Johannification;

DESCRIPTION

@@ -1,35 +1,37 @@
-Package: MARMoSET
-Type: Package
-Title: Get metadata out of raw files
-Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <yourself@somewhere.net>
-Description: This packages uses a c# command line tool to extract the meta data of a raw file into a json file.
-    It contains methods to collect data requred for publication by journal and to write them into a tab delimited text file. 
-License: What license is it under?
-Encoding: UTF-8
-LazyData: true
-Imports:
-    assertive.base,
-    assertive.files,
-    assertive.numbers,
-    assertive.properties,
-    assertive.reflection,
-    assertive.sets,
-    assertive.strings,
-    assertive.types,
-    dplyr,
-    jsonlite,
-    pathological,
-    rlist,
-    stringi,
-    tidyr,
-    magrittr
-Depends:
-    R (>= 2.10)
-Suggests:
-    readODS,
-    knitr,
-    rmarkdown
-RoxygenNote: 6.1.1
-VignetteBuilder: knitr
+Package: MARMoSET
+Type: Package
+Title: Get metadata out of raw files
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: Extraction of meta data from Thermo Fisher Scientific mass spectrometric raw data files into a json file via a
+    c# command line tool.
+    Also provided are methods to assemble data requred for publication by journals and to write them into a tab delimited text file. 
+License: GPL (>= 3)
+Encoding: UTF-8
+LazyData: true
+Imports:
+    assertive.base,
+    assertive.files,
+    assertive.numbers,
+    assertive.properties,
+    assertive.reflection,
+    assertive.sets,
+    assertive.strings,
+    assertive.types,
+    dplyr,
+    jsonlite,
+    magrittr,
+    pathological,
+    rlist,
+    stringi,
+    tidyr,
+    utils
+Depends:
+    R (>= 2.10)
+Suggests:
+    readODS,
+    knitr,
+    rmarkdown
+RoxygenNote: 6.1.1
+VignetteBuilder: knitr

MARMoSET.Rproj

@@ -1,19 +1,20 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageInstallArgs: --no-multiarch --with-keep.source
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran

R/additional_functions.R

@@ -1,80 +1,82 @@
-#' Number of groups in the json file
-#'
-#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
-#'
-#' @return Count of groups in the JSON file.
-#'
-#' @examples
-#' data <- system.file(
-#'    file.path('extdata', 'testfile.raw'),
-#'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- generate_json(data)
-#'
-#' group_count(json)
-#'
-#' @export
-
-group_count <- function(json)
-{
-  assertive.types::assert_is_list(json)
-
-  return(json[["Group"]] %>% length())
-}
-
-
-#' Filenames of one group
-#'
-#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
-#' @param group_number An index that determines the group.
-#'
-#' @return A list of filenames belonging to the choosen group.
-#'
-#' @examples
-#' data <- system.file(
-#'    file.path('extdata', 'testfile.raw'),
-#'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- generate_json(data)
-#'
-#' files_in_group(json, 1)
-#'
-#' @export
-
-files_in_group <- function(json, group_number)
-{
-  assertive.types::assert_is_list(json)
-  assertive.types::assert_is_a_number(group_number)
-  assertive.numbers::assert_all_are_less_than_or_equal_to(group_number, group_count(json))
-
-  return(json[["Group"]][[group_number]][["Names"]])
-}
-
-
-#' Get instrument names
-#'
-#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
-#' @param group_number An index that determines the group.
-#'
-#' @return A list of instruments used in the choosen group.
-#'
-#' @examples
-#' data <- system.file(
-#'    file.path('extdata', 'testfile.raw'),
-#'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- generate_json(data)
-#'
-#' instrument_names(json, 1)
-#'
-#' @export
-
-instrument_names <- function(json, group_number)
-{
-  assertive.types::assert_is_list(json)
-  assertive.types::assert_is_a_number(group_number)
-  assertive.numbers::assert_all_are_less_than_or_equal_to(group_number, group_count(json))
-
-  instruments <- json[["Group"]][[group_number]][["Instruments"]] %>%
-                  summary() %>%
-                  rownames()
-
-  return(instruments)
-}
+#' Number of groups in the json file
+#'
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
+#'
+#' @return Count of groups in the JSON file.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- generate_json(data)
+#'
+#' group_count(json)
+#'
+#' @export
+
+group_count <- function(json)
+{
+  assertive.types::assert_is_list(json)
+
+  return(json[["Group"]] %>% length())
+}
+
+
+#' Filenames of one group
+#'
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
+#' @param group_number An index that determines the group.
+#'
+#' @return A list of filenames belonging to the choosen group.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#'
+#' # Real-time JSON-generation: `json <- generate_json(data)`
+#' json <- MARMoSET::testfile_json
+#'
+#' files_in_group(json, 1)
+#'
+#' @export
+
+files_in_group <- function(json, group_number)
+{
+  assertive.types::assert_is_list(json)
+  assertive.types::assert_is_a_number(group_number)
+  assertive.numbers::assert_all_are_less_than_or_equal_to(group_number, group_count(json))
+
+  return(json[["Group"]][[group_number]][["Names"]])
+}
+
+
+#' Get instrument names
+#'
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
+#' @param group_number An index that determines the group.
+#'
+#' @return A list of instruments used in the choosen group.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- generate_json(data)
+#'
+#' instrument_names(json, 1)
+#'
+#' @export
+
+instrument_names <- function(json, group_number)
+{
+  assertive.types::assert_is_list(json)
+  assertive.types::assert_is_a_number(group_number)
+  assertive.numbers::assert_all_are_less_than_or_equal_to(group_number, group_count(json))
+
+  instruments <- json[["Group"]][[group_number]][["Instruments"]] %>%
+                  summary() %>%
+                  rownames()
+
+  return(instruments)
+}