fix all cran comments

Author: RichardHooijmaijers

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.5.0
-Date: 2024-11-11 14:52:47 UTC
-SHA: 6383cfbb58ebad20005d83d85265f7f010208320
+Date: 2024-11-12 15:06:04 UTC
+SHA: d52926094d51d21be79ff3d152278ffb53cb831b

DESCRIPTION

@@ -6,8 +6,9 @@ Authors@R: c(person("Richard", "Hooijmaijers", email = "richardhooijmaijers@gmai
              person("LAPP Consultants",email = "info@lapp.nl", role=c("fnd","cph")),
              person("Matthew Fidler",role=c("ctb")),
              person("Veerle van Leemput",role=c("ctb")))
-Description: An interface for the 'nlmixr2' package. Furthermore additional functions
-  are included to work with the 'nlmixr2' package through the command line.
+Description: An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package, 
+  designed to simplify the modeling process for users. Additionally, this package includes supplementary functions 
+  to further enhances the usage of 'nlmixr2'.
 Depends:
   R (>= 3.5.0),
   shiny,

R/fit_plot.r

@@ -42,7 +42,7 @@ fit_plot <- function(dfrm,type="xpose",by="ID",idv="TIME",obs="DV",pred="PRED",i
 
   if(type=="xpose"){
     if((length(by)==1 && by!="ID") || length(by)>1 || idv!="TIME" || obs!="DV" || pred!="PRED" || ipred!="IPRED" || grp!="ID") stop("Changing variables does not work with xpose type of plots")
-    if("nlmixr2" %in% rownames(installed.packages())){
+    if(length(find.package("nlmixr2", quiet = TRUE))>0){
       xpdb <- xpose.nlmixr2::xpose_data_nlmixr2(dfrm)
     }else{
       stop("nlmixr2 package is not installed")

R/get_meta.r

@@ -6,6 +6,7 @@
 #' @param mdl character with the path of the model function
 #'
 #' @export
+#' @return A list with the models meta data
 #' @examples
 #'
 #' \dontrun{

R/get_proj.r

@@ -1,13 +1,14 @@
 #------------------------------------------ get_proj ------------------------------------------
 #' Read in and update model results in project object
 #'
-#' This function creates or updates a project object with models and/or results emerged from nlmixr runs
+#' This function creates or updates a project object with models and/or results emerged from nlmixr2 runs.
 #' A check is performed to see if newer results are present and only updates these.
 #'
 #' @param projloc character with the base location of the shinyMixR project
 #' @param geteval logical indicating if the model functions should be evaluated
 #'
 #' @export
+#' @return A named list with information for each model in the 'projloc'
 #' @examples
 #'
 #' \dontrun{

R/gof_plot.r

@@ -34,7 +34,7 @@
 #' }
 gof_plot <- function(dfrm,type="xpose",mdlnm=NULL,colby=NULL,ptype="all",outnm=NULL,projloc=".",title=NULL,linscale=FALSE,...){
   if(type=="xpose" & !is.null(colby)) stop("Color by does not work with xpose type of plots")
-  if(type=="xpose" && "nlmixr2" %in% rownames(installed.packages())){
+  if(type=="xpose" && length(find.package("nlmixr2", quiet = TRUE))>0){
     dat <- xpose.nlmixr2::xpose_data_nlmixr2(dfrm)
   }else{
     dat <- as.data.frame(dfrm)

R/misc.r

@@ -5,6 +5,7 @@
 #' @param x a numerical vector
 #' @param sdig a single number defining the number of significant digits
 #' @export
+#' @return A character vector with formatted numbers
 sigdigs <- function(x,sdig=3){
   om <- floor(log10(abs(x)))
   dp <- sdig-om-1
@@ -20,6 +21,7 @@ sigdigs <- function(x,sdig=3){
 #' @param type character with the type of alert to display
 #' @param ... other arguments passed to class
 #' @export
+#' @return No return value, called for side effects
 myalert <- function(text,type,...){
   shinyWidgets::sendSweetAlert(text = text,type = type,
     showClass=list(backdrop='swal2-noanimation'),width="30%",
@@ -33,6 +35,7 @@ myalert <- function(text,type,...){
 #' This function provides a custom theme for ggplot output
 #' @param fontsize numeric with the default fontsize passed through to theme
 #' @export
+#' @return A list with ggplot theme elements
 theme_shinyMixR <- function(fontsize=12){
   ret <- theme_bw(base_size = fontsize) + 
     theme(panel.border     = element_rect(color="grey30", size=0.75),

R/module_dataexplore.R

@@ -6,6 +6,7 @@
 #' @param id Module id
 #' 
 #' @export
+#' @return A list of html tags used for th UI of the app
 module_dataexplore_ui <- function(id) {
   ns <- NS(id)
   tagList(
@@ -143,6 +144,7 @@ module_dataexplore_ui <- function(id) {
 #' @param r reactive values object that is defined top-level
 #' 
 #' @export
+#' @return No return value, called for side effects
 module_dataexplore_server <- function(id, r) {
   moduleServer(id, function(input, output, session) {
 

R/module_edit.R

@@ -6,6 +6,7 @@
 #' @param id Module id
 #' 
 #' @export
+#' @return A list of html tags used for th UI of the app
 module_edit_ui <- function(id) {
   ns <- NS(id)
   tagList(
@@ -25,6 +26,7 @@ module_edit_ui <- function(id) {
 #' @param settings reactive value with the app settings
 #' 
 #' @export
+#' @return No return value, called for side effects
 module_edit_server <- function(id, r, settings) {
   moduleServer(id, function(input, output, session) {
     # Adapt model list based on selected project location

R/module_fitplots.R

@@ -7,6 +7,7 @@
 #' @param proj_obj Project object
 #' 
 #' @export
+#' @return A list of html tags used for th UI of the app
 module_fitplots_ui <- function(id, proj_obj) {
   ns <- NS(id)
   tagList(
@@ -42,6 +43,7 @@ module_fitplots_ui <- function(id, proj_obj) {
 #' @param settings reactive value with the app settings
 #' 
 #' @export
+#' @return No return value, called for side effects
 module_fitplots_server <- function(id, r, settings) {
   moduleServer(id, function(input, output, session) {
     # Adapt model list based on selected project location