("header", "RD1", function(object) object@header)
 #' @export
-setMethod("footer", "RD1", function(x) x@footer)
+setMethod("footer", "RD1", function(object) object@footer)
 #' @export
-setMethod("rd1", "RD1", function(x) x@rd1)
+setMethod("rd1", "RD1", function(object) object@rd1)
 
 #' @export
-setMethod("content", "RD1", function(x) x@content)
+setMethod("content", "RD1", function(object) object@content)
 #' @export
-setMethod("country", "RD1", function(x) x@country)
+setMethod("country", "RD1", function(object) object@country)
 #' @export
-setMethod("protocol", "RD1", function(x) x@protocol)
+setMethod("protocol", "RD1", function(object) object@protocol)
 
 # slot setters
 #' @export
-setReplaceMethod("rd1", "RD1", function(x, value) {x@rd1 <- value; validObject(x); x})
+setReplaceMethod("rd1", "RD1", function(object, value) {object@rd1 <- value; validObject(object); object})
 
 # constructor
 #' @export
@@ -55,18 +55,18 @@ setMethod("show", "RD1",
 )
 
 #' @export
-setMethod("selectYears", "RD1", function(x, selectYears) {
+setMethod("selectYears", "RD1", function(object, selectYears) {
   Year <- NULL # evoid NOTE
-  .rd1 <- x@rd1[Year %in% selectYears]
-  return(new("RD1", header=x@header, footer=x@footer, rd1=.rd1, content=x@content, country=x@country, protocol=x@protocol))
+  .rd1 <- object@rd1[Year %in% selectYears]
+  return(new("RD1", header=object@header, footer=object@footer, rd1=.rd1, content=object@content, country=object@country, protocol=object@protocol))
 }
 )
 
 #' @export
-setMethod("selectRegion", "RD1", function(x, selectRegion) {
+setMethod("selectRegion", "RD1", function(object, selectRegion) {
   Region_Code <- NULL # evoid NOTE
-  .rd1 <- x@rd1[Region_Code %in% selectRegion]
-  return(new("RD1", header=x@header, footer=x@footer, rd1=.rd1, content=x@content, country=x@country, protocol=x@protocol))
+  .rd1 <- object@rd1[Region_Code %in% selectRegion]
+  return(new("RD1", header=object@header, footer=object@footer, rd1=.rd1, content=object@content, country=object@country, protocol=object@protocol))
 }
 )
 
@@ -105,22 +105,22 @@ setClass("RE1",
 
 # slot getters
 #' @export
-setMethod("header", "RE1", function(x) x@header)
+setMethod("header", "RE1", function(object) object@header)
 #' @export
-setMethod("footer", "RE1", function(x) x@footer)
+setMethod("footer", "RE1", function(object) object@footer)
 #' @export
-setMethod("re1", "RE1", function(x) x@re1)
+setMethod("re1", "RE1", function(object) object@re1)
 
 #' @export
-setMethod("content", "RE1", function(x) x@content)
+setMethod("content", "RE1", function(object) object@content)
 #' @export
-setMethod("country", "RE1", function(x) x@country)
+setMethod("country", "RE1", function(object) object@country)
 #' @export
-setMethod("protocol", "RE1", function(x) x@protocol)
+setMethod("protocol", "RE1", function(object) object@protocol)
 
 # slot setters
 #' @export
-setReplaceMethod("re1", "RE1", function(x, value) {x@re1 <- value; validObject(x); x})
+setReplaceMethod("re1", "RE1", function(object, value) {object@re1 <- value; validObject(object); object})
 
 # constructor
 #' @export
@@ -138,18 +138,18 @@ setMethod("show", "RE1",
 )
 
 #' @export
-setMethod("selectYears", "RE1", function(x, selectYears) {
+setMethod("selectYears", "RE1", function(object, selectYears) {
   Year <- NULL # evoid NOTE
-  .re1 <- x@re1[Year %in% selectYears]
-  return(new("RE1", header=x@header, footer=x@footer, re1=.re1, content=x@content, country=x@country, protocol=x@protocol))
+  .re1 <- object@re1[Year %in% selectYears]
+  return(new("RE1", header=object@header, footer=object@footer, re1=.re1, content=object@content, country=object@country, protocol=object@protocol))
 }
 )
 
 #' @export
-setMethod("selectRegion", "RE1", function(x, selectRegion) {
+setMethod("selectRegion", "RE1", function(object, selectRegion) {
   Region_Code <- NULL # evoid NOTE
-  .re1 <- x@re1[Region_Code %in% selectRegion]
-  return(new("RE1", header=x@header, footer=x@footer, re1=.re1, content=x@content, country=x@country, protocol=x@protocol))
+  .re1 <- object@re1[Region_Code %in% selectRegion]
+  return(new("RE1", header=object@header, footer=object@footer, re1=.re1, content=object@content, country=object@country, protocol=object@protocol))
 }
 )
 

R/HMDClasses.R

@@ -9,18 +9,21 @@ NULL
 ## S4 class definitions
 
 
-#' LT1 class for life-tables 1x1
+#' LT1 class for HMD life-tables 1x1
 #'
-#' The class \code{LT1} stores life-table information in a systematic way.
-#' It fits to Human Mortality Database (HMD) 1x1 period life tables.
+#' The class \code{LT1} stores HMD life table information in a systematic way.
+#'
+#' This \code{LT1} class fits to Human Mortality Database (HMD) 1x1 period life tables.
 #' See https://www.mortality.org/ for data details.
-#' An LT1 instance stores the raw header content and the life table as data.table.
-#' Further it adds a  pure numeric age AgeLow to the data.table.
+#' An LT1 instance stores the raw header, the content, 
+#' the version protocol and regional information and the
+#' life table as a data.table object.
+#' The validation adds a pure numeric age AgeLow to the life table.
 #'
 #' @slot content describes the content
 #' @slot country regional entity
 #' @slot header includes the raw header information
-#' @slot lt1 ist the life table (data.table)
+#' @slot lt1 stores the life table (data.table)
 #' @slot protocol contains the protocol information
 #' @export
 #' @rdname LT1-class
@@ -39,66 +42,116 @@ setClass("LT1",
 #' LT1 header
 #'
 #' The \code{header}-method gets the raw header information of an LT1 object
-#' @param x LT1-object
-#' @return raw header information
+#'
+#' @param object LT1-object
+#' @return The \code{header}-method returns the raw header information
 #' @export
 #' @rdname LT1-class
-setMethod("header", "LT1", function(x) x@header)
-#' @export
-setMethod("lt1", "LT1", function(x) x@lt1)
+setMethod("header", "LT1", function(object) object@header)
 
+#' LT1 lt1
+#'
+#' The \code{lt1}-method gets the life table information of an LT1 object
+#'
+#' @return The \code{lt1}-method returns the life-table
 #' @export
-setMethod("content", "LT1", function(x) x@content)
+#' @rdname LT1-class
+setMethod("lt1", "LT1", function(object) object@lt1)
+
+#' LT1 content
+#'
+#' The \code{content}-method gets the life table information of an LT1 object
+#'
+#' @return The \code{content}-method returns the content information
 #' @export
-setMethod("country", "LT1", function(x) x@country)
+#' @rdname LT1-class
+setMethod("content", "LT1", function(object) object@content)
+
+#' LT1 country
+#'
+#' The \code{country}-method gets the regional information of an LT1 object
+#'
+#' @return The \code{country}-method returns the regional information
 #' @export
-setMethod("protocol", "LT1", function(x) x@protocol)
+#' @rdname LT1-class
+setMethod("country", "LT1", function(object) object@country)
 
-# slot setters
+#' LT1 protocol
+#'
+#' The \code{protocol}-method gets the protocol information of an LT1 object
+#'
+#' @return The \code{protocol}-method returns the protocol information
 #' @export
-setReplaceMethod("lt1", "LT1", function(x, value) {x@lt1 <- value; validObject(x); x})
+#' @rdname LT1-class
+setMethod("protocol", "LT1", function(object) object@protocol)
 
+## slot setters
+
+#' LT1 lt1<-
+#'
+#' The \code{lt1<-}-method allows to modify the life table information in a LT1 object
+#'
+#' @param value data.table
+#' @return The \code{lt1<-}-method changes the life table information
+#' @export
+#' @rdname LT1-class
+setReplaceMethod("lt1", "LT1", function(object, value) {object@lt1 <- value; validObject(object); object})
 
 
 ## constructor
 
 #' LT1 constructor
 #'
 #' The \code{LTable1}-constructor creates an LT1 object
-#' @param object header lt1 content country protocol
-#' @return LT1 object
+#'
+#' @param header vector
+#' @param lt1 data.table
+#' @param content character
+#' @param country character
+#' @param  protocol character
+#' @return The \code{LTable1}-constructor returns an LT1 object
 #' @export
 #' @rdname LT1-class
 LTable1 <- function(header, lt1, content, country, protocol)
   new("LT1", header=header, lt1=lt1, content=content, country=country, protocol=protocol)
 
 ## methods
 
-
 #' LT1 length
 #'
 #' The \code{length}-method gets the number of rows int the LT1 lt1 data.table
 #' @param x LT1-object
-#' @return number of rows
+#' @return The \code{length}-method returns the number of rows
 #' @export
 #' @rdname LT1-class
 setMethod("length", "LT1", function(x) dim(x@lt1)[1])
 
+#' LT1 show
+#'
 #' @export
+#' @rdname LT1-class
 setMethod("show", "LT1",
           function(object)
             cat(class(object), "instance with length", length(object), "\n")
 )
 
+#' LT1 selectYears
+#'
+#' The \code{selectYears}-method gets a subset of an the LT1 object
+#'
+#' @param selectYears vector
+#' @return The \code{selectYears}-method returns an LT1 object
 #' @export
-setMethod("selectYears", "LT1", function(x, selectYears) {
+#' @rdname LT1-class
+setMethod("selectYears", "LT1", function(object, selectYears) {
   Year <- NULL # evoid NOTE
-  .lt1 <- x@lt1[Year %in% selectYears]
-            return(new("LT1", header=x@header, lt1=.lt1, content=x@content, country=x@country, protocol=x@protocol))
+  .lt1 <- object@lt1[Year %in% selectYears]
+            return(new("LT1", header=object@header, lt1=.lt1, content=object@content, country=object@country, protocol=object@protocol))
           }
 )
 
-# validity method
+## validity method
+
 #' @export
 setValidity("LT1",
             function(object) {
@@ -140,20 +193,20 @@ setClass("EX1",
 
 # slot getters
 #' @export
-setMethod("header", "EX1", function(x) x@header)
+setMethod("header", "EX1", function(object) object@header)
 #' @export
-setMethod("ex1", "EX1", function(x) x@ex1)
+setMethod("ex1", "EX1", function(object) object@ex1)
 
 #' @export
-setMethod("content", "EX1", function(x) x@content)
+setMethod("content", "EX1", function(object) object@content)
 #' @export
-setMethod("country", "EX1", function(x) x@country)
+setMethod("country", "EX1", function(object) object@country)
 #' @export
-setMethod("protocol", "EX1", function(x) x@protocol)
+setMethod("protocol", "EX1", function(object) object@protocol)
 
 # slot setters
 #' @export
-setReplaceMethod("ex1", "EX1", function(x, value) {x@ex1 <- value; validObject(x); x})
+setReplaceMethod("ex1", "EX1", function(object, value) {object@ex1 <- value; validObject(object); object})
 
 # constructor
 #' @export
@@ -170,10 +223,10 @@ setMethod("show", "EX1",
 )
 
 #' @export
-setMethod("selectYears", "EX1", function(x, selectYears) {
+setMethod("selectYears", "EX1", function(object, selectYears) {
   Year <- NULL # evoid NOTE
-  .ex1 <- x@ex1[Year %in% selectYears]
-  return(new("EX1", header=x@header, ex1=.ex1, content=x@content, country=x@country, protocol=x@protocol))
+  .ex1 <- object@ex1[Year %in% selectYears]
+  return(new("EX1", header=object@header, ex1=.ex1, content=object@content, country=object@country, protocol=object@protocol))
 }
 )