From 2776861cdd6a5e4fdfea5f617a54c5c7581fb8b0 Mon Sep 17 00:00:00 2001 From: Preston Burns Date: Tue, 5 Feb 2019 16:29:40 -0500 Subject: [PATCH 1/2] update description file --- DESCRIPTION | 2 ++ 1 file changed, 2 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 441d1ad5..9ab41ba1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -11,6 +11,8 @@ Authors@R: c( person("Rho Inc.", role = "cph")) Maintainer: Jeremy Wildfire Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries. +URL: https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics +BugReports: https://github.com/ASA-DIA-InteractiveSafetyGraphics/safetyGraphics/issues Depends: R (>= 3.5) License: MIT + file LICENSE Encoding: UTF-8 From 670c1646202b4ec4de35b392e6503a1964d3c944 Mon Sep 17 00:00:00 2001 From: Preston Burns Date: Wed, 6 Feb 2019 09:19:01 -0500 Subject: [PATCH 2/2] update manual --- R/checkColumnSetting.R | 1 + R/checkFieldSettings.R | 3 ++- R/checkNumericColumns.R | 1 + R/checkSettingProvided.R | 2 +- R/compare_cols.R | 2 +- R/getRequiredColumns.R | 1 + R/getSettingKeys.R | 2 +- R/getSettingValue.R | 1 + R/textKeysToList.R | 2 ++ man/checkColumnSetting.Rd | 1 + man/checkFieldSettings.Rd | 1 + man/checkNumericColumns.Rd | 1 + man/checkSettingProvided.Rd | 2 +- man/compare_cols.Rd | 2 +- man/getRequiredColumns.Rd | 1 + man/getSettingKeys.Rd | 1 + man/getSettingValue.Rd | 1 + man/textKeysToList.Rd | 2 ++ 18 files changed, 21 insertions(+), 6 deletions(-) diff --git a/R/checkColumnSetting.R b/R/checkColumnSetting.R index d3f334f7..b09e1107 100644 --- a/R/checkColumnSetting.R +++ b/R/checkColumnSetting.R @@ -32,6 +32,7 @@ #' #invalid column fails #' safetyGraphics:::checkColumnSetting(key=list("filters",3,"value_col"), #' settings=testSettings, adlbc) +#' @keywords internal checkColumnSetting <- function(key, settings, data){ stopifnot(typeof(key)=="list",typeof(settings)=="list") diff --git a/R/checkFieldSettings.R b/R/checkFieldSettings.R index d5095a3a..772ca3e6 100644 --- a/R/checkFieldSettings.R +++ b/R/checkFieldSettings.R @@ -20,7 +20,8 @@ #' @importFrom stringr str_split #' @importFrom magrittr "%>%" #' @importFrom purrr map -#' +#' @keywords internal + checkFieldSettings <- function(fieldKey, settings, data){ diff --git a/R/checkNumericColumns.R b/R/checkNumericColumns.R index d2ba46be..80e5581e 100644 --- a/R/checkNumericColumns.R +++ b/R/checkNumericColumns.R @@ -18,6 +18,7 @@ #' #fails since groups aren't specified by default #' safetyGraphics:::checkSettingProvided(key=list("groups",1,"value_col"),settings=testSettings) #' +#' @keywords internal checkNumericColumns <- function(key, settings, data){ stopifnot(typeof(key)=="list",typeof(settings)=="list") diff --git a/R/checkSettingProvided.R b/R/checkSettingProvided.R index f837e9ea..6032b38d 100644 --- a/R/checkSettingProvided.R +++ b/R/checkSettingProvided.R @@ -20,7 +20,7 @@ #' #fails since groups aren't specified by default #' safetyGraphics:::checkSettingProvided(key=list("groups",1,"value_col"), #' settings=testSettings) -#' +#' @keywords internal checkSettingProvided <- function(key, settings){ stopifnot(typeof(key)=="list",typeof(settings)=="list") diff --git a/R/compare_cols.R b/R/compare_cols.R index 47f2c3ac..32202fdb 100644 --- a/R/compare_cols.R +++ b/R/compare_cols.R @@ -15,7 +15,7 @@ #' # match == TRUE #' safetyGraphics:::compare_cols(names(adlbc), #' safetyGraphics:::getRequiredColumns(standard="ADaM")) -#' +#' @keywords internal compare_cols<-function(data_cols, standard_cols){ compare_summary <- list() diff --git a/R/getRequiredColumns.R b/R/getRequiredColumns.R index 8b1c6546..7c588adc 100644 --- a/R/getRequiredColumns.R +++ b/R/getRequiredColumns.R @@ -11,6 +11,7 @@ #' safetyGraphics:::getRequiredColumns(standard="SDTM") #' #' @importFrom rlang .data +#' @keywords internal getRequiredColumns<-function(standard,chart="eDish"){ stopifnot( diff --git a/R/getSettingKeys.R b/R/getSettingKeys.R index 4fcdbeff..90729da7 100644 --- a/R/getSettingKeys.R +++ b/R/getSettingKeys.R @@ -31,7 +31,7 @@ #' matchLists=TRUE) #' #' @importFrom stringr str_detect -#' +#' @keywords internal diff --git a/R/getSettingValue.R b/R/getSettingValue.R index c50382ca..9794482c 100644 --- a/R/getSettingValue.R +++ b/R/getSettingValue.R @@ -15,6 +15,7 @@ #' safetyGraphics:::getSettingValue(list("measure_values","ALP"),testSettings) #' safetyGraphics:::getSettingValue(list("NotASetting"),testSettings) #returns NULL #' +#' @keywords internal getSettingValue <- function(key,settings){ stopifnot(typeof(settings)=="list") diff --git a/R/textKeysToList.R b/R/textKeysToList.R index 62f89020..495d00e6 100644 --- a/R/textKeysToList.R +++ b/R/textKeysToList.R @@ -11,6 +11,8 @@ #' #' #list(list("id_col"),list("measure_col","label")) #' safetyGraphics:::textKeysToList(c("id_col","measure_col--label")) +#' +#' @keywords internal textKeysToList <- function(textKeys){ diff --git a/man/checkColumnSetting.Rd b/man/checkColumnSetting.Rd index a94b6126..01e113b8 100644 --- a/man/checkColumnSetting.Rd +++ b/man/checkColumnSetting.Rd @@ -45,3 +45,4 @@ safetyGraphics:::checkColumnSetting(key=list("filters",2,"value_col"), safetyGraphics:::checkColumnSetting(key=list("filters",3,"value_col"), settings=testSettings, adlbc) } +\keyword{internal} diff --git a/man/checkFieldSettings.Rd b/man/checkFieldSettings.Rd index a19243ef..708ad3ed 100644 --- a/man/checkFieldSettings.Rd +++ b/man/checkFieldSettings.Rd @@ -30,3 +30,4 @@ safetyGraphics:::checkFieldSettings(fieldKey=list("measure_values"), settings=testSettings, adlbc) } +\keyword{internal} diff --git a/man/checkNumericColumns.Rd b/man/checkNumericColumns.Rd index b70eaf1b..afc95c7f 100644 --- a/man/checkNumericColumns.Rd +++ b/man/checkNumericColumns.Rd @@ -31,3 +31,4 @@ safetyGraphics:::checkSettingProvided(key=list("filters"),settings=testSettings) safetyGraphics:::checkSettingProvided(key=list("groups",1,"value_col"),settings=testSettings) } +\keyword{internal} diff --git a/man/checkSettingProvided.Rd b/man/checkSettingProvided.Rd index 58af6a07..e08d407b 100644 --- a/man/checkSettingProvided.Rd +++ b/man/checkSettingProvided.Rd @@ -31,5 +31,5 @@ safetyGraphics:::checkSettingProvided(key=list("filters"), #fails since groups aren't specified by default safetyGraphics:::checkSettingProvided(key=list("groups",1,"value_col"), settings=testSettings) - } +\keyword{internal} diff --git a/man/compare_cols.Rd b/man/compare_cols.Rd index 47c50785..a5a67420 100644 --- a/man/compare_cols.Rd +++ b/man/compare_cols.Rd @@ -25,5 +25,5 @@ safetyGraphics:::compare_cols(data_cols=c("a","b","c"), # match == TRUE safetyGraphics:::compare_cols(names(adlbc), safetyGraphics:::getRequiredColumns(standard="ADaM")) - } +\keyword{internal} diff --git a/man/getRequiredColumns.Rd b/man/getRequiredColumns.Rd index a5643912..8ea9d63f 100644 --- a/man/getRequiredColumns.Rd +++ b/man/getRequiredColumns.Rd @@ -22,3 +22,4 @@ safetyGraphics:::getRequiredColumns(standard="ADAM") safetyGraphics:::getRequiredColumns(standard="SDTM") } +\keyword{internal} diff --git a/man/getSettingKeys.Rd b/man/getSettingKeys.Rd index 661ab999..349ae48f 100644 --- a/man/getSettingKeys.Rd +++ b/man/getSettingKeys.Rd @@ -45,3 +45,4 @@ safetyGraphics:::getSettingKeys(patterns=c("measure_values"), matchLists=TRUE) } +\keyword{internal} diff --git a/man/getSettingValue.Rd b/man/getSettingValue.Rd index ca3c989e..586668bf 100644 --- a/man/getSettingValue.Rd +++ b/man/getSettingValue.Rd @@ -26,3 +26,4 @@ safetyGraphics:::getSettingValue(list("measure_values","ALP"),testSettings) safetyGraphics:::getSettingValue(list("NotASetting"),testSettings) #returns NULL } +\keyword{internal} diff --git a/man/textKeysToList.Rd b/man/textKeysToList.Rd index 31cd0f86..9a11e91a 100644 --- a/man/textKeysToList.Rd +++ b/man/textKeysToList.Rd @@ -21,4 +21,6 @@ safetyGraphics:::textKeysToList("id_col") #list(list("id_col"),list("measure_col","label")) safetyGraphics:::textKeysToList(c("id_col","measure_col--label")) + } +\keyword{internal}