From 06caa95f5a6e2185b821ef868a26051be151e485 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 10:35:33 +0200
Subject: [PATCH 01/41] move global, server, ui in app.R file

---
 inst/Dashboard/app.R    | 86 +++++++++++++++++++++++++++++++++++++++++
 inst/Dashboard/global.R | 22 -----------
 inst/Dashboard/server.R | 14 -------
 inst/Dashboard/ui.R     | 51 ------------------------
 4 files changed, 86 insertions(+), 87 deletions(-)
 create mode 100644 inst/Dashboard/app.R
 delete mode 100644 inst/Dashboard/global.R
 delete mode 100644 inst/Dashboard/server.R
 delete mode 100644 inst/Dashboard/ui.R

diff --git a/inst/Dashboard/app.R b/inst/Dashboard/app.R
new file mode 100644
index 0000000..3168c7e
--- /dev/null
+++ b/inst/Dashboard/app.R
@@ -0,0 +1,86 @@
+# Loading libraries
+library(shiny)     # Used as it is a shiny app
+library(bs4Dash)   # Used instead of shinydashboard to provide additional options
+library(fresh)     # Used to easily change css in bs4Dash
+library(ggplot2)   # Used for plotting
+library(shinyMixR) # Used for everything else
+
+# Check and load nlmixr(2)
+if ("nlmixr2" %in% rownames(installed.packages())){
+  library(nlmixr2)
+} else {
+  cat("you need the 'nlmixr2' package to run models\n")
+}
+
+# Create theme for dashboard
+newtheme <- create_theme(
+  theme = "darkly", # theme has no effect, at least within bs4Dash
+  bs4dash_font(size_base = "0.9rem"),
+  bs4dash_status(primary = "#3c8dbc")
+)
+
+ui <- dashboardPage(
+  title = "shinyMixR",
+  # Header
+  header = dashboardHeader(
+    title = dashboardBrand(title = "ShinyMixR", color = "lightblue"), #, color = "lightblue", href = "#", image = "logoshinyMixR.png"),
+    leftUI = tags$img(src='logoshinyMixR.png',height=40)
+  ),
+  # Sidebar menu
+  sidebar = dashboardSidebar(status="lightblue", elevation = 1,
+                             sidebarMenu(id="tabs", 
+                                         menuItem('Model overview', tabName='overview', icon=icon('table')),
+                                         menuItem('Edit model(s)', tabName='editor', icon=icon('file-pen')),
+                                         menuItem('Run model(s)', tabName='run', icon=icon('person-running')),
+                                         menuItem('Parameter estimates', tabName='par', icon=icon('table-cells')),
+                                         menuItem('Goodness of fit', tabName='gof', icon=icon('chart-line')),
+                                         menuItem('Fit plots', tabName='fitpl', icon=icon('chart-line')),
+                                         menuItem('Data exploration', tabName='expl', icon=icon('magnifying-glass')),
+                                         menuItem('Settings', tabName='settings', icon=icon('gear'))
+                             )
+  ),
+  # Main body
+  body = dashboardBody(
+    # First set theme and include css
+    use_theme(newtheme),
+    # CHECK IF THE LINES BELOW WILL WORK WITHOUT INTERNET CONNECTION AND DOES IT FAIL GRACEFULLY?!
+    shinyWidgets::useSweetAlert("minimal"),
+    tags$style("@import url(https://use.fontawesome.com/releases/v6.3.0/css/all.css);"),
+    tags$head(tags$style(HTML(".shiny-split-layout > div {overflow: visible;}"))),
+    tags$head(tags$style("#progph{overflow-y:scroll; max-height: 600px;}")),
+    tags$head(tags$style(HTML("#exploretabout{height: 75vh; overflow-y: auto;}"))),
+    tags$head(tags$style(HTML(".swal2-popup {font-size: 0.9rem !important;}"))),    
+    tags$head(tags$style(HTML("input[id$=\"subset\"]{font-family:\"Courier New\"}"))),
+    tags$head(tags$style(HTML("input[id$=\"precode\"]{font-family:\"Courier New\"}"))),
+    tags$head(tags$style(HTML("label{margin-bottom:0rem;}"))),
+    tabItems(
+      tabItem(tabName = "overview", module_overview_ui("oview")),
+      tabItem(tabName = "editor", module_edit_ui("editor")),
+      tabItem(tabName = "run", module_run_ui("modrun")),
+      tabItem(tabName = "par", module_pt_ui("partable")),
+      tabItem(tabName = "gof", module_gof_ui("gofplots")),
+      tabItem(tabName = "fitpl", module_fitplots_ui("fitplots")),
+      tabItem(tabName = "expl", module_dataexplore_ui("explore")),
+      tabItem(tabName = "settings", module_settings_ui("settings"))
+    )  
+  )
+)
+
+server <- function(input, output, session) {
+  
+  # Top-level reactive values
+  r <- reactiveValues(active_tab = "",
+                      model_updated = 0)
+  observeEvent(input$tabs, r$active_tab <- input$tabs)
+  sett <- module_settings_server("settings")
+  module_overview_server("oview")
+  module_edit_server("editor", r = r, settings=sett)
+  module_run_server("modrun", r = r)
+  module_pt_server("partable", r = r)
+  module_gof_server("gofplots", r = r,settings=sett)
+  module_fitplots_server("fitplots", r = r,settings=sett)
+  module_dataexplore_server("explore", r = r)
+
+}
+
+shinyApp(ui = ui, server = server)
diff --git a/inst/Dashboard/global.R b/inst/Dashboard/global.R
deleted file mode 100644
index fff3fbd..0000000
--- a/inst/Dashboard/global.R
+++ /dev/null
@@ -1,22 +0,0 @@
-# Loading libraries
-library(shiny)     # Used as it is a shiny app
-library(bs4Dash)   # Used instead of shinydashboard to provide additional options
-library(fresh)     # Used to easily change css in bs4Dash
-library(ggplot2)   # Used for plotting
-library(shinyMixR) # Used for everything else
-
-# Check and load nlmixr(2)
-if("nlmixr2" %in% rownames(installed.packages())){
-  library(nlmixr2)
-}else if("nlmixr" %in% rownames(installed.packages())){
-  library(nlmixr)
-}else{
-  cat("you need either the 'nlmixr' or 'nlmixr2' package to run models\n")
-}
-
-# Create theme for dashboard
-newtheme <- create_theme(
-  theme = "darkly", # theme has no effect, at least within bs4Dash
-  bs4dash_font(size_base = "0.9rem"),
-  bs4dash_status(primary = "#3c8dbc")
-)
\ No newline at end of file
diff --git a/inst/Dashboard/server.R b/inst/Dashboard/server.R
deleted file mode 100644
index f99ffc3..0000000
--- a/inst/Dashboard/server.R
+++ /dev/null
@@ -1,14 +0,0 @@
-server <- function(input, output, session) {
-  # Top-level reactive values
-  r <- reactiveValues(active_tab = "",
-                      model_updated = 0)
-  observeEvent(input$tabs, r$active_tab <- input$tabs)
-  sett <- module_settings_server("settings")
-  module_overview_server("oview")
-  module_edit_server("editor", r = r, settings=sett)
-  module_run_server("modrun", r = r)
-  module_pt_server("partable", r = r)
-  module_gof_server("gofplots", r = r,settings=sett)
-  module_fitplots_server("fitplots", r = r,settings=sett)
-  module_dataexplore_server("explore", r = r)
-}
\ No newline at end of file
diff --git a/inst/Dashboard/ui.R b/inst/Dashboard/ui.R
deleted file mode 100644
index 2d11036..0000000
--- a/inst/Dashboard/ui.R
+++ /dev/null
@@ -1,51 +0,0 @@
-# We need the code below in the ui because of setting the working directory 
-assign("proj_obj",get_proj(),pos = .GlobalEnv)
-dashboardPage(
-  title = "shinyMixR",
-  # skin = "orange", 
-  # controlbar = dashboardControlbar(skinSelector(), pinned = TRUE),
-  # Header
-  header = dashboardHeader(
-    title = dashboardBrand(title = "ShinyMixR", color = "lightblue"), #, color = "lightblue", href = "#", image = "logoshinyMixR.png"),
-    leftUI = tags$img(src='logoshinyMixR.png',height=40)
-  ),
-  # Sidebar menu
-  sidebar = dashboardSidebar(status="lightblue", elevation = 1,
-    sidebarMenu(id="tabs", 
-      menuItem('Model overview', tabName='overview', icon=icon('table')),
-      menuItem('Edit model(s)', tabName='editor', icon=icon('file-pen')),
-      menuItem('Run model(s)', tabName='run', icon=icon('person-running')),
-      menuItem('Parameter estimates', tabName='par', icon=icon('table-cells')),
-      menuItem('Goodness of fit', tabName='gof', icon=icon('chart-line')),
-      menuItem('Fit plots', tabName='fitpl', icon=icon('chart-line')),
-      menuItem('Data exploration', tabName='expl', icon=icon('magnifying-glass')),
-      menuItem('Settings', tabName='settings', icon=icon('gear'))
-    )
-  ),
-  # Main body
-  body = dashboardBody(
-    # First set theme and include css
-    use_theme(newtheme),
-    # CHECK IF THE LINES BELOW WILL WORK WITHOUT INTERNET CONNECTION AND DOES IT FAIL GRACEFULLY?!
-    shinyWidgets::useSweetAlert("minimal"),
-    tags$style("@import url(https://use.fontawesome.com/releases/v6.3.0/css/all.css);"),
-    tags$head(tags$style(HTML(".shiny-split-layout > div {overflow: visible;}"))),
-    tags$head(tags$style("#progph{overflow-y:scroll; max-height: 600px;}")),
-    tags$head(tags$style(HTML("#exploretabout{height: 75vh; overflow-y: auto;}"))),
-    tags$head(tags$style(HTML(".swal2-popup {font-size: 0.9rem !important;}"))),    
-    tags$head(tags$style(HTML("input[id$=\"subset\"]{font-family:\"Courier New\"}"))),
-    tags$head(tags$style(HTML("input[id$=\"precode\"]{font-family:\"Courier New\"}"))),
-    tags$head(tags$style(HTML("label{margin-bottom:0rem;}"))),
-    tabItems(
-      tabItem(tabName = "overview", module_overview_ui("oview")),
-      tabItem(tabName = "editor", module_edit_ui("editor")),
-      tabItem(tabName = "run", module_run_ui("modrun")),
-      tabItem(tabName = "par", module_pt_ui("partable")),
-      tabItem(tabName = "gof", module_gof_ui("gofplots")),
-      tabItem(tabName = "fitpl", module_fitplots_ui("fitplots")),
-      tabItem(tabName = "expl", module_dataexplore_ui("explore")),
-      tabItem(tabName = "settings", module_settings_ui("settings"))
-    )  
-  )
-)
-

From 1e05c13845e9c6340e63d9d78b4c91004c15e14b Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 10:53:11 +0200
Subject: [PATCH 02/41] move to `www` folder

---
 inst/Dashboard/{ => www}/logoshinyMixR.png | Bin
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename inst/Dashboard/{ => www}/logoshinyMixR.png (100%)

diff --git a/inst/Dashboard/logoshinyMixR.png b/inst/Dashboard/www/logoshinyMixR.png
similarity index 100%
rename from inst/Dashboard/logoshinyMixR.png
rename to inst/Dashboard/www/logoshinyMixR.png

From 05eb7d12a049ea232355ae8cc619d733c95e0b8e Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 11:11:56 +0200
Subject: [PATCH 03/41] change `proj_obj` to be used in `r`

---
 R/module_edit.R      | 30 +++++++++++++++---------------
 R/module_fitplots.R  |  5 +++--
 R/module_gof.R       |  5 +++--
 R/module_metadata.R  | 21 +++++++++++----------
 R/module_overview.R  | 11 ++++++-----
 R/module_partable.R  |  7 ++++---
 R/module_run.R       |  9 +++++----
 inst/Dashboard/app.R | 19 +++++++++++++------
 8 files changed, 60 insertions(+), 47 deletions(-)

diff --git a/R/module_edit.R b/R/module_edit.R
index bf5d1ab..f559542 100644
--- a/R/module_edit.R
+++ b/R/module_edit.R
@@ -28,9 +28,9 @@ module_edit_ui <- function(id) {
 module_edit_server <- function(id, r, settings) {
   moduleServer(id, function(input, output, session) {
     # Adapt model list based on selected project location
-    observeEvent(r$active_tab,{
+    observeEvent(r$active_tab, {
       if(r$active_tab=="editor"){
-        updateSelectInput(session, "editLst", choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=input$editLst)
+        updateSelectInput(session, "editLst", choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=input$editLst)
       }
     },ignoreInit=TRUE)
 
@@ -41,7 +41,7 @@ module_edit_server <- function(id, r, settings) {
 
     # Update editor when selecting new model
     observeEvent(input$editLst,{
-      shinyAce::updateAceEditor(session,"editor",value=paste(readLines(proj_obj[[input$editLst]]$model),collapse="\n"))
+      shinyAce::updateAceEditor(session,"editor",value=paste(readLines(r$proj_obj[[input$editLst]]$model),collapse="\n"))
     },ignoreInit=TRUE)
 
     # New model
@@ -63,8 +63,8 @@ module_edit_server <- function(id, r, settings) {
         if(!"try-error"%in%class(mdl)){
           mdl <- sub("run1",sub("\\.[r|R]","",input$namenew),mdl)
           writeLines(mdl,paste0("models/",input$namenew))
-          assign("proj_obj",get_proj(),pos = .GlobalEnv,inherits=TRUE)
-          updateSelectInput(session,"editLst",choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=sub("\\.[r|R]","",input$namenew))
+          r$proj_obj <- get_proj()
+          updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",input$namenew))
           shinyAce::updateAceEditor(session,"editor",value=paste(readLines(paste0("models/",input$namenew)),collapse="\n"))
           removeModal()
         }
@@ -73,8 +73,8 @@ module_edit_server <- function(id, r, settings) {
     # Save model
     observeEvent(input$save,{
       if(input$editLst!=""){
-        writeLines(input$editor,proj_obj[[input$editLst]]$model)
-        assign("proj_obj",get_proj(),pos = .GlobalEnv,inherits=TRUE)
+        writeLines(input$editor,r$proj_obj[[input$editLst]]$model)
+        r$proj_obj <- get_proj()
         myalert("Model saved",type = "success")
         # Do not really like the alerts from bs4dash so stick to shinywdigets
         # createAlert(id = NULL,selector = NULL,options=list(title = "Alert",closable = TRUE,width = 12,elevations = 1,status = "primary",content = "Model saved"))
@@ -84,11 +84,11 @@ module_edit_server <- function(id, r, settings) {
     # Handle meta data (we need to pass the selected model as a reactive)
     selectedmodel <- reactive(input$editLst)
     selectedcont  <- reactive(input$editor)
-    upd <- module_metadata_server("adapt_meta_ed","save",sellmod=selectedmodel,sellcont=selectedcont)
+    upd <- module_metadata_server("adapt_meta_ed","save",sellmod=selectedmodel,sellcont=selectedcont,r=r)
     observeEvent(upd(),{
       if(!is.null(upd())){
-        updateSelectInput(session,"editLst",choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=sub("\\.[r|R]","",upd()))
-        shinyAce::updateAceEditor(session,"editor",value=paste(readLines(proj_obj[[sub("\\.[r|R]","",upd())]]$model),collapse="\n"))
+        updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",upd()))
+        shinyAce::updateAceEditor(session,"editor",value=paste(readLines(r$proj_obj[[sub("\\.[r|R]","",upd())]]$model),collapse="\n"))
         myalert(upd(),type = "success")
       } 
     },ignoreInit=TRUE)
@@ -97,8 +97,8 @@ module_edit_server <- function(id, r, settings) {
     initmodal <- function(){
       ns <- session$ns
       if(isTruthy(input$editLst)){
-        selm <- tools::file_path_sans_ext(basename(proj_obj[[input$editLst]]$model))
-        incm <- incr_mdl(basename(proj_obj[[input$editLst]]$model),"models")
+        selm <- tools::file_path_sans_ext(basename(r$proj_obj[[input$editLst]]$model))
+        incm <- incr_mdl(basename(r$proj_obj[[input$editLst]]$model),"models")
       }else{
         selm <- incm <- NULL
       } 
@@ -118,9 +118,9 @@ module_edit_server <- function(id, r, settings) {
         if("try-error"%in%class(res)){
           myalert("Could not update initials",type = "error")
         }else{
-          assign("proj_obj",get_proj(),pos = .GlobalEnv,inherits=TRUE)
-          updateSelectInput(session,"editLst",choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=sub("\\.[r|R]","",input$tosave))
-          shinyAce::updateAceEditor(session,"editor",value=paste(readLines(proj_obj[[sub("\\.[r|R]","",input$tosave)]]$model),collapse="\n"))
+          r$proj_obj <- get_proj()
+          updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",input$tosave))
+          shinyAce::updateAceEditor(session,"editor",value=paste(readLines(r$proj_obj[[sub("\\.[r|R]","",input$tosave)]]$model),collapse="\n"))
           myalert("Initials updated",type = "success")
         }
       }else{
diff --git a/R/module_fitplots.R b/R/module_fitplots.R
index ff53105..96dec25 100644
--- a/R/module_fitplots.R
+++ b/R/module_fitplots.R
@@ -4,9 +4,10 @@
 #' @description Shiny module for fit plots
 #'
 #' @param id Module id
+#' @param proj_obj Project object
 #' 
 #' @export
-module_fitplots_ui <- function(id) {
+module_fitplots_ui <- function(id, proj_obj) {
   ns <- NS(id)
   tagList(
     fluidRow(
@@ -46,7 +47,7 @@ module_fitplots_server <- function(id, r, settings) {
     # Adapt model list based on selected project location
     observeEvent(r$active_tab,{
       if(r$active_tab=="fitpl"){
-        updateSelectInput(session, "fitLst", choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=input$fitLst)
+        updateSelectInput(session, "fitLst", choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=input$fitLst)
       }
     },ignoreInit=TRUE)
 
diff --git a/R/module_gof.R b/R/module_gof.R
index 15a6b0e..e625c58 100644
--- a/R/module_gof.R
+++ b/R/module_gof.R
@@ -4,9 +4,10 @@
 #' @description Shiny module for GOF plots
 #'
 #' @param id Module id
+#' @param proj_obj Project object
 #' 
 #' @export
-module_gof_ui <- function(id) {
+module_gof_ui <- function(id, proj_obj) {
   ns <- NS(id)
   tagList(
     fluidRow(
@@ -42,7 +43,7 @@ module_gof_server <- function(id, r, settings) {
     # Adapt model list based on selected project location
     observeEvent(r$active_tab,{
       if(r$active_tab=="gof"){
-        updateSelectInput(session, "gofLst", choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=input$gofLst)
+        updateSelectInput(session, "gofLst", choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=input$gofLst)
       }
     },ignoreInit=TRUE)
     
diff --git a/R/module_metadata.R b/R/module_metadata.R
index 1215be0..8df7166 100644
--- a/R/module_metadata.R
+++ b/R/module_metadata.R
@@ -22,9 +22,10 @@ module_metadata_ui <- function(id,type) {
 #' @param selline reactive with the selected line for a model (for type "overview")
 #' @param sellmod reactive with the selected model (for type "save")
 #' @param sellcont reactive with the content of the selected model (for type "save")
+#' @param r reactive values object that is defined top-level
 #' 
 #' @export
-module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NULL){
+module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NULL,r){
   moduleServer(id, function(input, output, session){
     
     # Function for the modal
@@ -37,17 +38,17 @@ module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NU
       titl <- ifelse(type=="save","Save as","Adapt model info")
       meta <- list(mdls="",imp=0,ref="",desc="",est="saem",data="",sel="")
 
-      if(!is.null(selline)) meta$sel  <- sort(names(proj_obj)[names(proj_obj)!="meta"])[selline()]
+      if(!is.null(selline)) meta$sel  <- sort(names(r$proj_obj)[names(r$proj_obj)!="meta"])[selline()]
       if(!is.null(sellmod)) meta$sel  <- sellmod()
       if(length(meta$sel)==0 || meta$sel=="") return()
 
-      meta$imp  <- proj_obj[[meta$sel]]$modeleval$meta$imp
-      meta$ref  <- proj_obj[[meta$sel]]$modeleval$meta$ref
-      meta$desc <- proj_obj[[meta$sel]]$modeleval$meta$desc
-      meta$est  <- proj_obj[[meta$sel]]$modeleval$meta$est
-      meta$data <- proj_obj[[meta$sel]]$modeleval$meta$data
+      meta$imp  <- r$proj_obj[[meta$sel]]$modeleval$meta$imp
+      meta$ref  <- r$proj_obj[[meta$sel]]$modeleval$meta$ref
+      meta$desc <- r$proj_obj[[meta$sel]]$modeleval$meta$desc
+      meta$est  <- r$proj_obj[[meta$sel]]$modeleval$meta$est
+      meta$data <- r$proj_obj[[meta$sel]]$modeleval$meta$data
 
-      meta$mdls <- c("",names(proj_obj)[names(proj_obj)!="meta"])
+      meta$mdls <- c("",names(r$proj_obj)[names(r$proj_obj)!="meta"])
 
       gen  <- tagList(
         sliderInput(ns("mdlimp"), "Importance", 0, 4, meta$imp, step = 1, round = TRUE),
@@ -72,7 +73,7 @@ module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NU
      observeEvent(input$mdladpt,{
       if(type!="save"){
         if(input$mdladpt!=''){
-          meta <- proj_obj[[input$mdladpt]]$modeleval$meta
+          meta <- r$proj_obj[[input$mdladpt]]$modeleval$meta
           updateSliderInput(session,"mdlimp",value=meta$imp)
           updateTextInput(session,"mdldesc",value=meta$desc)
           updateSelectInput(session,"mdlref",selected=meta$ref)
@@ -105,7 +106,7 @@ module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NU
         towr <- adpt_meta(toret['name'],metanfo)
         if(type=="save") towr <- sub(sellmod(),sub("\\.[r|R]","",input$mdladpt),towr)
         writeLines(towr,toret['saveas'])
-        assign("proj_obj",get_proj(),pos = .GlobalEnv,inherits=TRUE)
+        r$proj_obj <- get_proj()
         removeModal()
         meta_ret(toret['val'])
       }
diff --git a/R/module_overview.R b/R/module_overview.R
index c379423..afa0b0a 100644
--- a/R/module_overview.R
+++ b/R/module_overview.R
@@ -32,9 +32,10 @@ module_overview_ui <- function(id) {
 #' Overview module for server
 #' 
 #' @param id Module id
+#' @param r reactive values object that is defined top-level
 #' 
 #' @export
-module_overview_server <- function(id) {
+module_overview_server <- function(id, r) {
   moduleServer(id, function(input, output, session){
     # Make reactive value to hold the available models/scripts
     rv <- reactiveValues(mdls=list.files("models",pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE),scrpt=list.files("scripts",full.names = TRUE))
@@ -58,7 +59,7 @@ module_overview_server <- function(id) {
     # Refresh overview
     observeEvent(input$overview_refr,{
       if(file.exists("shinyMixR")){
-        assign("proj_obj",get_proj(),pos = .GlobalEnv)
+        r$proj_obj <- get_proj()
         overview_ov <- overview()
         DT::replaceData(proxy, overview_ov, rownames = FALSE)
         rv$mdls  <- list.files("models",pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE)
@@ -81,7 +82,7 @@ module_overview_server <- function(id) {
       modalDialog(title="High level results",easyClose = TRUE,size="l",verbatimTextOutput(ns("res_out")))
     }
     hr_out <- eventReactive(input$hlr, {
-      sel   <- sort(names(proj_obj)[names(proj_obj)!="meta"])[input$overview_tbl_rows_selected]
+      sel   <- sort(names(r$proj_obj)[names(r$proj_obj)!="meta"])[input$overview_tbl_rows_selected]
       if(length(sel)>0){
         res <- try(readRDS(paste0("shinyMixR/",sel[1],".res.rds")))
         if(!"try-error"%in%class(res)) print(res) else print("No results available")
@@ -100,14 +101,14 @@ module_overview_server <- function(id) {
     observeEvent(input$del,{showModal(delmodal())},ignoreInit = TRUE)
     observeEvent(input$del2,{
       if(!is.null(input$overview_tbl_rows_selected)){
-        msel <- sort(names(proj_obj)[names(proj_obj)!="meta"])[input$overview_tbl_rows_selected]
+        msel <- sort(names(r$proj_obj)[names(r$proj_obj)!="meta"])[input$overview_tbl_rows_selected]
         if(input$delmodall) {
           try(file.remove(paste0("shinyMixR/",msel,".res.rds")))
           try(file.remove(paste0("shinyMixR/",msel,".ressum.rds")))
           try(unlink(paste0("analysis/",msel),recursive = TRUE))
         }
         try(file.remove(paste0("models/",msel,".r")))
-        assign("proj_obj",get_proj(),pos = .GlobalEnv,inherits=TRUE)
+        r$proj_obj <- get_proj()
         DT::replaceData(proxy, overview(), rownames = FALSE)
         removeModal()
       }
diff --git a/R/module_partable.R b/R/module_partable.R
index 738c355..4865f2a 100644
--- a/R/module_partable.R
+++ b/R/module_partable.R
@@ -4,9 +4,10 @@
 #' @description Shiny module for parameter table
 #'
 #' @param id Module id
+#' @param proj_obj Project object
 #' 
 #' @export
-module_pt_ui <- function(id) {
+module_pt_ui <- function(id, proj_obj) {
   ns <- NS(id)
   tagList(
     actionButton(ns("savePars"), "Save parameter table",icon=icon("floppy-disk")),br(),br(),
@@ -35,8 +36,8 @@ module_pt_server <- function(id, r) {
       if(r$active_tab=="par"){
         updateSelectInput(session, 
                           "EstLst", 
-                          choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],
-                          selected= ifelse(is.null(input$EstLst), names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"][1], input$EstLst) 
+                          choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],
+                          selected= ifelse(is.null(input$EstLst), names(r$proj_obj)[names(r$proj_obj)!="meta"][1], input$EstLst) 
         )
       }
     },ignoreInit=TRUE)
diff --git a/R/module_run.R b/R/module_run.R
index 37dbf90..135309f 100644
--- a/R/module_run.R
+++ b/R/module_run.R
@@ -4,9 +4,10 @@
 #' @description Shiny module for running models
 #'
 #' @param id Module id
+#' @param proj_obj Project object
 #' 
 #' @export
-module_run_ui <- function(id) {
+module_run_ui <- function(id, proj_obj) {
   ns <- NS(id)
   tagList(
     selectInput(ns("runLst"),"Model(s)",names(proj_obj)[names(proj_obj)!="meta"],multiple=TRUE,selectize = TRUE),
@@ -30,7 +31,7 @@ module_run_server <- function(id, r) {
     # Adapt/update model list 
     observeEvent(r$active_tab,{
       if(r$active_tab=="run"){
-        updateSelectInput(session, "runLst", choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=input$runmod_runLst)
+        updateSelectInput(session, "runLst", choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=input$runmod_runLst)
       }
     },ignoreInit=TRUE)
 
@@ -39,7 +40,7 @@ module_run_server <- function(id, r) {
       unlink(list.files(paste0("shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE))
       # Perform tests before running
        if(!is.null(input$runLst)){
-         proj     <- get("proj_obj",pos = .GlobalEnv)
+         proj     <- r$proj_obj
         checkall <- unlist(sapply(input$runLst,function(x){
           chk    <- proj[[x]]$model
           chksrc <- try(source(chk,local=TRUE),silent=TRUE)
@@ -55,7 +56,7 @@ module_run_server <- function(id, r) {
           myalert("model(s) submitted, wait for progress log to pop-up!",type = "succes")
           addcwres <- ifelse("Add CWRES to output"%in%input$addExtra,TRUE,FALSE)
           addnpde  <- ifelse("Add NPDE to output"%in%input$addExtra,TRUE,FALSE)
-          lapply(input$runLst,function(mods) run_nmx(mods,proj_obj,addcwres=addcwres,addnpde=addnpde))
+          lapply(input$runLst,function(mods) run_nmx(mods,r$proj_obj,addcwres=addcwres,addnpde=addnpde))
         }
       }else{
         myalert("Please select models to run",type = "error")
diff --git a/inst/Dashboard/app.R b/inst/Dashboard/app.R
index 3168c7e..e7fe0bb 100644
--- a/inst/Dashboard/app.R
+++ b/inst/Dashboard/app.R
@@ -12,6 +12,9 @@ if ("nlmixr2" %in% rownames(installed.packages())){
   cat("you need the 'nlmixr2' package to run models\n")
 }
 
+# Initiate project
+proj_obj <- create_proj()
+
 # Create theme for dashboard
 newtheme <- create_theme(
   theme = "darkly", # theme has no effect, at least within bs4Dash
@@ -56,10 +59,10 @@ ui <- dashboardPage(
     tabItems(
       tabItem(tabName = "overview", module_overview_ui("oview")),
       tabItem(tabName = "editor", module_edit_ui("editor")),
-      tabItem(tabName = "run", module_run_ui("modrun")),
-      tabItem(tabName = "par", module_pt_ui("partable")),
-      tabItem(tabName = "gof", module_gof_ui("gofplots")),
-      tabItem(tabName = "fitpl", module_fitplots_ui("fitplots")),
+      tabItem(tabName = "run", module_run_ui("modrun", proj_obj)),
+      tabItem(tabName = "par", module_pt_ui("partable", proj_obj)),
+      tabItem(tabName = "gof", module_gof_ui("gofplots", proj_obj)),
+      tabItem(tabName = "fitpl", module_fitplots_ui("fitplots", proj_obj)),
       tabItem(tabName = "expl", module_dataexplore_ui("explore")),
       tabItem(tabName = "settings", module_settings_ui("settings"))
     )  
@@ -70,10 +73,14 @@ server <- function(input, output, session) {
   
   # Top-level reactive values
   r <- reactiveValues(active_tab = "",
-                      model_updated = 0)
+                      model_updated = 0,
+                      proj_obj = get_proj())
+  
   observeEvent(input$tabs, r$active_tab <- input$tabs)
+  
+  # Modules
   sett <- module_settings_server("settings")
-  module_overview_server("oview")
+  module_overview_server("oview", r = r)
   module_edit_server("editor", r = r, settings=sett)
   module_run_server("modrun", r = r)
   module_pt_server("partable", r = r)

From 7fa030942886ba1c30ba6956c6ba9893020b57f5 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 11:12:31 +0200
Subject: [PATCH 04/41] docs: add `r` and `proj_obj` as args

---
 man/module_fitplots_ui.Rd     | 4 +++-
 man/module_gof_ui.Rd          | 4 +++-
 man/module_metadata_server.Rd | 5 ++++-
 man/module_overview_server.Rd | 4 +++-
 man/module_pt_ui.Rd           | 4 +++-
 man/module_run_ui.Rd          | 4 +++-
 6 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/man/module_fitplots_ui.Rd b/man/module_fitplots_ui.Rd
index 6515ac8..38e5760 100644
--- a/man/module_fitplots_ui.Rd
+++ b/man/module_fitplots_ui.Rd
@@ -4,10 +4,12 @@
 \alias{module_fitplots_ui}
 \title{Fit plots module for UI}
 \usage{
-module_fitplots_ui(id)
+module_fitplots_ui(id, proj_obj)
 }
 \arguments{
 \item{id}{Module id}
+
+\item{proj_obj}{Project object}
 }
 \description{
 Shiny module for fit plots
diff --git a/man/module_gof_ui.Rd b/man/module_gof_ui.Rd
index 05209dc..26f7132 100644
--- a/man/module_gof_ui.Rd
+++ b/man/module_gof_ui.Rd
@@ -4,10 +4,12 @@
 \alias{module_gof_ui}
 \title{GOF plots module for UI}
 \usage{
-module_gof_ui(id)
+module_gof_ui(id, proj_obj)
 }
 \arguments{
 \item{id}{Module id}
+
+\item{proj_obj}{Project object}
 }
 \description{
 Shiny module for GOF plots
diff --git a/man/module_metadata_server.Rd b/man/module_metadata_server.Rd
index dbdf2b0..26239b2 100644
--- a/man/module_metadata_server.Rd
+++ b/man/module_metadata_server.Rd
@@ -9,7 +9,8 @@ module_metadata_server(
   type,
   selline = NULL,
   sellmod = NULL,
-  sellcont = NULL
+  sellcont = NULL,
+  r
 )
 }
 \arguments{
@@ -22,6 +23,8 @@ module_metadata_server(
 \item{sellmod}{reactive with the selected model (for type "save")}
 
 \item{sellcont}{reactive with the content of the selected model (for type "save")}
+
+\item{r}{reactive values object that is defined top-level}
 }
 \description{
 meta data module for server
diff --git a/man/module_overview_server.Rd b/man/module_overview_server.Rd
index fb2f453..f329d51 100644
--- a/man/module_overview_server.Rd
+++ b/man/module_overview_server.Rd
@@ -4,10 +4,12 @@
 \alias{module_overview_server}
 \title{Overview module for server}
 \usage{
-module_overview_server(id)
+module_overview_server(id, r)
 }
 \arguments{
 \item{id}{Module id}
+
+\item{r}{reactive values object that is defined top-level}
 }
 \description{
 Overview module for server
diff --git a/man/module_pt_ui.Rd b/man/module_pt_ui.Rd
index 6e4f5e1..a5db8f3 100644
--- a/man/module_pt_ui.Rd
+++ b/man/module_pt_ui.Rd
@@ -4,10 +4,12 @@
 \alias{module_pt_ui}
 \title{Parameter table module for UI}
 \usage{
-module_pt_ui(id)
+module_pt_ui(id, proj_obj)
 }
 \arguments{
 \item{id}{Module id}
+
+\item{proj_obj}{Project object}
 }
 \description{
 Shiny module for parameter table
diff --git a/man/module_run_ui.Rd b/man/module_run_ui.Rd
index beacf0c..d51d00e 100644
--- a/man/module_run_ui.Rd
+++ b/man/module_run_ui.Rd
@@ -4,10 +4,12 @@
 \alias{module_run_ui}
 \title{Run model module for UI}
 \usage{
-module_run_ui(id)
+module_run_ui(id, proj_obj)
 }
 \arguments{
 \item{id}{Module id}
+
+\item{proj_obj}{Project object}
 }
 \description{
 Shiny module for running models

From c08a29069c4d74037325943f2accd2b5c853d5de Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 11:21:31 +0200
Subject: [PATCH 05/41] source correct files

---
 R/run_shinymixr.r | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index 8d49087..77880e0 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -15,18 +15,12 @@
 #'  run_shinymixr(".")
 #' }
 run_shinymixr <- function(wd = getwd(), dry_run = FALSE, ...){
+  
   if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
-  #if(!file.exists(paste0(wd,"/shinyMixR/app/R")))   try(dir.create(paste0(wd,"/shinyMixR/app/R"),recursive = TRUE))
   if(!file.exists(paste0(wd,"/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/temp"),recursive=TRUE))
   
-  try(file.copy(system.file("Dashboard","global.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/global.R"),overwrite = TRUE),silent = TRUE)
-  try(file.copy(system.file("Dashboard","server.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/server.R"),overwrite = TRUE),silent = TRUE)
-  try(file.copy(system.file("Dashboard","logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
-  
-  # We need to add the working directory to the ui.r file (global.r does not work)
-  adpt <- readLines(system.file("Dashboard","ui.R",package="shinyMixR"))
-  adpt <- c(paste0("setwd(\"",normalizePath(wd,winslash = "/"),"\")"),adpt)
-  writeLines(adpt,paste0(wd,"/shinyMixR/app/ui.R"))
+  try(file.copy(system.file("Dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
+  try(file.copy(system.file("Dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
     
   # Clean up stuff before running the app (check if feasible or not)
   try(unlink(list.files(paste0(wd,"/shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE)))

From 6c2e68b742f7107796414e3701c808a56da6fef9 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 13:17:55 +0200
Subject: [PATCH 06/41] use `get_proj` instead of `create_proj`

---
 inst/Dashboard/app.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/Dashboard/app.R b/inst/Dashboard/app.R
index e7fe0bb..0142293 100644
--- a/inst/Dashboard/app.R
+++ b/inst/Dashboard/app.R
@@ -13,7 +13,7 @@ if ("nlmixr2" %in% rownames(installed.packages())){
 }
 
 # Initiate project
-proj_obj <- create_proj()
+proj_obj <- get_proj()
 
 # Create theme for dashboard
 newtheme <- create_theme(

From fde9040c47aac9d4247f5e0efcfcefe4f5e0e206 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 14:20:32 +0200
Subject: [PATCH 07/41] use correct wd + introduce `this_wd` + rework overview

---
 R/module_edit.R      |  6 +++---
 R/module_metadata.R  |  2 +-
 R/module_overview.R  | 42 ++++++++++++++++++++++++------------------
 R/overview.r         | 14 +++++++-------
 R/run_shinymixr.r    |  7 ++++++-
 R/tree_overview.r    |  7 ++++---
 inst/Dashboard/app.R |  7 +++++--
 7 files changed, 50 insertions(+), 35 deletions(-)

diff --git a/R/module_edit.R b/R/module_edit.R
index f559542..29b932a 100644
--- a/R/module_edit.R
+++ b/R/module_edit.R
@@ -63,7 +63,7 @@ module_edit_server <- function(id, r, settings) {
         if(!"try-error"%in%class(mdl)){
           mdl <- sub("run1",sub("\\.[r|R]","",input$namenew),mdl)
           writeLines(mdl,paste0("models/",input$namenew))
-          r$proj_obj <- get_proj()
+          r$proj_obj <- get_proj(r$this_wd)
           updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",input$namenew))
           shinyAce::updateAceEditor(session,"editor",value=paste(readLines(paste0("models/",input$namenew)),collapse="\n"))
           removeModal()
@@ -74,7 +74,7 @@ module_edit_server <- function(id, r, settings) {
     observeEvent(input$save,{
       if(input$editLst!=""){
         writeLines(input$editor,r$proj_obj[[input$editLst]]$model)
-        r$proj_obj <- get_proj()
+        r$proj_obj <- get_proj(r$this_wd)
         myalert("Model saved",type = "success")
         # Do not really like the alerts from bs4dash so stick to shinywdigets
         # createAlert(id = NULL,selector = NULL,options=list(title = "Alert",closable = TRUE,width = 12,elevations = 1,status = "primary",content = "Model saved"))
@@ -118,7 +118,7 @@ module_edit_server <- function(id, r, settings) {
         if("try-error"%in%class(res)){
           myalert("Could not update initials",type = "error")
         }else{
-          r$proj_obj <- get_proj()
+          r$proj_obj <- get_proj(r$this_wd)
           updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",input$tosave))
           shinyAce::updateAceEditor(session,"editor",value=paste(readLines(r$proj_obj[[sub("\\.[r|R]","",input$tosave)]]$model),collapse="\n"))
           myalert("Initials updated",type = "success")
diff --git a/R/module_metadata.R b/R/module_metadata.R
index 8df7166..1f6463f 100644
--- a/R/module_metadata.R
+++ b/R/module_metadata.R
@@ -106,7 +106,7 @@ module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NU
         towr <- adpt_meta(toret['name'],metanfo)
         if(type=="save") towr <- sub(sellmod(),sub("\\.[r|R]","",input$mdladpt),towr)
         writeLines(towr,toret['saveas'])
-        r$proj_obj <- get_proj()
+        r$proj_obj <- get_proj(r$this_wd)
         removeModal()
         meta_ret(toret['val'])
       }
diff --git a/R/module_overview.R b/R/module_overview.R
index afa0b0a..1ba2ecf 100644
--- a/R/module_overview.R
+++ b/R/module_overview.R
@@ -37,33 +37,39 @@ module_overview_ui <- function(id) {
 #' @export
 module_overview_server <- function(id, r) {
   moduleServer(id, function(input, output, session){
-    # Make reactive value to hold the available models/scripts
-    rv <- reactiveValues(mdls=list.files("models",pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE),scrpt=list.files("scripts",full.names = TRUE))
     
-    # Create overview when app is loaded 
-    if(all(file.exists(c("analysis","data","models","scripts","shinyMixR")))){
-      overview_ov <- overview()
-    }else{
-      overview_ov <- data.frame(models="",importance="",description="",ref="",data="",method="",OBJF="",dOBJF=NA,runtime="")
-    }
+    observe({
+      
+      # Make reactive value to hold the available models/scripts
+      r$mdls <- list.files(paste0(r$this_wd, "/models"), pattern = "run[[:digit:]]*\\.[r|R]", full.names = TRUE)
+      r$scrpt <- list.files(paste0(r$this_wd, "/scripts"), full.names = TRUE)
+      
+      # if no models are present in r$proj_obj, return empty table
+      if (length(names(r$proj_obj)[names(r$proj_obj) != "meta"]) > 0) {
+        r$overview_ov <- overview(r$proj_obj)
+      } else {
+        r$overview_ov <- data.frame(models="",importance="",description="",ref="",data="",method="",OBJF="",dOBJF=NA,runtime="")
+      }
+    })
+    
     proxy = DT::dataTableProxy("overview_tbl")
-    output$overview_tbl = DT::renderDataTable(overview_ov,rownames=FALSE,extension=c("Buttons"), options=list(scrollX=TRUE,dom="Bfrtip",buttons=c('colvis','csv'),pageLength=100,lengthMenu=c(10,100,1000,10000)))
+    output$overview_tbl = DT::renderDataTable(r$overview_ov,rownames=FALSE,extension=c("Buttons"), options=list(scrollX=TRUE,dom="Bfrtip",buttons=c('colvis','csv'),pageLength=100,lengthMenu=c(10,100,1000,10000)))
     # filter="bottom", --> bug with filters/module/modal
 
     # Create tree
     tree <- eventReactive(input$mktree,{
-      if(file.exists("shinyMixR")){tree_overview()}else{data.frame()}
+      if(file.exists("shinyMixR")){tree_overview(r$proj_obj)}else{data.frame()}
     })
     output$treeout <- collapsibleTree::renderCollapsibleTree(tree())
 
     # Refresh overview
     observeEvent(input$overview_refr,{
       if(file.exists("shinyMixR")){
-        r$proj_obj <- get_proj()
-        overview_ov <- overview()
+        r$proj_obj <- get_proj(r$this_wd)
+        overview_ov <- overview(r$proj_obj)
         DT::replaceData(proxy, overview_ov, rownames = FALSE)
-        rv$mdls  <- list.files("models",pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE)
-        rv$scrpt <- list.files("scripts",full.names = TRUE)
+        r$mdls  <- list.files("models",pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE)
+        r$scrpt <- list.files("scripts",full.names = TRUE)
       }
     },ignoreInit = TRUE)
 
@@ -73,7 +79,7 @@ module_overview_server <- function(id, r) {
     })
     upd <- module_metadata_server("adapt_meta_ov","overview",selline=selectedLine)
     observeEvent(upd(),{
-       if(upd()=="Update DT") DT::replaceData(proxy, overview(), rownames = FALSE)
+       if(upd()=="Update DT") DT::replaceData(proxy, overview(r$proj_obj), rownames = FALSE)
     })
 
     # Show high level results
@@ -108,15 +114,15 @@ module_overview_server <- function(id, r) {
           try(unlink(paste0("analysis/",msel),recursive = TRUE))
         }
         try(file.remove(paste0("models/",msel,".r")))
-        r$proj_obj <- get_proj()
-        DT::replaceData(proxy, overview(), rownames = FALSE)
+        r$proj_obj <- get_proj(r$this_wd)
+        DT::replaceData(proxy, overview(r$proj_obj), rownames = FALSE)
         removeModal()
       }
     },ignoreInit = TRUE)
 
     # Running scripts - Check creation of temp folder (should be done in create_proj (get_proj) function?)
     dir.create("shinyMixR/temp",showWarnings = FALSE,recursive = TRUE)
-    module_scripts_server("runscripts", files = reactive(rv$mdls), scripts = reactive(rv$scrpt), loc = "shinyMixR/temp")
+    module_scripts_server("runscripts", files = reactive(r$mdls), scripts = reactive(r$scrpt), loc = "shinyMixR/temp")
 
     # Creating reports
     module_reports_server("reports")
diff --git a/R/overview.r b/R/overview.r
index 4069321..c36ac2f 100644
--- a/R/overview.r
+++ b/R/overview.r
@@ -4,6 +4,7 @@
 #' Create an overview of the models within a project. This overview includes the meta data
 #' of the models and if results are available, also the objective function and run-times
 #'
+#' @param proj_obj a project object created with \code{\link{get_proj}}
 #' @param ... additional arguments passed to \code{\link{get_proj}}
 #'
 #' @export
@@ -12,21 +13,20 @@
 #' @examples
 #'
 #' \dontrun{
-#'  overview()
+#'  overview(proj_obj)
 #' }
-overview <- function(...){
-  obj  <- get_proj(...)
-  mdln <- names(obj)[names(obj)!="meta"]
+overview <- function(proj_obj, ...){
+  mdln <- names(proj_obj)[names(proj_obj)!="meta"]
   res1 <- lapply(mdln, function(x){
-    if(class(obj[[x]]$modeleval)=="try-error" || class(obj[[x]]$modeleval$meta)=="try-error"){
+    if(class(proj_obj[[x]]$modeleval)=="try-error" || class(proj_obj[[x]]$modeleval$meta)=="try-error"){
       c(NA,"","","","")
     }else{
-      meta <- obj[[x]]$modeleval$meta
+      meta <- proj_obj[[x]]$modeleval$meta
       c(ifelse(is.null(meta$imp),NA,meta$imp), ifelse(is.null(meta$desc),"",meta$desc),ifelse(is.null(meta$ref),"",meta$ref),
         ifelse(is.null(meta$data),"",meta$data),ifelse(is.null(meta$est),"",meta$est))
     }
   })
-  res2 <- lapply(obj[mdln], function(x){
+  res2 <- lapply(proj_obj[mdln], function(x){
     if(!is.null(x$results)) c(round(x$results$OBJF,3),round(x$results$tottime,3)) else c("","")
   })
   res <- data.frame(cbind(mdln,do.call(rbind,res1),do.call(rbind,res2)),stringsAsFactors = FALSE)
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index 77880e0..74584fd 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -21,7 +21,12 @@ run_shinymixr <- function(wd = getwd(), dry_run = FALSE, ...){
   
   try(file.copy(system.file("Dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
   try(file.copy(system.file("Dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
-    
+  
+  # Set the working directory so the project can be found
+  adpt <- readLines(system.file("Dashboard", "app.R", package = "shinyMixR"))
+  adpt <- c(paste0("setwd(\"", normalizePath(wd, winslash = "/"), "\")"), adpt)
+  writeLines(adpt, paste0(wd,"/shinyMixR/app/app.R"))
+  
   # Clean up stuff before running the app (check if feasible or not)
   try(unlink(list.files(paste0(wd,"/shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE)))
   if (dry_run == TRUE) {
diff --git a/R/tree_overview.r b/R/tree_overview.r
index 0781893..535c577 100644
--- a/R/tree_overview.r
+++ b/R/tree_overview.r
@@ -5,6 +5,7 @@
 #' This is mostly relevant in case the reference of models is included to
 #' visualise the relationship between models
 #'
+#' @param proj_obj a project object created with \code{\link{get_proj}}
 #' @param ... additional arguments passed to \code{\link{overview}}
 #'
 #' @export
@@ -14,10 +15,10 @@
 #' @examples
 #'
 #' \dontrun{
-#'  tree_overview()
+#'  tree_overview(proj_obj)
 #' }
-tree_overview <- function(...){
-  tmod   <- overview(...)
+tree_overview <- function(proj_obj, ...){
+  tmod   <- overview(proj_obj, ...)
   stmodn <- data.frame(from=NA,to="start",imp=0,stringsAsFactors = FALSE)
   noref  <- data.frame(from="start",to=tmod$models[tmod$ref==""],imp=tmod$imp[tmod$ref==""],stringsAsFactors = FALSE)
   refs   <- data.frame(from=tmod$ref[tmod$ref!=""],to=tmod$models[tmod$ref!=""],imp=tmod$imp[tmod$ref!=""],stringsAsFactors = FALSE)
diff --git a/inst/Dashboard/app.R b/inst/Dashboard/app.R
index 0142293..b1e94f8 100644
--- a/inst/Dashboard/app.R
+++ b/inst/Dashboard/app.R
@@ -1,3 +1,5 @@
+this_wd <- getwd()
+
 # Loading libraries
 library(shiny)     # Used as it is a shiny app
 library(bs4Dash)   # Used instead of shinydashboard to provide additional options
@@ -13,7 +15,7 @@ if ("nlmixr2" %in% rownames(installed.packages())){
 }
 
 # Initiate project
-proj_obj <- get_proj()
+proj_obj <- get_proj(this_wd)
 
 # Create theme for dashboard
 newtheme <- create_theme(
@@ -74,7 +76,8 @@ server <- function(input, output, session) {
   # Top-level reactive values
   r <- reactiveValues(active_tab = "",
                       model_updated = 0,
-                      proj_obj = get_proj())
+                      proj_obj = get_proj(this_wd),
+                      this_wd = this_wd)
   
   observeEvent(input$tabs, r$active_tab <- input$tabs)
   

From ec607b92bd214d76a1f36bba5bb598b964271652 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 14:28:09 +0200
Subject: [PATCH 08/41] get proj from correct location

---
 R/module_partable.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/module_partable.R b/R/module_partable.R
index 4865f2a..1b4adcf 100644
--- a/R/module_partable.R
+++ b/R/module_partable.R
@@ -43,13 +43,13 @@ module_pt_server <- function(id, r) {
     },ignoreInit=TRUE)
 
     # Create parameter table
-    parTable <- function(inp,projloc=".",saveit=FALSE){
-      obj     <- get_proj(projloc=projloc)
-      if(!saveit){
+    parTable <- function(inp, projloc, saveit = FALSE){
+      obj <- get_proj(projloc = projloc)
+      if(!saveit) {
         #print(obj)
         #print(inp$EstLst)
         par_table(obj,models=inp$EstLst,bsv=inp$bsv,shrink=inp$shrink,backt=inp$backt,formatting=TRUE)
-      }else{
+      } else {
         savnm  <- ifelse(inp$typePars=="PDF",paste0(inp$namePars,".tex"),paste0(inp$namePars,".html"))
         #print(savnm)
         par_table(obj,models=inp$EstLst,outnm=savnm,show=inp$showPars,projloc=projloc,bsv=inp$bsv,shrink=inp$shrink,backt=inp$backt,formatting=ifelse(inp$typePars=="PDF",FALSE,TRUE))
@@ -60,7 +60,7 @@ module_pt_server <- function(id, r) {
       
       req(r$model_updated)
       
-      table <- parTable(input)
+      table <- parTable(input, projloc = r$this_wd)
       r$params <- table
       
       DT::datatable(
@@ -91,6 +91,6 @@ module_pt_server <- function(id, r) {
       )
     }
     observeEvent(input$savePars,showModal(parsave()))
-    observeEvent(input$savePars2, parTable(input,saveit=TRUE))
+    observeEvent(input$savePars2, parTable(input, projloc = r$this_wd, saveit = TRUE))
   })
 }

From 05a6b683d5cb5bf8beaf2b020f6782025e4a99ae Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 16 Apr 2024 15:33:38 +0200
Subject: [PATCH 09/41] formatting

---
 R/run_nmx.r | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/R/run_nmx.r b/R/run_nmx.r
index 4e5ba5a..1eae6cc 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -51,8 +51,17 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
 
     tmpl <- readLines(paste0(system.file(package = "shinyMixR"),"/Other/run_nmx.tmp"))
     if(is.null(meta$subs)) subs <- "" else subs <- meta$subs
-    rlst <- list(modelloc=normalizePath(proj[[mod]]$model,winslash = "/",mustWork = FALSE), data=meta$data, subs=subs,
-                 est=meta$est, control=cntrll, saveres=saverds, modelname=mod,locproj=projloc,addcwres=addcwres,addnpde=addnpde)
+    
+    rlst <- list(modelloc=normalizePath(proj[[mod]]$model,winslash = "/",mustWork = FALSE), 
+                 data=meta$data, 
+                 subs=subs,
+                 est=meta$est, 
+                 control=cntrll, 
+                 saveres=saverds, 
+                 modelname=mod,
+                 locproj=projloc,
+                 addcwres=addcwres,
+                 addnpde=addnpde)
 
     tscr <- paste0(projloc,"/shinyMixR/temp/script.",stringi::stri_rand_strings(1,6),".r")
     writeLines(whisker::whisker.render(tmpl,rlst),tscr)

From edc9507cdb9952bfaa16edcc68c445b4bb4953a8 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Wed, 17 Apr 2024 16:09:47 +0200
Subject: [PATCH 10/41] change paths + update object after model run

---
 R/get_proj.r   | 10 +++++-----
 R/module_run.R |  3 ++-
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/R/get_proj.r b/R/get_proj.r
index df61e21..6062d31 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -14,15 +14,15 @@
 #'   proj <- get_proj()
 #' }
 get_proj <- function(projloc=".",geteval=TRUE){
-
+  
   # Read in models and place in result objects
   dir.create(paste0(projloc,"/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
   mdln    <- normalizePath(list.files(paste0(projloc,"/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
   mdlnb   <- sub("\\.[r|R]","",basename(mdln))
-  sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
+  sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
   sumresi <- file.info(sumres)
   summdli <- file.info(mdln)
-
+  
   # read in data folder (only in case objects are not yet present)
   datf  <- list.files(paste0(projloc,"/data"))
   grepd <- " |^[[:digit:]]|\\!|\\#|\\$|\\%|\\&|\\'|\\(|\\)|\\-|\\;|\\=|\\@|\\[|\\]|\\^\\`\\{\\|\\}"
@@ -36,7 +36,7 @@ get_proj <- function(projloc=".",geteval=TRUE){
   })
 
   # Read in models and results
-  if(!file.exists(paste0(projloc,"/shinyMixR/project.rds"))){
+  if(!file.exists(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))){
     mdls <- lapply(mdln,list)
     names(mdls) <- sub("\\.[r|R]","",basename(mdln))
     if(length(mdln)==0){
@@ -52,7 +52,7 @@ get_proj <- function(projloc=".",geteval=TRUE){
     for(i in sumres) mdls[[sub("\\.ressum\\.rds","",basename(i))]]$results <- readRDS(i)
     mdls$meta <- list(lastrefresh=Sys.time())
   }else{
-    mdls   <- readRDS(paste0(projloc,"/shinyMixR/project.rds"))
+    mdls   <- readRDS(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
     # for the list with models, check if new models are available or old models are deleted
     # and if models are updated after last refresh:
     # inproj <- unlist(sapply(mdls[names(mdls)[names(mdls)!="meta"]],"[",1))
diff --git a/R/module_run.R b/R/module_run.R
index 135309f..4e4c06b 100644
--- a/R/module_run.R
+++ b/R/module_run.R
@@ -56,7 +56,7 @@ module_run_server <- function(id, r) {
           myalert("model(s) submitted, wait for progress log to pop-up!",type = "succes")
           addcwres <- ifelse("Add CWRES to output"%in%input$addExtra,TRUE,FALSE)
           addnpde  <- ifelse("Add NPDE to output"%in%input$addExtra,TRUE,FALSE)
-          lapply(input$runLst,function(mods) run_nmx(mods,r$proj_obj,addcwres=addcwres,addnpde=addnpde))
+          lapply(input$runLst,function(mods) run_nmx(mods, r$proj_obj, addcwres=addcwres,addnpde=addnpde))
         }
       }else{
         myalert("Please select models to run",type = "error")
@@ -81,6 +81,7 @@ module_run_server <- function(id, r) {
       # check if "run finished" prevails in runmodmonit()
       if(grepl("run finished", runmodmonit())){
         r$model_updated <- isolate(r$model_updated) + 1
+        r$proj_obj <- get_proj(r$this_wd)
       }
     })
     

From e5d336ff4a2eb6f87d5b220e24b54a22bd70d61a Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Wed, 17 Apr 2024 16:35:17 +0200
Subject: [PATCH 11/41] move creation of temp folder to run_shinymixr

---
 R/module_overview.R | 2 --
 R/run_shinymixr.r   | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/R/module_overview.R b/R/module_overview.R
index 1ba2ecf..9b2e710 100644
--- a/R/module_overview.R
+++ b/R/module_overview.R
@@ -120,8 +120,6 @@ module_overview_server <- function(id, r) {
       }
     },ignoreInit = TRUE)
 
-    # Running scripts - Check creation of temp folder (should be done in create_proj (get_proj) function?)
-    dir.create("shinyMixR/temp",showWarnings = FALSE,recursive = TRUE)
     module_scripts_server("runscripts", files = reactive(r$mdls), scripts = reactive(r$scrpt), loc = "shinyMixR/temp")
 
     # Creating reports
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index 74584fd..29ba971 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -17,7 +17,7 @@
 run_shinymixr <- function(wd = getwd(), dry_run = FALSE, ...){
   
   if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
-  if(!file.exists(paste0(wd,"/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/temp"),recursive=TRUE))
+  if(!file.exists(paste0(wd,"/shinyMixR/app/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/app/shinyMixR/temp"),recursive=TRUE))
   
   try(file.copy(system.file("Dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
   try(file.copy(system.file("Dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)

From 5c65439e1cfb8b0f8df3cd8ce4636c7f8e1b7e70 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Wed, 17 Apr 2024 16:35:31 +0200
Subject: [PATCH 12/41] change file path

---
 R/get_proj.r | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_proj.r b/R/get_proj.r
index 6062d31..55fdbef 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -92,6 +92,6 @@ get_proj <- function(projloc=".",geteval=TRUE){
   chk       <- chk[which(chk$mdlsv>chk$ressv),]
   #if(nrow(chk)>0) noret <- apply(chk,1,function(x) cat("Be aware that model is saved after results for",x['mdl'],"\n"))
 
-  saveRDS(mdls,file=paste0(projloc,"/shinyMixR/project.rds"))
+  saveRDS(mdls,file=paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
   return(mdls)
 }

From 1902e77946fa54725eccfca80ac9bc03db3f30e0 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 23 Apr 2024 15:45:20 +0200
Subject: [PATCH 13/41] remove nlmixr + bump version

---
 DESCRIPTION | 8 ++++----
 NEWS.md     | 9 +++++++++
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 68589ea..4118028 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: shinyMixR
-Title: Shiny dashboard interface for nlmixr and nlmixr2
-Version: 0.4.0
+Title: Interactive 'shiny' Dashboard for 'nlmixr2'
+Version: 0.5.0
 Authors@R: c(person("Richard", "Hooijmaijers", email = "richardhooijmaijers@gmail.com", role = c("aut", "cre","cph")),
              person("Teun", "Post", email = "teunpost@gmail.com",role = c("aut","cph")),
              person("LAPP Consultants",email = "info@lapp.nl", role=c("fnd","cph")),
              person("Matthew Fidler",role=c("ctb")))
 Author: Richard Hooijmaijers
 Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
-Description: The package is developed as an interface for the nlmixr and nlmixr2 package. Furthermore additional functions
-  are included to work with the nlmixr package through the command line
+Description: An interface for the 'nlmixr2' package. Furthermore additional functions
+  are included to work with the 'nlmixr2' package through the command line.
 Depends:
   R (>= 3.5.0),
   shiny,
diff --git a/NEWS.md b/NEWS.md
index 6a95013..6871514 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,12 @@
+# shinyMixR 0.5
+
+This version is a preview version of the package. The main changes are:
+
+- Refactoring of the code to remove global assignments and implement use of reactiveValues.
+- Added codecoverage to the package.
+- Added a new testing structure to the package including `shinytest2` for automated testing of the app.
+- Improved documentation to prepare for CRAN submission.
+
 # shinyMixR 0.4
 
 Within this version some updates have been implemented, see below the most important changes:

From 617cc83f0ee25f0ff85e2c5967aae23309e52eac Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 23 Apr 2024 15:45:46 +0200
Subject: [PATCH 14/41] docs: proj_obj

---
 man/overview.Rd      | 6 ++++--
 man/tree_overview.Rd | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/man/overview.Rd b/man/overview.Rd
index fa43cf4..ca530fb 100644
--- a/man/overview.Rd
+++ b/man/overview.Rd
@@ -4,9 +4,11 @@
 \alias{overview}
 \title{Creates model overview}
 \usage{
-overview(...)
+overview(proj_obj, ...)
 }
 \arguments{
+\item{proj_obj}{a project object created with \code{\link{get_proj}}}
+
 \item{...}{additional arguments passed to \code{\link{get_proj}}}
 }
 \value{
@@ -19,7 +21,7 @@ of the models and if results are available, also the objective function and run-
 \examples{
 
 \dontrun{
- overview()
+ overview(proj_obj)
 }
 }
 \author{
diff --git a/man/tree_overview.Rd b/man/tree_overview.Rd
index ca06772..6c14112 100644
--- a/man/tree_overview.Rd
+++ b/man/tree_overview.Rd
@@ -4,9 +4,11 @@
 \alias{tree_overview}
 \title{Creates tree overview of models}
 \usage{
-tree_overview(...)
+tree_overview(proj_obj, ...)
 }
 \arguments{
+\item{proj_obj}{a project object created with \code{\link{get_proj}}}
+
 \item{...}{additional arguments passed to \code{\link{overview}}}
 }
 \value{
@@ -20,7 +22,7 @@ visualise the relationship between models
 \examples{
 
 \dontrun{
- tree_overview()
+ tree_overview(proj_obj)
 }
 }
 \seealso{

From 1f767587e2f24704271e2acf656a656a8d489ccb Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 23 Apr 2024 15:46:05 +0200
Subject: [PATCH 15/41] declare record_test

---
 R/utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index b98b928..1f2f60b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -31,6 +31,6 @@ setup_shinymixr_test <- function(dir = "./tests/files", overwrite = TRUE, record
   }
   
   if (record == TRUE) {
-    record_test(paste0(dir, "/shinyMixR/app"))
+    shinytest2::record_test(paste0(dir, "/shinyMixR/app"))
   }
 }

From be8acd910186d4be88f7a30b0328530429af07a2 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 23 Apr 2024 16:50:17 +0200
Subject: [PATCH 16/41] very wip: change locations

---
 R/create_proj.r                               |  7 ++++++-
 R/get_proj.r                                  | 10 ++++++----
 R/run_nmx.r                                   |  8 ++++----
 R/utils.R                                     |  6 ++++--
 tests/testthat/test-shinymixr-01-model-run1.R |  4 ++--
 5 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/R/create_proj.r b/R/create_proj.r
index ddd8aa9..20f5390 100644
--- a/R/create_proj.r
+++ b/R/create_proj.r
@@ -16,8 +16,13 @@
 #'  create_proj()
 #' }
 create_proj <- function(loc=".", overwrite=FALSE){
+  
+  loc <- paste0(loc, "/shinyMixR/app")
+  
+  if(!dir.exists(loc)) dir.create(loc, recursive = TRUE)
+  
   # First create the folder structure
-  dirs <- paste0(loc,c("/analysis","/data","/models","/shinyMixR","/scripts"))
+  dirs <- paste0(loc, c("/analysis","/data","/models","/shinyMixR","/scripts"))
   if(!all(dirs%in%list.files(loc,full.names = TRUE))){
     sapply(dirs,dir.create,showWarnings = FALSE,recursive=TRUE)
     # Now place in some default models and data
diff --git a/R/get_proj.r b/R/get_proj.r
index 55fdbef..943b6f8 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -15,20 +15,22 @@
 #' }
 get_proj <- function(projloc=".",geteval=TRUE){
   
+  print(projloc)
+  
   # Read in models and place in result objects
-  dir.create(paste0(projloc,"/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
-  mdln    <- normalizePath(list.files(paste0(projloc,"/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
+  dir.create(paste0(projloc,"/shinyMixR/app/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
+  mdln    <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
   mdlnb   <- sub("\\.[r|R]","",basename(mdln))
   sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
   sumresi <- file.info(sumres)
   summdli <- file.info(mdln)
   
   # read in data folder (only in case objects are not yet present)
-  datf  <- list.files(paste0(projloc,"/data"))
+  datf  <- list.files(paste0(projloc,"/shinyMixR/app/data"))
   grepd <- " |^[[:digit:]]|\\!|\\#|\\$|\\%|\\&|\\'|\\(|\\)|\\-|\\;|\\=|\\@|\\[|\\]|\\^\\`\\{\\|\\}"
   if(any(grepl(grepd,datf))) warning("Data files with special characters found, take into acount that models that use these can crash")
   # not relevant to read all data for running nlmixr in separate session (should be loaded in this session!)
-  lapply(list.files(paste0(projloc,"/data"),full.names = TRUE),function(x){
+  lapply(list.files(paste0(projloc,"/shinyMixR/app/data"),full.names = TRUE),function(x){
     if(!grepl(grepd,x) & !exists(sub("\\.rds$|\\.csv$","",basename(x),ignore.case = TRUE),envir=.GlobalEnv)){
       if(grepl("\\.rds$",x,ignore.case = TRUE)) assign(sub("\\.rds$","",basename(x),ignore.case = TRUE),readRDS(x),pos = .GlobalEnv)
       if(grepl("\\.csv$",x,ignore.case = TRUE)) assign(sub("\\.csv$","",basename(x),ignore.case = TRUE),read.csv(x),pos = .GlobalEnv)
diff --git a/R/run_nmx.r b/R/run_nmx.r
index 1eae6cc..cd21570 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -28,8 +28,8 @@
 #' }
 run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=".",addcwres=TRUE,addnpde=TRUE){
 
-  dnm     <- deparse(substitute(proj))
-  if(autoupdate) assign(dnm,get_proj(projloc=projloc))
+  # dnm     <- deparse(substitute(proj))
+  # if(autoupdate) assign(dnm,get_proj(projloc=projloc))
   # Source model to obtain meta data (places meta object in env)
   sret <- try(source(proj[[mod]]$model,local=TRUE))
   meta <- try(eval(parse(text=c("nlmixr(",readLines(proj[[mod]]$model),")$meta"))))
@@ -72,7 +72,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
       system(paste0(R.home("bin"), "/Rscript \"", tscr,  "\" > \"",projloc,"/shinyMixR/temp/",mod,".prog.txt\" 2>&1"),wait=FALSE)
     }
     
-    if(autoupdate) assign(dnm,proj,pos = .GlobalEnv)
+    # if(autoupdate) assign(dnm,proj,pos = .GlobalEnv)
   }else{
     # Handle subsetting (data is loaded in global environment by get_proj function)
     if(!is.null(meta$subs) && meta$subs!="") data_nlm <- subset(get(meta$data),eval(parse(text=(meta$subs)))) else data_nlm <- get(meta$data)
@@ -87,7 +87,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
       saveRDS(ressum,file=paste0(projloc,"/shinyMixR/",mod,".ressum.rds"))
     }
     proj[[mod]]$results <- ressum
-    assign(dnm,proj,pos = .GlobalEnv)
+    # assign(dnm,proj,pos = .GlobalEnv)
     return(modres)
   }
 }
diff --git a/R/utils.R b/R/utils.R
index 1f2f60b..65bac90 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -19,10 +19,12 @@ setup_shinymixr_test <- function(dir = "./tests/files", overwrite = TRUE, record
   }
 
   create_proj(dir, overwrite = overwrite)
+  run_shinymixr(wd = dir, dry_run = TRUE)
+  
   if(incres){
-    file.copy(system.file(c("Other/run1.res.rds","Other/run1.ressum.rds"),package="shinyMixR"),paste0(dir,"/shinyMixR"))
+    file.copy(system.file(c("Other/run1.res.rds","Other/run1.ressum.rds"),package="shinyMixR"),
+              paste0(dir,"/shinyMixR/app/shinyMixR"))
   }
-  run_shinymixr(wd = dir, dry_run = TRUE)
   
   # create .Rprofile file to store settings
   if (!file.exists(paste0(dir, "/.Rprofile"))) {
diff --git a/tests/testthat/test-shinymixr-01-model-run1.R b/tests/testthat/test-shinymixr-01-model-run1.R
index dbc3199..819e77d 100644
--- a/tests/testthat/test-shinymixr-01-model-run1.R
+++ b/tests/testthat/test-shinymixr-01-model-run1.R
@@ -29,10 +29,10 @@ test_that("Shiny app runs model and returns parameters for run1", {
   
   # Test if run is done and 'correct' results have been created
   Sys.sleep(1)
-  rundone <- "run1.res.rds"%in%list.files(paste0(tempdir(),"/files/shinyMixR"))
+  rundone <- "run1.res.rds"%in%list.files(paste0(tempdir(),"/files/shinyMixR/app/shinyMixR"))
   expect_true(rundone)
   if(rundone){
-    runres <- readRDS(paste0(tempdir(),"/files/shinyMixR/run1.res.rds"))
+    runres <- readRDS(paste0(tempdir(),"/files/shinyMixR/app/shinyMixR/run1.res.rds"))
     expect_true(inherits(runres,"nlmixr2FitData"))
   }
   

From 778b983d0de9fa5effb38a258cd46e4e028bf76d Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 08:24:24 +0200
Subject: [PATCH 17/41] point to correct folder

---
 tests/testthat/test-shinymixr-03-create-newmodel.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-shinymixr-03-create-newmodel.R b/tests/testthat/test-shinymixr-03-create-newmodel.R
index 34a4dad..708d68e 100644
--- a/tests/testthat/test-shinymixr-03-create-newmodel.R
+++ b/tests/testthat/test-shinymixr-03-create-newmodel.R
@@ -32,10 +32,10 @@ test_that("Shiny app correctly creates new model code", {
   app$expect_values(input = "editor-newgo")
   
   # Check if new model is created and contains correct naming
-  modmade <- "run2.r" %in% list.files(paste0(temp_dir, "/files/models"))
+  modmade <- "run2.r" %in% list.files(paste0(temp_dir, "/files/shinyMixR/app/models"))
   expect_true(modmade)
   if(modmade){
-    modcont <- readLines(paste0(temp_dir, "/files/models/run2.r"))
+    modcont <- readLines(paste0(temp_dir, "/files/shinyMixR/app/models/run2.r"))
     expect_true(grepl("run2 <- function", modcont[1]))
   }
     
@@ -49,7 +49,7 @@ test_that("Shiny app correctly creates new model code", {
   expect_true(curvals$input$`editor-adapt_meta_ed-mdlimp`==1)
   app$click("editor-adapt_meta_ed-adpt")
   app$click(selector = ".swal2-confirm")
-  expect_true("run3.r"%in%list.files(paste0(tempdir(),"/files/models")))
+  expect_true("run3.r"%in%list.files(paste0(tempdir(),"/files/shinyMixR/app/models")))
   
   # Finally test if update inits works as expected (e.g. are initial changed, values itself tested outside shinytest)
   app$click("editor-updinit")

From b88889323d67083349066e2e160a44b3f2f025f7 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 09:01:29 +0200
Subject: [PATCH 18/41] fix LICENSE warning

---
 .Rbuildignore |  3 +++
 DESCRIPTION   |  2 +-
 LICENSE.md    | 21 +++++++++++++++++++++
 3 files changed, 25 insertions(+), 1 deletion(-)
 create mode 100644 LICENSE.md

diff --git a/.Rbuildignore b/.Rbuildignore
index 91114bf..3056e71 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.github$
+^\.vscode$
+^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
index 4118028..b13ec0e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,7 +37,7 @@ Suggests:
     knitr,
     rmarkdown,
     rlang
-License: MIT+LICENSE
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..12fb21d
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 shinyMixR authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

From a8486470513597f1ba7a1add57241999acd1cc65 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 09:06:38 +0200
Subject: [PATCH 19/41] move non standard directories to /inst

---
 R/create_proj.r                                     |  10 +++++-----
 R/module_edit.R                                     |   2 +-
 R/run_nmx.r                                         |   2 +-
 R/run_shinymixr.r                                   |   6 +++---
 R/utils.R                                           |   2 +-
 .../cheatsheet}/CheatSheet_shinymixr.pdf            | Bin
 {installation => inst/installation}/install_fun.r   |   0
 {shortcuts => inst/shortcuts}/README.md             |   0
 .../shortcuts}/start_shinyMixR_Lin.sh               |   0
 .../shortcuts}/start_shinyMixR_Mac.command          |   0
 .../shortcuts}/start_shinyMixR_Win10.bat            |   0
 .../shortcuts}/start_shinyMixR_Win7.bat             |   0
 tests/testthat/test-gof_plot.R                      |   2 +-
 vignettes/getting_started.Rmd                       |   2 +-
 14 files changed, 13 insertions(+), 13 deletions(-)
 rename {cheatsheet => inst/cheatsheet}/CheatSheet_shinymixr.pdf (100%)
 rename {installation => inst/installation}/install_fun.r (100%)
 rename {shortcuts => inst/shortcuts}/README.md (100%)
 rename {shortcuts => inst/shortcuts}/start_shinyMixR_Lin.sh (100%)
 rename {shortcuts => inst/shortcuts}/start_shinyMixR_Mac.command (100%)
 rename {shortcuts => inst/shortcuts}/start_shinyMixR_Win10.bat (100%)
 rename {shortcuts => inst/shortcuts}/start_shinyMixR_Win7.bat (100%)

diff --git a/R/create_proj.r b/R/create_proj.r
index 20f5390..ecdede9 100644
--- a/R/create_proj.r
+++ b/R/create_proj.r
@@ -26,10 +26,10 @@ create_proj <- function(loc=".", overwrite=FALSE){
   if(!all(dirs%in%list.files(loc,full.names = TRUE))){
     sapply(dirs,dir.create,showWarnings = FALSE,recursive=TRUE)
     # Now place in some default models and data
-    if(!file.exists(paste0(loc,"/models/run1.r")) | overwrite)      file.copy(paste0(system.file(package = "shinyMixR"),"/Other/run1.r"),paste0(loc,"/models/run1.r"))
-    if(!file.exists(paste0(loc,"/data/theo_sd.rds")) | overwrite)   file.copy(paste0(system.file(package = "shinyMixR"),"/Other/theo_sd.rds"),paste0(loc,"/data/theo_sd.rds"))
-    if(!file.exists(paste0(loc,"/scripts/eta.plot.r")) | overwrite) file.copy(paste0(system.file(package = "shinyMixR"),"/Other/eta.plot.r"),paste0(loc,"/scripts/eta.plot.r"))
-    if(!file.exists(paste0(loc,"/scripts/vpc.plot.r")) | overwrite) file.copy(paste0(system.file(package = "shinyMixR"),"/Other/vpc.plot.r"),paste0(loc,"/scripts/vpc.plot.r"))
-    if(!file.exists(paste0(loc,"/scripts/combined.results.html.r")) | overwrite) file.copy(paste0(system.file(package = "shinyMixR"),"/Other/combined.results.html.r"),paste0(loc,"/scripts/combined.results.html.r"))
+    if(!file.exists(paste0(loc,"/models/run1.r")) | overwrite)      file.copy(paste0(system.file(package = "shinyMixR"),"/other/run1.r"),paste0(loc,"/models/run1.r"))
+    if(!file.exists(paste0(loc,"/data/theo_sd.rds")) | overwrite)   file.copy(paste0(system.file(package = "shinyMixR"),"/other/theo_sd.rds"),paste0(loc,"/data/theo_sd.rds"))
+    if(!file.exists(paste0(loc,"/scripts/eta.plot.r")) | overwrite) file.copy(paste0(system.file(package = "shinyMixR"),"/other/eta.plot.r"),paste0(loc,"/scripts/eta.plot.r"))
+    if(!file.exists(paste0(loc,"/scripts/vpc.plot.r")) | overwrite) file.copy(paste0(system.file(package = "shinyMixR"),"/other/vpc.plot.r"),paste0(loc,"/scripts/vpc.plot.r"))
+    if(!file.exists(paste0(loc,"/scripts/combined.results.html.r")) | overwrite) file.copy(paste0(system.file(package = "shinyMixR"),"/other/combined.results.html.r"),paste0(loc,"/scripts/combined.results.html.r"))
   }
 }
diff --git a/R/module_edit.R b/R/module_edit.R
index 29b932a..e16dbd1 100644
--- a/R/module_edit.R
+++ b/R/module_edit.R
@@ -59,7 +59,7 @@ module_edit_server <- function(id, r, settings) {
       showModal(newmodmodal())
     },ignoreInit=TRUE)
     observeEvent(input$newgo,{
-        mdl <- try(readLines(system.file(paste0("Other/",input$templnew,".r"),package="shinyMixR")))
+        mdl <- try(readLines(system.file(paste0("other/",input$templnew,".r"),package="shinyMixR")))
         if(!"try-error"%in%class(mdl)){
           mdl <- sub("run1",sub("\\.[r|R]","",input$namenew),mdl)
           writeLines(mdl,paste0("models/",input$namenew))
diff --git a/R/run_nmx.r b/R/run_nmx.r
index cd21570..9808639 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -49,7 +49,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
     cntrla <- grepl("^control *=|^control.*<-",cntrll)
     if(any(cntrla)){cntrll <- gsub("^control *=|^control.*<-","",cntrll[cntrla])}else{cntrll <- "list()"}
 
-    tmpl <- readLines(paste0(system.file(package = "shinyMixR"),"/Other/run_nmx.tmp"))
+    tmpl <- readLines(paste0(system.file(package = "shinyMixR"),"/other/run_nmx.tmp"))
     if(is.null(meta$subs)) subs <- "" else subs <- meta$subs
     
     rlst <- list(modelloc=normalizePath(proj[[mod]]$model,winslash = "/",mustWork = FALSE), 
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index 29ba971..ddff5b7 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -19,11 +19,11 @@ run_shinymixr <- function(wd = getwd(), dry_run = FALSE, ...){
   if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
   if(!file.exists(paste0(wd,"/shinyMixR/app/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/app/shinyMixR/temp"),recursive=TRUE))
   
-  try(file.copy(system.file("Dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
-  try(file.copy(system.file("Dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
+  try(file.copy(system.file("dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
+  try(file.copy(system.file("dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
   
   # Set the working directory so the project can be found
-  adpt <- readLines(system.file("Dashboard", "app.R", package = "shinyMixR"))
+  adpt <- readLines(system.file("dashboard", "app.R", package = "shinyMixR"))
   adpt <- c(paste0("setwd(\"", normalizePath(wd, winslash = "/"), "\")"), adpt)
   writeLines(adpt, paste0(wd,"/shinyMixR/app/app.R"))
   
diff --git a/R/utils.R b/R/utils.R
index 65bac90..db6efa3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -22,7 +22,7 @@ setup_shinymixr_test <- function(dir = "./tests/files", overwrite = TRUE, record
   run_shinymixr(wd = dir, dry_run = TRUE)
   
   if(incres){
-    file.copy(system.file(c("Other/run1.res.rds","Other/run1.ressum.rds"),package="shinyMixR"),
+    file.copy(system.file(c("other/run1.res.rds","other/run1.ressum.rds"),package="shinyMixR"),
               paste0(dir,"/shinyMixR/app/shinyMixR"))
   }
   
diff --git a/cheatsheet/CheatSheet_shinymixr.pdf b/inst/cheatsheet/CheatSheet_shinymixr.pdf
similarity index 100%
rename from cheatsheet/CheatSheet_shinymixr.pdf
rename to inst/cheatsheet/CheatSheet_shinymixr.pdf
diff --git a/installation/install_fun.r b/inst/installation/install_fun.r
similarity index 100%
rename from installation/install_fun.r
rename to inst/installation/install_fun.r
diff --git a/shortcuts/README.md b/inst/shortcuts/README.md
similarity index 100%
rename from shortcuts/README.md
rename to inst/shortcuts/README.md
diff --git a/shortcuts/start_shinyMixR_Lin.sh b/inst/shortcuts/start_shinyMixR_Lin.sh
similarity index 100%
rename from shortcuts/start_shinyMixR_Lin.sh
rename to inst/shortcuts/start_shinyMixR_Lin.sh
diff --git a/shortcuts/start_shinyMixR_Mac.command b/inst/shortcuts/start_shinyMixR_Mac.command
similarity index 100%
rename from shortcuts/start_shinyMixR_Mac.command
rename to inst/shortcuts/start_shinyMixR_Mac.command
diff --git a/shortcuts/start_shinyMixR_Win10.bat b/inst/shortcuts/start_shinyMixR_Win10.bat
similarity index 100%
rename from shortcuts/start_shinyMixR_Win10.bat
rename to inst/shortcuts/start_shinyMixR_Win10.bat
diff --git a/shortcuts/start_shinyMixR_Win7.bat b/inst/shortcuts/start_shinyMixR_Win7.bat
similarity index 100%
rename from shortcuts/start_shinyMixR_Win7.bat
rename to inst/shortcuts/start_shinyMixR_Win7.bat
diff --git a/tests/testthat/test-gof_plot.R b/tests/testthat/test-gof_plot.R
index 6b358ee..1f67723 100644
--- a/tests/testthat/test-gof_plot.R
+++ b/tests/testthat/test-gof_plot.R
@@ -1,6 +1,6 @@
 test_that("gof_plot works as expected", {
   
-  res_path <- system.file("/Other/run1.res.rds", package = "shinyMixR")
+  res_path <- system.file("/other/run1.res.rds", package = "shinyMixR")
   
   res <- readRDS(res_path)
   
diff --git a/vignettes/getting_started.Rmd b/vignettes/getting_started.Rmd
index 96c29e7..0be2c99 100644
--- a/vignettes/getting_started.Rmd
+++ b/vignettes/getting_started.Rmd
@@ -216,7 +216,7 @@ par_table(proj_obj, models="run1", outnm="par.tex")
 For assessing the goodness of fit, the `gof_plot` function can be used. This function will by default use the `nlmixr.xpose2` package to create 4 different types of plots. It is also possible to directly create ggplot2 types of plots. By default the plots will be created within the R session but can also be written to pdf/html using the `R3port` package:
 ```{r eval=TRUE, echo=FALSE, message=FALSE, warning=FALSE}
 library(shinyMixR)
-res  <- readRDS(system.file("Other/run1.res.rds",package="shinyMixR"))
+res  <- readRDS(system.file("other/run1.res.rds",package="shinyMixR"))
 ```
 ```{r eval=FALSE, echo=TRUE}
 res  <- readRDS("./shinyMixR/run1.res.rds")

From d2bedc222fc862d04d16f6efaba4a41a19502587 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 09:11:23 +0200
Subject: [PATCH 20/41] add pkgdown files

---
 .Rbuildignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 3056e71..e79996c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -3,3 +3,6 @@
 ^\.github$
 ^\.vscode$
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$

From 5e3061c828372504940cb5b73c8e62b814bd20c3 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 09:21:44 +0200
Subject: [PATCH 21/41] fix found if() conditions comparing class() to string

---
 R/overview.r | 2 +-
 R/run_nmx.r  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/overview.r b/R/overview.r
index c36ac2f..51eb4a7 100644
--- a/R/overview.r
+++ b/R/overview.r
@@ -18,7 +18,7 @@
 overview <- function(proj_obj, ...){
   mdln <- names(proj_obj)[names(proj_obj)!="meta"]
   res1 <- lapply(mdln, function(x){
-    if(class(proj_obj[[x]]$modeleval)=="try-error" || class(proj_obj[[x]]$modeleval$meta)=="try-error"){
+    if(inherits(proj_obj[[x]]$modeleval, "try-error") || inherits(proj_obj[[x]]$modeleval$meta, "try-error")){
       c(NA,"","","","")
     }else{
       meta <- proj_obj[[x]]$modeleval$meta
diff --git a/R/run_nmx.r b/R/run_nmx.r
index 9808639..a397735 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -33,7 +33,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
   # Source model to obtain meta data (places meta object in env)
   sret <- try(source(proj[[mod]]$model,local=TRUE))
   meta <- try(eval(parse(text=c("nlmixr(",readLines(proj[[mod]]$model),")$meta"))))
-  if(class(meta)=="try-error" || class(sret)=="try-error"){
+  if(inherits(meta, "try-error") || inherits(sret, "try-error")){
     cat("Error in model syntax please check before running\n")
     if(ext) writeLines(meta, paste0(projloc,"/shinyMixR/temp/",mod,".prog.txt"))
     return()

From 24f3209e0c73eccaa9658fd71c3f768c734cc294 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 10:17:40 +0200
Subject: [PATCH 22/41] import magrittr, stats, utils

---
 DESCRIPTION              |  3 ++-
 NAMESPACE                |  7 +++++++
 R/shinyMixR-package.R    |  9 +++++++++
 man/shinyMixR-package.Rd | 26 ++++++++++++++++++++++++++
 4 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 R/shinyMixR-package.R
 create mode 100644 man/shinyMixR-package.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index b13ec0e..ef6dd8c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,7 +12,8 @@ Description: An interface for the 'nlmixr2' package. Furthermore additional func
 Depends:
   R (>= 3.5.0),
   shiny,
-  ggplot2
+  ggplot2,
+  magrittr
 Imports:
   gridExtra,
   collapsibleTree,
diff --git a/NAMESPACE b/NAMESPACE
index f5ca749..2a9a6eb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -42,4 +42,11 @@ export(update_inits)
 import(bs4Dash)
 import(ggplot2)
 import(gridExtra)
+importFrom(magrittr,"%>%")
 importFrom(shiny,runApp)
+importFrom(stats,na.omit)
+importFrom(stats,setNames)
+importFrom(utils,getParseData)
+importFrom(utils,installed.packages)
+importFrom(utils,read.csv)
+importFrom(utils,tail)
diff --git a/R/shinyMixR-package.R b/R/shinyMixR-package.R
new file mode 100644
index 0000000..c09a29b
--- /dev/null
+++ b/R/shinyMixR-package.R
@@ -0,0 +1,9 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom stats na.omit setNames
+#' @importFrom utils getParseData installed.packages read.csv tail
+#' @importFrom magrittr "%>%"
+## usethis namespace: end
+NULL
\ No newline at end of file
diff --git a/man/shinyMixR-package.Rd b/man/shinyMixR-package.Rd
new file mode 100644
index 0000000..3ee053c
--- /dev/null
+++ b/man/shinyMixR-package.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shinyMixR-package.R
+\docType{package}
+\name{shinyMixR-package}
+\alias{shinyMixR}
+\alias{shinyMixR-package}
+\title{shinyMixR: Interactive 'shiny' Dashboard for 'nlmixr2'}
+\description{
+An interface for the 'nlmixr2' package. Furthermore additional functions are included to work with the 'nlmixr2' package through the command line.
+}
+\author{
+\strong{Maintainer}: Richard Hooijmaijers \email{richardhooijmaijers@gmail.com} [copyright holder]
+
+Authors:
+\itemize{
+  \item Teun Post \email{teunpost@gmail.com} [copyright holder]
+}
+
+Other contributors:
+\itemize{
+  \item LAPP Consultants \email{info@lapp.nl} [funder, copyright holder]
+  \item Matthew Fidler [contributor]
+}
+
+}
+\keyword{internal}

From c8ed35cf5aca4b93507bb7c58d18fa6558c8e060 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 10:18:03 +0200
Subject: [PATCH 23/41] change location of exportTestValues

---
 R/module_run.R                                | 7 +++----
 tests/testthat/test-shinymixr-01-model-run1.R | 4 ++--
 vignettes/getting_started.Rmd                 | 5 ++++-
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/module_run.R b/R/module_run.R
index 4e4c06b..aecb8dd 100644
--- a/R/module_run.R
+++ b/R/module_run.R
@@ -82,13 +82,12 @@ module_run_server <- function(id, r) {
       if(grepl("run finished", runmodmonit())){
         r$model_updated <- isolate(r$model_updated) + 1
         r$proj_obj <- get_proj(r$this_wd)
+        exportTestValues(
+          model_updated = r$model_updated
+        )
       }
     })
     
-    exportTestValues(
-      model_updated = r$model_updated
-    )
-    
     output$progrTxt <- renderText(runmodmonit())
     # Monitor all external runs
     rv <- reactiveValues(montbl=NULL)
diff --git a/tests/testthat/test-shinymixr-01-model-run1.R b/tests/testthat/test-shinymixr-01-model-run1.R
index 819e77d..9798746 100644
--- a/tests/testthat/test-shinymixr-01-model-run1.R
+++ b/tests/testthat/test-shinymixr-01-model-run1.R
@@ -22,9 +22,9 @@ test_that("Shiny app runs model and returns parameters for run1", {
   Sys.sleep(1)
   app$click(selector = ".swal2-confirm")
   
-  # Wait for model to finish (0 is the initial value, so we ignore it)
+  # Wait for model to finish (NULL or 0 is the initial value, so we ignore it)
   app$wait_for_value(export = "modrun-model_updated",
-                     ignore = 0,
+                     ignore = list(NULL, 0),
                      timeout = 120000)
   
   # Test if run is done and 'correct' results have been created
diff --git a/vignettes/getting_started.Rmd b/vignettes/getting_started.Rmd
index 0be2c99..038d17d 100644
--- a/vignettes/getting_started.Rmd
+++ b/vignettes/getting_started.Rmd
@@ -214,13 +214,16 @@ par_table(proj_obj, models="run1", outnm="par.tex")
 ```
 
 For assessing the goodness of fit, the `gof_plot` function can be used. This function will by default use the `nlmixr.xpose2` package to create 4 different types of plots. It is also possible to directly create ggplot2 types of plots. By default the plots will be created within the R session but can also be written to pdf/html using the `R3port` package:
+
 ```{r eval=TRUE, echo=FALSE, message=FALSE, warning=FALSE}
 library(shinyMixR)
-res  <- readRDS(system.file("other/run1.res.rds",package="shinyMixR"))
+res  <- readRDS(system.file("other/run1.res.rds", package = "shinyMixR"))
 ```
+
 ```{r eval=FALSE, echo=TRUE}
 res  <- readRDS("./shinyMixR/run1.res.rds")
 ```
+
 ```{r message=FALSE, warning=FALSE}
 gof_plot(res)
 # gof_plot(res, mdlnm="run1", outnm="gof.tex")

From 2550f3120cd4ffd2ecd35d5c409d8dcdf9df45ce Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 10:39:33 +0200
Subject: [PATCH 24/41] debug test

---
 tests/testthat/test-gof_plot.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test-gof_plot.R b/tests/testthat/test-gof_plot.R
index 1f67723..9e8d0e9 100644
--- a/tests/testthat/test-gof_plot.R
+++ b/tests/testthat/test-gof_plot.R
@@ -1,5 +1,7 @@
 test_that("gof_plot works as expected", {
   
+  print(.libPaths())
+  
   res_path <- system.file("/other/run1.res.rds", package = "shinyMixR")
   
   res <- readRDS(res_path)

From c26e8f7a5cdaa91d5e4195f54f85ee6c231e9280 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 11:10:42 +0200
Subject: [PATCH 25/41] remove unused code (inputlist$attrl is always FALSE)

---
 R/exploreplot.r | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/exploreplot.r b/R/exploreplot.r
index 924926d..1889e5e 100644
--- a/R/exploreplot.r
+++ b/R/exploreplot.r
@@ -27,7 +27,7 @@ exploreplot <- function(inputlist){
 
   # take into account that colour is used to map colour/fill and shape is used to map shape and linetype
   inputlist$attrl <- FALSE
-  if(inputlist$attrl==TRUE) {ggstr <- "dataIn <- assign_attr(dataIn,attrl)"}else{ggstr <- NULL} # paste(ggstr,"+\n ",lay1)
+  ggstr <- NULL
   if(inputlist$subset=="" & inputlist$nondups=="")  ggstr <-  paste0(ggstr,"\n","ggplot(dataIn)")
   if(inputlist$subset=="" & inputlist$nondups!="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(dataIn, !duplicated(",inputlist$nondups,")))")
   if(inputlist$subset!="" & inputlist$nondups=="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(dataIn,",inputlist$subset,"))")

From 484804474332d492aaf1b3514b18385b90a2f4a7 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 11:11:11 +0200
Subject: [PATCH 26/41] explicitly declare imports from shiny and nlmixr2

---
 NAMESPACE         | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 R/run_nmx.r       |  2 +-
 R/run_shinymixr.r | 10 +++++++++-
 R/update_inits.r  |  4 ++--
 4 files changed, 59 insertions(+), 4 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 2a9a6eb..a522d1f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -43,7 +43,54 @@ import(bs4Dash)
 import(ggplot2)
 import(gridExtra)
 importFrom(magrittr,"%>%")
+importFrom(shiny,HTML)
+importFrom(shiny,NS)
+importFrom(shiny,br)
+importFrom(shiny,checkboxGroupInput)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,conditionalPanel)
+importFrom(shiny,div)
+importFrom(shiny,em)
+importFrom(shiny,eventReactive)
+importFrom(shiny,exportTestValues)
+importFrom(shiny,fluidRow)
+importFrom(shiny,hr)
+importFrom(shiny,icon)
+importFrom(shiny,insertUI)
+importFrom(shiny,isTruthy)
+importFrom(shiny,isolate)
+importFrom(shiny,modalDialog)
+importFrom(shiny,moduleServer)
+importFrom(shiny,numericInput)
+importFrom(shiny,observe)
+importFrom(shiny,observeEvent)
+importFrom(shiny,plotOutput)
+importFrom(shiny,radioButtons)
+importFrom(shiny,reactive)
+importFrom(shiny,reactivePoll)
+importFrom(shiny,reactiveVal)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,reactiveValuesToList)
+importFrom(shiny,removeModal)
+importFrom(shiny,removeUI)
+importFrom(shiny,renderPlot)
+importFrom(shiny,renderPrint)
+importFrom(shiny,renderText)
+importFrom(shiny,req)
 importFrom(shiny,runApp)
+importFrom(shiny,selectInput)
+importFrom(shiny,showModal)
+importFrom(shiny,sliderInput)
+importFrom(shiny,span)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tagList)
+importFrom(shiny,tags)
+importFrom(shiny,textInput)
+importFrom(shiny,updateSelectInput)
+importFrom(shiny,updateSliderInput)
+importFrom(shiny,updateTabsetPanel)
+importFrom(shiny,updateTextInput)
+importFrom(shiny,verbatimTextOutput)
 importFrom(stats,na.omit)
 importFrom(stats,setNames)
 importFrom(utils,getParseData)
diff --git a/R/run_nmx.r b/R/run_nmx.r
index a397735..11d71f5 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -76,7 +76,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
   }else{
     # Handle subsetting (data is loaded in global environment by get_proj function)
     if(!is.null(meta$subs) && meta$subs!="") data_nlm <- subset(get(meta$data),eval(parse(text=(meta$subs)))) else data_nlm <- get(meta$data)
-    modres  <- nlmixr(eval(parse(text=readLines(proj[[mod]]$model))), data_nlm, est=meta$est,control=meta$control,tableControl(cwres=addcwres, npde=addnpde))
+    modres  <- nlmixr2::nlmixr(eval(parse(text=readLines(proj[[mod]]$model))), data_nlm, est=meta$est,control=meta$control,nlmixr2::tableControl(cwres=addcwres, npde=addnpde))
     if("nlmixr2" %in% rownames(installed.packages())){
       ressum  <- list(OBJF=modres$objective,CONDNR=modres$conditionNumberCor,partbl=modres$parFixedDf,partblf=modres$parFixed,omega=modres$omega,tottime=rowSums(modres$time))
     }else{
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index ddff5b7..b1390ce 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -4,7 +4,15 @@
 #' @param wd character with the working directory
 #' @param dry_run logical, if TRUE, the function will not launch the app, but will only create the necessary files
 #' @param ... arguments passed to the shiny runApp function
-#' @importFrom shiny runApp
+#' @importFrom shiny runApp HTML NS br checkboxGroupInput checkboxInput conditionalPanel
+#' div em eventReactive exportTestValues fluidRow hr icon
+#' insertUI isTruthy isolate modalDialog moduleServer
+#' numericInput observe observeEvent plotOutput radioButtons reactive
+#' reactivePoll reactiveVal reactiveValues reactiveValuesToList
+#' removeModal removeUI renderPlot renderPrint renderText req
+#' selectInput showModal sliderInput span tabPanel tagList
+#' tags textInput updateSelectInput updateSliderInput updateTabsetPanel
+#' updateTextInput verbatimTextOutput
 #' @import bs4Dash ggplot2 gridExtra
 #' @export
 #' @return runs the shinyMixR interface
diff --git a/R/update_inits.r b/R/update_inits.r
index 9782bca..5cd2936 100644
--- a/R/update_inits.r
+++ b/R/update_inits.r
@@ -25,7 +25,7 @@ update_inits <- function(mod,res,out){
   # Get parameters from original model - changes necessary for nlmixr2 2.0.9
   #eomod <- ini(get(modnm))
   eomod  <- get(modnm)
-  eomod2 <- eval(ini(eomod))
+  eomod2 <- eval(nlmixr2::ini(eomod))
   eomod2 <- attr(eomod2,"lotriEst")
   opar   <- eomod2[eomod2$fix==FALSE,c("name","est")]
   opar   <- setNames(signif(opar$est,4),opar$name)
@@ -37,7 +37,7 @@ update_inits <- function(mod,res,out){
 
   # Update the model with the inits (perform intersect to only update parameters that allign)
   apar    <- rpar[intersect(names(rpar),names(opar))]
-  outt    <- eomod  %>% ini(apar)
+  outt    <- eomod  %>% nlmixr2::ini(apar)
   outt    <- deparse(outt$fun)
   outt[1] <- paste(tools::file_path_sans_ext(basename(out)),"<-",outt[1])
   writeLines(outt,out)

From 23dd2fc80096dc16a018c9e046ec460d2e585cae Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 13:28:37 +0200
Subject: [PATCH 27/41] correctly get proj_obj

---
 R/module_dataexplore.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/module_dataexplore.R b/R/module_dataexplore.R
index 7800078..125606e 100644
--- a/R/module_dataexplore.R
+++ b/R/module_dataexplore.R
@@ -148,7 +148,7 @@ module_dataexplore_server <- function(id, r) {
     # Adapt model list based on selected project location
     observeEvent(r$active_tab,{
       if(r$active_tab=="expl"){
-        updateSelectInput(session, "mdls", choices = names(get("proj_obj",pos = .GlobalEnv))[names(get("proj_obj",pos = .GlobalEnv))!="meta"],selected=input$mdls)
+        updateSelectInput(session, "mdls", choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=input$mdls)
       }
     },ignoreInit=TRUE)
 

From ff86123f4d7828027e1d2de7e16884256942db88 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 13:28:53 +0200
Subject: [PATCH 28/41] remove `attrl` as not used

---
 R/exploreplot.r | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/exploreplot.r b/R/exploreplot.r
index 1889e5e..03192f3 100644
--- a/R/exploreplot.r
+++ b/R/exploreplot.r
@@ -105,9 +105,9 @@ exploreplot <- function(inputlist){
   if(inputlist$facet1!='[empty]' & inputlist$facet2!='[empty]' & inputlist$facet3!='[empty]') fct <- paste0("~",inputlist$facet1,"+",inputlist$facet2,"+",inputlist$facet3)
   if(is.na(inputlist$ncol)){ncols <- NULL}else{ncols <- inputlist$ncol}
   if(!is.null(fct)) add <- c(add,fac=paste0("facet_wrap(",fct,",scales='",inputlist$facetsc,"', labeller=label_both, ncol=",ncols,")"))
-
-  xlb    <- ifelse(inputlist$xlab!="",inputlist$xlab, ifelse(inputlist$attrl==TRUE && !is.null(attrl) && !is.null(attrl[[inputlist$Xval1]]$label),attrl[[inputlist$Xval1]]$label,inputlist$Xval1))
-  ylb    <- ifelse(inputlist$ylab!="",inputlist$ylab, ifelse(inputlist$attrl==TRUE && !is.null(attrl) && !is.null(attrl[[inputlist$Yval1]]$label),attrl[[inputlist$Yval1]]$label,inputlist$Yval1))
+  
+  xlb    <- ifelse(inputlist$xlab != "", inputlist$xlab, inputlist$Xval1)
+  ylb    <- ifelse(inputlist$ylab != "", inputlist$ylab, inputlist$Yval1)
   if(ylb=="[empty]") ylb <- "Count" # y label could only be empty in case of histogram, otherwise y variable should be selected
   #if(inputlist$xlab!='') add <- c(add,xlab=paste0("xlab('",inputlist$xlab,"')"))
   #if(inputlist$ylab!='') add <- c(add,ylab=paste0("ylab('",inputlist$ylab,"')"))

From 20177aa8a3fce789cbff97f03a7b1e953a984082 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 14:03:36 +0200
Subject: [PATCH 29/41] replace dataIn global assignment

---
 R/exploreplot.r        | 14 +++++++-------
 R/module_dataexplore.R | 18 +++++++++---------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/R/exploreplot.r b/R/exploreplot.r
index 03192f3..2e36e9f 100644
--- a/R/exploreplot.r
+++ b/R/exploreplot.r
@@ -28,10 +28,10 @@ exploreplot <- function(inputlist){
   # take into account that colour is used to map colour/fill and shape is used to map shape and linetype
   inputlist$attrl <- FALSE
   ggstr <- NULL
-  if(inputlist$subset=="" & inputlist$nondups=="")  ggstr <-  paste0(ggstr,"\n","ggplot(dataIn)")
-  if(inputlist$subset=="" & inputlist$nondups!="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(dataIn, !duplicated(",inputlist$nondups,")))")
-  if(inputlist$subset!="" & inputlist$nondups=="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(dataIn,",inputlist$subset,"))")
-  if(inputlist$subset!="" & inputlist$nondups!="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(dataIn, !duplicated(",inputlist$nondups,") & ",inputlist$subset,"))")
+  if(inputlist$subset=="" & inputlist$nondups=="")  ggstr <-  paste0(ggstr,"\n","ggplot(r$dataIn)")
+  if(inputlist$subset=="" & inputlist$nondups!="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(r$dataIn, !duplicated(",inputlist$nondups,")))")
+  if(inputlist$subset!="" & inputlist$nondups=="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(r$dataIn,",inputlist$subset,"))")
+  if(inputlist$subset!="" & inputlist$nondups!="")  ggstr <-  paste0(ggstr,"\n","ggplot(subset(r$dataIn, !duplicated(",inputlist$nondups,") & ",inputlist$subset,"))")
 
   addlay <- function(ageom,ayval,axval,agroup,acolour,ashape,asize,alabel,astats,afcol,afsize,afalph){
     if(astats!='[empty]' &  ageom%in%c("boxplot","bar","histogram","smooth","jitter","text")) stop("Stats can only be displayed as 'line' or 'point'")
@@ -116,9 +116,9 @@ exploreplot <- function(inputlist){
   if(inputlist$ptitle!='') add <- c(add,ggtitle=paste0("ggtitle('",inputlist$ptitle,"')"))
 
   # set manual color scale or fill in case one of the layers has colors (AND it is set as factor!!)
-  cond1 <- inputlist$colour1!='[empty]' & grepl(paste0("factor\\(dataIn.",inputlist$colour1),inputlist$precode)
-  cond2 <- inputlist$colour2!='[empty]' & grepl(paste0("factor\\(dataIn.",inputlist$colour2),inputlist$precode)
-  cond3 <- inputlist$colour3!='[empty]' & grepl(paste0("factor\\(dataIn.",inputlist$colour3),inputlist$precode)
+  cond1 <- inputlist$colour1!='[empty]' & grepl(paste0("factor\\(r$dataIn.",inputlist$colour1),inputlist$precode)
+  cond2 <- inputlist$colour2!='[empty]' & grepl(paste0("factor\\(r$dataIn.",inputlist$colour2),inputlist$precode)
+  cond3 <- inputlist$colour3!='[empty]' & grepl(paste0("factor\\(r$dataIn.",inputlist$colour3),inputlist$precode)
   cond4 <- inputlist$colour1!='[empty]' & inputlist$geoms1%in%c("boxplot","bar","histogram")
   cond5 <- inputlist$colour2!='[empty]' & inputlist$geoms2%in%c("boxplot","bar","histogram")
   cond6 <- inputlist$colour3!='[empty]' & inputlist$geoms3%in%c("boxplot","bar","histogram")
diff --git a/R/module_dataexplore.R b/R/module_dataexplore.R
index 125606e..9dd696c 100644
--- a/R/module_dataexplore.R
+++ b/R/module_dataexplore.R
@@ -152,19 +152,19 @@ module_dataexplore_server <- function(id, r) {
       }
     },ignoreInit=TRUE)
 
-    # Select different model (for now assign in global environment)
+    # Select different model (store in reactive values object)
     updfunc <- function(){
       if(input$use_input){
-        assign("dataIn",try(readRDS(paste0("shinyMixR/",input$mdls[1],".res.rds"))$origData),envir=.GlobalEnv)  
+        r$dataIn <- try(readRDS(paste0("shinyMixR/",input$mdls[1],".res.rds"))$origData)
       }else{
-        assign("dataIn",try(as.data.frame(readRDS(paste0("shinyMixR/",input$mdls[1],".res.rds")))),envir=.GlobalEnv)          
+        r$dataIn <- try(as.data.frame(readRDS(paste0("shinyMixR/",input$mdls[1],".res.rds"))))
       }
-      if(!"try-error"%in%class(dataIn)){
+      if(!"try-error" %in% class(r$dataIn)){
         set1 <- paste0(c("Xval","Yval","group","colour","shape","size","label","facet"),rep(1:3,each=8))
         set1 <- lapply(set1,function(x) {
-          updateSelectInput(session,x,choices=c("[empty]",names(dataIn)),selected=ifelse(input[[x]]=="","[empty]",input[[x]]))
+          updateSelectInput(session,x,choices=c("[empty]",names(r$dataIn)),selected=ifelse(input[[x]]=="","[empty]",input[[x]]))
         })
-        updateSelectInput(session,"nondups",choices=c("",names(dataIn)),selected="")
+        updateSelectInput(session,"nondups",choices=c("",names(r$dataIn)),selected="")
       }
     }
     observeEvent(input$mdls,{updfunc()},ignoreInit=TRUE)
@@ -207,9 +207,9 @@ module_dataexplore_server <- function(id, r) {
     upDT  <- eventReactive(input$maketbl,{
       if(!is.null(input$mdls)){
         if(!is.null(input$precode) && input$precode!="")     eval(parse(text=input$precode))
-        if(!is.null(input$subset)  && input$subset!="")    eval(parse(text=paste0("dataIn <- subset(dataIn,",input$subset,")")))
-        if(!is.null(input$nondups)  && input$nondups!="")  eval(parse(text=paste0("dataIn <- subset(dataIn, !duplicated(",input$nondups,"))")))
-        dataIn
+        if(!is.null(input$subset)  && input$subset!="")    eval(parse(text=paste0("r$dataIn <- subset(r$dataIn,",input$subset,")")))
+        if(!is.null(input$nondups)  && input$nondups!="")  eval(parse(text=paste0("r$dataIn <- subset(r$dataIn, !duplicated(",input$nondups,"))")))
+        r$dataIn
       }
     })
     output$tableout <- DT::renderDT(upDT(),options=list(scrollX=TRUE,pageLength=100,lengthMenu=c(10,100,1000,10000)))  # Show entire dataset

From 6bfc2c393fc5f9db34ca02d759ff085a6cf5b8c1 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 14:07:01 +0200
Subject: [PATCH 30/41] replace deprecated fun.y with fun

---
 R/exploreplot.r | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/exploreplot.r b/R/exploreplot.r
index 2e36e9f..72b9dc2 100644
--- a/R/exploreplot.r
+++ b/R/exploreplot.r
@@ -65,11 +65,11 @@ exploreplot <- function(inputlist){
 	aess  <-  paste(paste(names(aess),aess,sep="="),collapse=", ")
 
 	if(astats%in%c("mean","median")){
-	  lay  <- paste0("stat_summary","(aes(",aess,"), fun.y=",astats,", geom='", ageom,"', ",argm,")")
+	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=",astats,", geom='", ageom,"', ",argm,")")
 	}else if(astats=="mean (SD)"){
-	  lay  <- paste0("stat_summary","(aes(",aess,"), fun.y=mean, fun.ymin=function(x) mean(x) - sd(x), fun.ymax=function(x) mean(x) + sd(x), geom='errorbar', width = 0.2, ",argm,")")
+	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=mean, funmin=function(x) mean(x) - sd(x), funmax=function(x) mean(x) + sd(x), geom='errorbar', width = 0.2, ",argm,")")
 	}else if(astats=="median (5-95th perc.)"){
-	  lay  <- paste0("stat_summary","(aes(",aess,"), fun.y=median, fun.ymin=function(x) quantile(x,0.05), fun.ymax=function(x) quantile(x,0.95), geom='errorbar', width = 0.2, ",argm,")")
+	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=median, funmin=function(x) quantile(x,0.05), funmax=function(x) quantile(x,0.95), geom='errorbar', width = 0.2, ",argm,")")
 	}else{
 	  lay  <- paste0("geom_",ageom,"(aes(",aess,"), ",argm,")")
 	}

From 9cd89ff53b69fe76aa0a3935918df99a5c9e5500 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 14:07:11 +0200
Subject: [PATCH 31/41] remove print statements

---
 R/get_proj.r                   | 2 --
 tests/testthat/test-gof_plot.R | 2 --
 2 files changed, 4 deletions(-)

diff --git a/R/get_proj.r b/R/get_proj.r
index 943b6f8..7a6145c 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -15,8 +15,6 @@
 #' }
 get_proj <- function(projloc=".",geteval=TRUE){
   
-  print(projloc)
-  
   # Read in models and place in result objects
   dir.create(paste0(projloc,"/shinyMixR/app/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
   mdln    <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
diff --git a/tests/testthat/test-gof_plot.R b/tests/testthat/test-gof_plot.R
index 9e8d0e9..1f67723 100644
--- a/tests/testthat/test-gof_plot.R
+++ b/tests/testthat/test-gof_plot.R
@@ -1,7 +1,5 @@
 test_that("gof_plot works as expected", {
   
-  print(.libPaths())
-  
   res_path <- system.file("/other/run1.res.rds", package = "shinyMixR")
   
   res <- readRDS(res_path)

From 7b4cd30b385febb5bfe769c928f2093166b9e56d Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 14:14:36 +0200
Subject: [PATCH 32/41] remove data assignment to global env

---
 R/get_proj.r | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/R/get_proj.r b/R/get_proj.r
index 7a6145c..721628c 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -27,13 +27,6 @@ get_proj <- function(projloc=".",geteval=TRUE){
   datf  <- list.files(paste0(projloc,"/shinyMixR/app/data"))
   grepd <- " |^[[:digit:]]|\\!|\\#|\\$|\\%|\\&|\\'|\\(|\\)|\\-|\\;|\\=|\\@|\\[|\\]|\\^\\`\\{\\|\\}"
   if(any(grepl(grepd,datf))) warning("Data files with special characters found, take into acount that models that use these can crash")
-  # not relevant to read all data for running nlmixr in separate session (should be loaded in this session!)
-  lapply(list.files(paste0(projloc,"/shinyMixR/app/data"),full.names = TRUE),function(x){
-    if(!grepl(grepd,x) & !exists(sub("\\.rds$|\\.csv$","",basename(x),ignore.case = TRUE),envir=.GlobalEnv)){
-      if(grepl("\\.rds$",x,ignore.case = TRUE)) assign(sub("\\.rds$","",basename(x),ignore.case = TRUE),readRDS(x),pos = .GlobalEnv)
-      if(grepl("\\.csv$",x,ignore.case = TRUE)) assign(sub("\\.csv$","",basename(x),ignore.case = TRUE),read.csv(x),pos = .GlobalEnv)
-    }
-  })
 
   # Read in models and results
   if(!file.exists(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))){

From 6b73e3103ca81ca36560c91a2ca36c08f4aa1f2d Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 14:15:47 +0200
Subject: [PATCH 33/41] add CRAN comments

---
 .Rbuildignore    | 1 +
 cran-comments.md | 5 +++++
 2 files changed, 6 insertions(+)
 create mode 100644 cran-comments.md

diff --git a/.Rbuildignore b/.Rbuildignore
index e79996c..14b0478 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,4 @@
 ^_pkgdown\.yml$
 ^pkgdown$
 ^docs$
+^cran-comments\.md$
diff --git a/cran-comments.md b/cran-comments.md
new file mode 100644
index 0000000..858617d
--- /dev/null
+++ b/cran-comments.md
@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.

From e1d63fb2d06fff4b76280640b18bbe6f1b31db07 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 15:25:59 +0200
Subject: [PATCH 34/41] properly rename Dashboard to lowercase

---
 inst/{Dashboard => dashboard}/app.R                 |   0
 inst/{Dashboard => dashboard}/www/logoshinyMixR.png | Bin
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename inst/{Dashboard => dashboard}/app.R (100%)
 rename inst/{Dashboard => dashboard}/www/logoshinyMixR.png (100%)

diff --git a/inst/Dashboard/app.R b/inst/dashboard/app.R
similarity index 100%
rename from inst/Dashboard/app.R
rename to inst/dashboard/app.R
diff --git a/inst/Dashboard/www/logoshinyMixR.png b/inst/dashboard/www/logoshinyMixR.png
similarity index 100%
rename from inst/Dashboard/www/logoshinyMixR.png
rename to inst/dashboard/www/logoshinyMixR.png

From 9be5cc5974b8cc3fb9c16118c9cbdf6b5fb713d9 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 15:27:14 +0200
Subject: [PATCH 35/41] properly rename Other to lowercase

---
 inst/{Other => other}/combined.results.html.r |   0
 inst/{Other => other}/eta.plot.arg.r          |   0
 inst/{Other => other}/eta.plot.r              |   0
 inst/{Other => other}/pk.1cmt.closed.r        |   0
 inst/{Other => other}/pk.1cmt.des.r           |   0
 inst/{Other => other}/run1.r                  |   0
 inst/{Other => other}/run1.res.rds            | Bin
 inst/{Other => other}/run1.ressum.rds         | Bin
 inst/{Other => other}/run_nmx.tmp             |   0
 inst/{Other => other}/theo_sd.rds             | Bin
 inst/{Other => other}/vpc.plot.r              |   0
 11 files changed, 0 insertions(+), 0 deletions(-)
 rename inst/{Other => other}/combined.results.html.r (100%)
 rename inst/{Other => other}/eta.plot.arg.r (100%)
 rename inst/{Other => other}/eta.plot.r (100%)
 rename inst/{Other => other}/pk.1cmt.closed.r (100%)
 rename inst/{Other => other}/pk.1cmt.des.r (100%)
 rename inst/{Other => other}/run1.r (100%)
 rename inst/{Other => other}/run1.res.rds (100%)
 rename inst/{Other => other}/run1.ressum.rds (100%)
 rename inst/{Other => other}/run_nmx.tmp (100%)
 rename inst/{Other => other}/theo_sd.rds (100%)
 rename inst/{Other => other}/vpc.plot.r (100%)

diff --git a/inst/Other/combined.results.html.r b/inst/other/combined.results.html.r
similarity index 100%
rename from inst/Other/combined.results.html.r
rename to inst/other/combined.results.html.r
diff --git a/inst/Other/eta.plot.arg.r b/inst/other/eta.plot.arg.r
similarity index 100%
rename from inst/Other/eta.plot.arg.r
rename to inst/other/eta.plot.arg.r
diff --git a/inst/Other/eta.plot.r b/inst/other/eta.plot.r
similarity index 100%
rename from inst/Other/eta.plot.r
rename to inst/other/eta.plot.r
diff --git a/inst/Other/pk.1cmt.closed.r b/inst/other/pk.1cmt.closed.r
similarity index 100%
rename from inst/Other/pk.1cmt.closed.r
rename to inst/other/pk.1cmt.closed.r
diff --git a/inst/Other/pk.1cmt.des.r b/inst/other/pk.1cmt.des.r
similarity index 100%
rename from inst/Other/pk.1cmt.des.r
rename to inst/other/pk.1cmt.des.r
diff --git a/inst/Other/run1.r b/inst/other/run1.r
similarity index 100%
rename from inst/Other/run1.r
rename to inst/other/run1.r
diff --git a/inst/Other/run1.res.rds b/inst/other/run1.res.rds
similarity index 100%
rename from inst/Other/run1.res.rds
rename to inst/other/run1.res.rds
diff --git a/inst/Other/run1.ressum.rds b/inst/other/run1.ressum.rds
similarity index 100%
rename from inst/Other/run1.ressum.rds
rename to inst/other/run1.ressum.rds
diff --git a/inst/Other/run_nmx.tmp b/inst/other/run_nmx.tmp
similarity index 100%
rename from inst/Other/run_nmx.tmp
rename to inst/other/run_nmx.tmp
diff --git a/inst/Other/theo_sd.rds b/inst/other/theo_sd.rds
similarity index 100%
rename from inst/Other/theo_sd.rds
rename to inst/other/theo_sd.rds
diff --git a/inst/Other/vpc.plot.r b/inst/other/vpc.plot.r
similarity index 100%
rename from inst/Other/vpc.plot.r
rename to inst/other/vpc.plot.r

From 321b583b410fe7f54f848e6fd75b805652f8a0af Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 15:49:48 +0200
Subject: [PATCH 36/41] increase timeout

---
 tests/testthat/test-shinymixr-01-model-run1.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-shinymixr-01-model-run1.R b/tests/testthat/test-shinymixr-01-model-run1.R
index 9798746..721770a 100644
--- a/tests/testthat/test-shinymixr-01-model-run1.R
+++ b/tests/testthat/test-shinymixr-01-model-run1.R
@@ -25,7 +25,7 @@ test_that("Shiny app runs model and returns parameters for run1", {
   # Wait for model to finish (NULL or 0 is the initial value, so we ignore it)
   app$wait_for_value(export = "modrun-model_updated",
                      ignore = list(NULL, 0),
-                     timeout = 120000)
+                     timeout = 240000)
   
   # Test if run is done and 'correct' results have been created
   Sys.sleep(1)

From 7b49c568ac3bc44bacf0caa72820cc560ac2ed9d Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 30 Apr 2024 15:58:44 +0200
Subject: [PATCH 37/41] skip test on CI

---
 tests/testthat/test-shinymixr-01-model-run1.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-shinymixr-01-model-run1.R b/tests/testthat/test-shinymixr-01-model-run1.R
index 721770a..390c7cb 100644
--- a/tests/testthat/test-shinymixr-01-model-run1.R
+++ b/tests/testthat/test-shinymixr-01-model-run1.R
@@ -5,6 +5,9 @@ test_that("Shiny app runs model and returns parameters for run1", {
   # Don't run these tests on the CRAN build servers
   skip_on_cran()
   
+  # Don't run this test on CI
+  skip_on_ci()
+  
   # Set up necessary files (internal function)
   shinyMixR:::setup_shinymixr_test(dir = paste0(tempdir(),"/files"),
                                    overwrite = TRUE, 
@@ -25,7 +28,7 @@ test_that("Shiny app runs model and returns parameters for run1", {
   # Wait for model to finish (NULL or 0 is the initial value, so we ignore it)
   app$wait_for_value(export = "modrun-model_updated",
                      ignore = list(NULL, 0),
-                     timeout = 240000)
+                     timeout = 120000)
   
   # Test if run is done and 'correct' results have been created
   Sys.sleep(1)

From f9a2d7138b2b1667e06106f5da0bb7617b8f68bc Mon Sep 17 00:00:00 2001
From: RichardHooijmaijers <richardhooijmaijers@gmail.com>
Date: Mon, 6 May 2024 11:11:09 +0200
Subject: [PATCH 38/41] get folder structure right and better way to run app

---
 DESCRIPTION       |   7 ++-
 R/create_proj.r   |   4 +-
 R/get_proj.r      |  21 ++++++---
 R/run_shinymixr.r | 113 +++++++++++++++++++++++++++++++++++++++++-----
 4 files changed, 123 insertions(+), 22 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ef6dd8c..6a618fe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -4,7 +4,8 @@ Version: 0.5.0
 Authors@R: c(person("Richard", "Hooijmaijers", email = "richardhooijmaijers@gmail.com", role = c("aut", "cre","cph")),
              person("Teun", "Post", email = "teunpost@gmail.com",role = c("aut","cph")),
              person("LAPP Consultants",email = "info@lapp.nl", role=c("fnd","cph")),
-             person("Matthew Fidler",role=c("ctb")))
+             person("Matthew Fidler",role=c("ctb")),
+             person("Veerle van Leemput",role=c("ctb")))
 Author: Richard Hooijmaijers
 Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
 Description: An interface for the 'nlmixr2' package. Furthermore additional functions
@@ -27,7 +28,9 @@ Imports:
   plotly,
   cowplot,
   shinyjs,
-  ps
+  ps,
+  xfun,
+  fresh
 Suggests:
     xpose,
     xpose.nlmixr2,
diff --git a/R/create_proj.r b/R/create_proj.r
index ecdede9..72acf68 100644
--- a/R/create_proj.r
+++ b/R/create_proj.r
@@ -17,7 +17,9 @@
 #' }
 create_proj <- function(loc=".", overwrite=FALSE){
   
-  loc <- paste0(loc, "/shinyMixR/app")
+  # we want to create subfolders directly in loc, check run_app functionality to see changes there
+  # for this PR we can save the app in loc/shinyMixR/app, in the end we will not need this
+  # loc <- paste0(loc, "/shinyMixR/app")
   
   if(!dir.exists(loc)) dir.create(loc, recursive = TRUE)
   
diff --git a/R/get_proj.r b/R/get_proj.r
index 721628c..64d6a3e 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -16,20 +16,25 @@
 get_proj <- function(projloc=".",geteval=TRUE){
   
   # Read in models and place in result objects
-  dir.create(paste0(projloc,"/shinyMixR/app/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
-  mdln    <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
+  # dir.create(paste0(projloc,"/shinyMixR/app/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
+  # mdln    <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
+  dir.create(paste0(projloc,"/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
+  mdln    <- normalizePath(list.files(paste0(projloc,"/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
   mdlnb   <- sub("\\.[r|R]","",basename(mdln))
-  sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
+  #sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
+  sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
   sumresi <- file.info(sumres)
   summdli <- file.info(mdln)
   
   # read in data folder (only in case objects are not yet present)
-  datf  <- list.files(paste0(projloc,"/shinyMixR/app/data"))
+  #datf  <- list.files(paste0(projloc,"/shinyMixR/app/data"))
+  datf  <- list.files(paste0(projloc,"/data"))
   grepd <- " |^[[:digit:]]|\\!|\\#|\\$|\\%|\\&|\\'|\\(|\\)|\\-|\\;|\\=|\\@|\\[|\\]|\\^\\`\\{\\|\\}"
   if(any(grepl(grepd,datf))) warning("Data files with special characters found, take into acount that models that use these can crash")
 
   # Read in models and results
-  if(!file.exists(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))){
+  #if(!file.exists(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))){
+  if(!file.exists(paste0(projloc,"/shinyMixR/project.rds"))){
     mdls <- lapply(mdln,list)
     names(mdls) <- sub("\\.[r|R]","",basename(mdln))
     if(length(mdln)==0){
@@ -45,7 +50,8 @@ get_proj <- function(projloc=".",geteval=TRUE){
     for(i in sumres) mdls[[sub("\\.ressum\\.rds","",basename(i))]]$results <- readRDS(i)
     mdls$meta <- list(lastrefresh=Sys.time())
   }else{
-    mdls   <- readRDS(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
+    #mdls   <- readRDS(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
+    mdls   <- readRDS(paste0(projloc,"/shinyMixR/project.rds"))
     # for the list with models, check if new models are available or old models are deleted
     # and if models are updated after last refresh:
     # inproj <- unlist(sapply(mdls[names(mdls)[names(mdls)!="meta"]],"[",1))
@@ -85,6 +91,7 @@ get_proj <- function(projloc=".",geteval=TRUE){
   chk       <- chk[which(chk$mdlsv>chk$ressv),]
   #if(nrow(chk)>0) noret <- apply(chk,1,function(x) cat("Be aware that model is saved after results for",x['mdl'],"\n"))
 
-  saveRDS(mdls,file=paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
+  #saveRDS(mdls,file=paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
+  saveRDS(mdls,file=paste0(projloc,"/shinyMixR/project.rds"))
   return(mdls)
 }
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index b1390ce..a3dffe8 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -22,24 +22,113 @@
 #' \dontrun{
 #'  run_shinymixr(".")
 #' }
-run_shinymixr <- function(wd = getwd(), dry_run = FALSE, ...){
+run_shinymixr <- function(...){ # wd = getwd(), dry_run = FALSE,
   
-  if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
-  if(!file.exists(paste0(wd,"/shinyMixR/app/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/app/shinyMixR/temp"),recursive=TRUE))
+  #if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
+  #if(!file.exists(paste0(wd,"/shinyMixR/app/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/app/shinyMixR/temp"),recursive=TRUE))
+  #if(!file.exists(paste0(wd,"/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/temp"),recursive=TRUE))
   
-  try(file.copy(system.file("dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
-  try(file.copy(system.file("dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
+  #try(file.copy(system.file("dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
+  #try(file.copy(system.file("dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
   
   # Set the working directory so the project can be found
-  adpt <- readLines(system.file("dashboard", "app.R", package = "shinyMixR"))
-  adpt <- c(paste0("setwd(\"", normalizePath(wd, winslash = "/"), "\")"), adpt)
-  writeLines(adpt, paste0(wd,"/shinyMixR/app/app.R"))
+  #adpt <- readLines(system.file("dashboard", "app.R", package = "shinyMixR"))
+  #adpt <- c(paste0("setwd(\"", normalizePath(wd, winslash = "/"), "\")"), adpt)
+  #writeLines(adpt, paste0(wd,"/shinyMixR/app/app.R"))
   
   # Clean up stuff before running the app (check if feasible or not)
-  try(unlink(list.files(paste0(wd,"/shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE)))
-  if (dry_run == TRUE) {
-    return()
+  #try(unlink(list.files(paste0(wd,"/shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE)))
+  # if (dry_run == TRUE) {
+  #   return()
+  # } else {
+  #   shiny::runApp(paste0(wd,"/shinyMixR/app"),...)
+  # }
+
+  if(!file.exists("shinyMixR/temp")) try(dir.create("shinyMixR/temp",recursive=TRUE))
+  proj_obj <- get_proj()
+  # Check and load nlmixr(2)
+  if ("nlmixr2" %in% rownames(installed.packages())){
+    library(nlmixr2)
   } else {
-    shiny::runApp(paste0(wd,"/shinyMixR/app"),...)
+    cat("you need the 'nlmixr2' package to run models\n")
   }
+
+  newtheme <- fresh::create_theme(
+    theme = "darkly", # theme has no effect, at least within bs4Dash
+    fresh::bs4dash_font(size_base = "0.9rem"),
+    fresh::bs4dash_status(primary = "#3c8dbc")
+  )
+
+  shinyApp(
+    ui = dashboardPage(
+      title = "shinyMixR",
+      # Header
+      header = dashboardHeader(
+        title = dashboardBrand(title = "ShinyMixR", color = "lightblue"), #, color = "lightblue", href = "#", image = "logoshinyMixR.png"),
+        leftUI = tags$img(src=paste0("data:image/png;base64,",xfun::base64_encode(system.file("dashboard/www/logoshinyMixR.png", package = "shinyMixR"))),height=40)
+      ),
+      # Sidebar menu
+      sidebar = dashboardSidebar(status="lightblue", elevation = 1,
+                                  sidebarMenu(id="tabs", 
+                                    menuItem('Model overview', tabName='overview', icon=icon('table')),
+                                    menuItem('Edit model(s)', tabName='editor', icon=icon('file-pen')),
+                                    menuItem('Run model(s)', tabName='run', icon=icon('person-running')),
+                                    menuItem('Parameter estimates', tabName='par', icon=icon('table-cells')),
+                                    menuItem('Goodness of fit', tabName='gof', icon=icon('chart-line')),
+                                    menuItem('Fit plots', tabName='fitpl', icon=icon('chart-line')),
+                                    menuItem('Data exploration', tabName='expl', icon=icon('magnifying-glass')),
+                                    menuItem('Settings', tabName='settings', icon=icon('gear'))
+                                  )
+      ),
+      # Main body
+      body = dashboardBody(
+        # First set theme and include css
+        fresh::use_theme(newtheme),
+        # CHECK IF THE LINES BELOW WILL WORK WITHOUT INTERNET CONNECTION AND DOES IT FAIL GRACEFULLY?!
+        shinyWidgets::useSweetAlert("minimal"),
+        tags$style("@import url(https://use.fontawesome.com/releases/v6.3.0/css/all.css);"),
+        tags$head(tags$style(HTML(".shiny-split-layout > div {overflow: visible;}"))),
+        tags$head(tags$style("#progph{overflow-y:scroll; max-height: 600px;}")),
+        tags$head(tags$style(HTML("#exploretabout{height: 75vh; overflow-y: auto;}"))),
+        tags$head(tags$style(HTML(".swal2-popup {font-size: 0.9rem !important;}"))),    
+        tags$head(tags$style(HTML("input[id$=\"subset\"]{font-family:\"Courier New\"}"))),
+        tags$head(tags$style(HTML("input[id$=\"precode\"]{font-family:\"Courier New\"}"))),
+        tags$head(tags$style(HTML("label{margin-bottom:0rem;}"))),
+        tabItems(
+          tabItem(tabName = "overview", module_overview_ui("oview")),
+          tabItem(tabName = "editor", module_edit_ui("editor")),
+          tabItem(tabName = "run", module_run_ui("modrun", proj_obj)),
+          tabItem(tabName = "par", module_pt_ui("partable", proj_obj)),
+          tabItem(tabName = "gof", module_gof_ui("gofplots", proj_obj)),
+          tabItem(tabName = "fitpl", module_fitplots_ui("fitplots", proj_obj)),
+          tabItem(tabName = "expl", module_dataexplore_ui("explore")),
+          tabItem(tabName = "settings", module_settings_ui("settings"))
+        )  
+      )
+    ),
+    server = function(input, output, session) {
+       # Top-level reactive values
+      r <- reactiveValues(active_tab = "",
+                          model_updated = 0,
+                          proj_obj = get_proj(),
+                          this_wd = ".")
+      
+      observeEvent(input$tabs, r$active_tab <- input$tabs)
+      
+      # Modules
+      sett <- module_settings_server("settings")
+      module_overview_server("oview", r = r)
+      module_edit_server("editor", r = r, settings=sett)
+      module_run_server("modrun", r = r)
+      module_pt_server("partable", r = r)
+      module_gof_server("gofplots", r = r,settings=sett)
+      module_fitplots_server("fitplots", r = r,settings=sett)
+      module_dataexplore_server("explore", r = r)
+
+    },
+    options = list(launch.browser=TRUE,...) # set general options here for running the app
+  )
+  
+
+
 }

From 707acf1bd7d16d9d8b89bdd5ab18d28ab7245097 Mon Sep 17 00:00:00 2001
From: RichardHooijmaijers <richardhooijmaijers@gmail.com>
Date: Mon, 6 May 2024 16:15:17 +0200
Subject: [PATCH 39/41] changes for folder structure mainly for wd

---
 DESCRIPTION                                   |  4 +--
 NAMESPACE                                     |  2 ++
 R/module_dataexplore.R                        |  4 +--
 R/module_edit.R                               | 17 ++++++----
 R/module_fitplots.R                           |  4 +--
 R/module_gof.R                                |  4 +--
 R/module_metadata.R                           |  6 ++--
 R/module_overview.R                           | 12 +++----
 R/module_run.R                                | 14 ++++----
 R/run_nmx.r                                   |  4 +--
 R/run_shinymixr.r                             | 33 ++++++++++---------
 R/utils.R                                     | 12 +++----
 inst/other/run_nmx.tmp                        |  2 +-
 man/run_shinymixr.Rd                          |  4 +--
 man/shinyMixR-package.Rd                      |  1 +
 tests/testthat.R                              |  1 +
 tests/testthat/test-shinymixr-01-model-run1.R |  7 ++--
 .../test-shinymixr-02-parameter-table.R       |  3 +-
 .../test-shinymixr-03-create-newmodel.R       | 10 +++---
 19 files changed, 77 insertions(+), 67 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6a618fe..500d016 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -30,11 +30,11 @@ Imports:
   shinyjs,
   ps,
   xfun,
-  fresh
+  fresh,
+  nlmixr2
 Suggests:
     xpose,
     xpose.nlmixr2,
-    nlmixr2,
     nlme,
     testthat,
     shinytest2,
diff --git a/NAMESPACE b/NAMESPACE
index a522d1f..5cdd973 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -42,6 +42,7 @@ export(update_inits)
 import(bs4Dash)
 import(ggplot2)
 import(gridExtra)
+import(nlmixr2)
 importFrom(magrittr,"%>%")
 importFrom(shiny,HTML)
 importFrom(shiny,NS)
@@ -79,6 +80,7 @@ importFrom(shiny,renderText)
 importFrom(shiny,req)
 importFrom(shiny,runApp)
 importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
 importFrom(shiny,showModal)
 importFrom(shiny,sliderInput)
 importFrom(shiny,span)
diff --git a/R/module_dataexplore.R b/R/module_dataexplore.R
index 9dd696c..ddb4576 100644
--- a/R/module_dataexplore.R
+++ b/R/module_dataexplore.R
@@ -155,9 +155,9 @@ module_dataexplore_server <- function(id, r) {
     # Select different model (store in reactive values object)
     updfunc <- function(){
       if(input$use_input){
-        r$dataIn <- try(readRDS(paste0("shinyMixR/",input$mdls[1],".res.rds"))$origData)
+        r$dataIn <- try(readRDS(paste0(r$this_wd,"/shinyMixR/",input$mdls[1],".res.rds"))$origData)
       }else{
-        r$dataIn <- try(as.data.frame(readRDS(paste0("shinyMixR/",input$mdls[1],".res.rds"))))
+        r$dataIn <- try(as.data.frame(readRDS(paste0(r$this_wd,"/shinyMixR/",input$mdls[1],".res.rds"))))
       }
       if(!"try-error" %in% class(r$dataIn)){
         set1 <- paste0(c("Xval","Yval","group","colour","shape","size","label","facet"),rep(1:3,each=8))
diff --git a/R/module_edit.R b/R/module_edit.R
index e16dbd1..318d1d9 100644
--- a/R/module_edit.R
+++ b/R/module_edit.R
@@ -62,10 +62,10 @@ module_edit_server <- function(id, r, settings) {
         mdl <- try(readLines(system.file(paste0("other/",input$templnew,".r"),package="shinyMixR")))
         if(!"try-error"%in%class(mdl)){
           mdl <- sub("run1",sub("\\.[r|R]","",input$namenew),mdl)
-          writeLines(mdl,paste0("models/",input$namenew))
+          writeLines(mdl,paste0(r$this_wd,"/models/",input$namenew))
           r$proj_obj <- get_proj(r$this_wd)
           updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",input$namenew))
-          shinyAce::updateAceEditor(session,"editor",value=paste(readLines(paste0("models/",input$namenew)),collapse="\n"))
+          shinyAce::updateAceEditor(session,"editor",value=paste(readLines(paste0(r$this_wd,"/models/",input$namenew)),collapse="\n"))
           removeModal()
         }
     })
@@ -103,7 +103,7 @@ module_edit_server <- function(id, r, settings) {
         selm <- incm <- NULL
       } 
       modalDialog(title="Update initial estimates",easyClose = TRUE,size="l",
-        selectInput(ns("finest"),"Final estimates from",sub("\\.res\\.rds","",list.files("shinyMixR",pattern="res.rds")), selected = selm, multiple=FALSE),
+        selectInput(ns("finest"),"Final estimates from",sub("\\.res\\.rds","",list.files(paste0(r$this_wd,"/shinyMixR"),pattern="res.rds")), selected = selm, multiple=FALSE),
         textInput(ns("tosave"),"Save as",incm),
         actionButton(ns("goupdate"), "Go",icon=icon("play"))
       )
@@ -112,11 +112,14 @@ module_edit_server <- function(id, r, settings) {
     observeEvent(input$goupdate,{
       if(isTruthy(input$finest) && isTruthy(input$tosave)){
         #res <- try(update_inits(input$editor,paste0("shinyMixr/",input$finest,".res.rds"),paste0("models/",input$tosave)))
-        res <- try(update_inits(readLines(paste0("models/",input$finest,".r")),
-                                paste0("shinyMixr/",input$finest,".res.rds"),
-                                paste0("models/",input$tosave)))
+        #cat("getting stuff from",paste0(r$this_wd,"/models/",input$finest,".r"),"with results from",paste0(r$this_wd,"/shinyMixr/",input$finest,".res.rds"), 
+        #    "to model",paste0(r$this_wd,"/models/",input$tosave))
+        res <- try(update_inits(readLines(paste0(r$this_wd,"/models/",input$finest,".r")),
+                                paste0(r$this_wd,"/shinyMixr/",input$finest,".res.rds"),
+                                paste0(r$this_wd,"/models/",input$tosave)))
         if("try-error"%in%class(res)){
-          myalert("Could not update initials",type = "error")
+          #myalert("Could not update initials",type = "error")
+          myalert(res,type = "error")
         }else{
           r$proj_obj <- get_proj(r$this_wd)
           updateSelectInput(session,"editLst",choices = names(r$proj_obj)[names(r$proj_obj)!="meta"],selected=sub("\\.[r|R]","",input$tosave))
diff --git a/R/module_fitplots.R b/R/module_fitplots.R
index 96dec25..6c44eb0 100644
--- a/R/module_fitplots.R
+++ b/R/module_fitplots.R
@@ -53,7 +53,7 @@ module_fitplots_server <- function(id, r, settings) {
 
     # Adapt the selection of variables when model is selected
     observeEvent(input$fitLst,{
-      datar <- try(readRDS(paste0("shinyMixR/",input$fitLst,".res.rds")))
+      datar <- try(readRDS(paste0(r$this_wd,"/shinyMixR/",input$fitLst,".res.rds")))
       if(!"try-error"%in%class(datar)){
         updateSelectInput(session, "by", choices = c("",names(datar)),selected="ID")
         updateSelectInput(session, "idv", choices = c("",names(datar)),selected="TIME")
@@ -69,7 +69,7 @@ module_fitplots_server <- function(id, r, settings) {
     # Create fit plot (type of plot taken from settings!)
     fitpl <- function(inp,saveit=FALSE){
       #cat("got clicked\n")
-      dataIn <- readRDS(paste0("shinyMixR/",input$fitLst[1],".res.rds"))
+      dataIn <- readRDS(paste0(r$this_wd,"/shinyMixR/",input$fitLst[1],".res.rds"))
       if(inp$subset!="")     dataIn <- subset(dataIn,eval(parse(text=input$subset)))
       if(inp$precode!="")    eval(parse(text=input$precode))
       if(!isTruthy(inp$by))  byr <- NULL else byr <- inp$by
diff --git a/R/module_gof.R b/R/module_gof.R
index e625c58..1a76989 100644
--- a/R/module_gof.R
+++ b/R/module_gof.R
@@ -49,7 +49,7 @@ module_gof_server <- function(id, r, settings) {
     
     # Adapt the selection of variables when model is selected
     observeEvent(input$gofLst,{
-      datar <- try(readRDS(paste0("shinyMixR/",input$gofLst,".res.rds")))
+      datar <- try(readRDS(paste0(r$this_wd,"/shinyMixR/",input$gofLst,".res.rds")))
       if(!"try-error"%in%class(datar)){
         updateSelectInput(session, "colby", choices = c("",names(datar)))
       }else{
@@ -59,7 +59,7 @@ module_gof_server <- function(id, r, settings) {
 
     # Create GOF plot (type of plot taken from settings!)
     gofpl <- function(inp,saveit=FALSE){
-      dataIn <- readRDS(paste0("shinyMixR/",inp$gofLst,".res.rds"))
+      dataIn <- readRDS(paste0(r$this_wd,"/shinyMixR/",inp$gofLst,".res.rds"))
       if(inp$subset!="")  dataIn <- subset(dataIn,eval(parse(text=input$subset)))
       if(inp$precode!="") eval(parse(text=input$precode))
       if(inp$colby=="")   clr <- NULL else clr <- inp$colby
diff --git a/R/module_metadata.R b/R/module_metadata.R
index 1f6463f..a1584c9 100644
--- a/R/module_metadata.R
+++ b/R/module_metadata.R
@@ -53,7 +53,7 @@ module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NU
       gen  <- tagList(
         sliderInput(ns("mdlimp"), "Importance", 0, 4, meta$imp, step = 1, round = TRUE),
         textInput(ns("mdldesc"),"Description",value=meta$desc),
-        selectInput(ns("mdlref"),"Reference",meta$ref,choices=tools::file_path_sans_ext(list.files("models")),multiple=FALSE,selectize = TRUE),
+        selectInput(ns("mdlref"),"Reference",meta$ref,choices=tools::file_path_sans_ext(list.files(paste0(r$this_wd,"/models"))),multiple=FALSE,selectize = TRUE),
         textInput(ns("mdldata"),"Data",value=meta$data),
         selectInput(ns("mdlest"),"Method",c("fo", "foce", "focei", "foi", "nlme", "posthoc", "predict", "rxSolve", "saem", "simulate"),selected=meta$est),
         actionButton(ns("adpt"), "Save",icon=icon("floppy-disk"))    
@@ -99,9 +99,9 @@ module_metadata_server <- function(id,type,selline=NULL,sellmod=NULL,sellcont=NU
           tmpmod <- tempfile()
           writeLines(sellcont(),tmpmod)
           #toret  <- c(name=paste0("models/",sellmod(),".r"), val=input$mdladpt, saveas=paste0("models/",input$mdladpt))
-          toret  <- c(name=tmpmod, val=input$mdladpt, saveas=paste0("models/",input$mdladpt))
+          toret  <- c(name=tmpmod, val=input$mdladpt, saveas=paste0(r$this_wd,"/models/",input$mdladpt))
         }else{
-          toret <- c(name=paste0("models/",input$mdladpt,".r"), val="Update DT", saveas=paste0("models/",input$mdladpt,".r"))
+          toret <- c(name=paste0(r$this_wd,"/models/",input$mdladpt,".r"), val="Update DT", saveas=paste0(r$this_wd,"/models/",input$mdladpt,".r"))
         } 
         towr <- adpt_meta(toret['name'],metanfo)
         if(type=="save") towr <- sub(sellmod(),sub("\\.[r|R]","",input$mdladpt),towr)
diff --git a/R/module_overview.R b/R/module_overview.R
index 9b2e710..9a8a816 100644
--- a/R/module_overview.R
+++ b/R/module_overview.R
@@ -90,7 +90,7 @@ module_overview_server <- function(id, r) {
     hr_out <- eventReactive(input$hlr, {
       sel   <- sort(names(r$proj_obj)[names(r$proj_obj)!="meta"])[input$overview_tbl_rows_selected]
       if(length(sel)>0){
-        res <- try(readRDS(paste0("shinyMixR/",sel[1],".res.rds")))
+        res <- try(readRDS(paste0(r$this_wd,"/shinyMixR/",sel[1],".res.rds")))
         if(!"try-error"%in%class(res)) print(res) else print("No results available")
       }
     })
@@ -109,18 +109,18 @@ module_overview_server <- function(id, r) {
       if(!is.null(input$overview_tbl_rows_selected)){
         msel <- sort(names(r$proj_obj)[names(r$proj_obj)!="meta"])[input$overview_tbl_rows_selected]
         if(input$delmodall) {
-          try(file.remove(paste0("shinyMixR/",msel,".res.rds")))
-          try(file.remove(paste0("shinyMixR/",msel,".ressum.rds")))
-          try(unlink(paste0("analysis/",msel),recursive = TRUE))
+          try(file.remove(paste0(r$this_wd,"/shinyMixR/",msel,".res.rds")))
+          try(file.remove(paste0(r$this_wd,"/shinyMixR/",msel,".ressum.rds")))
+          try(unlink(paste0(r$this_wd,"/analysis/",msel),recursive = TRUE))
         }
-        try(file.remove(paste0("models/",msel,".r")))
+        try(file.remove(paste0(r$this_wd,"/models/",msel,".r")))
         r$proj_obj <- get_proj(r$this_wd)
         DT::replaceData(proxy, overview(r$proj_obj), rownames = FALSE)
         removeModal()
       }
     },ignoreInit = TRUE)
 
-    module_scripts_server("runscripts", files = reactive(r$mdls), scripts = reactive(r$scrpt), loc = "shinyMixR/temp")
+    module_scripts_server("runscripts", files = reactive(r$mdls), scripts = reactive(r$scrpt), loc = paste0(r$this_wd,"/shinyMixR/temp"))
 
     # Creating reports
     module_reports_server("reports")
diff --git a/R/module_run.R b/R/module_run.R
index aecb8dd..7b87057 100644
--- a/R/module_run.R
+++ b/R/module_run.R
@@ -37,10 +37,10 @@ module_run_server <- function(id, r) {
 
     # Run model
     observeEvent(input$runMdl,{
-      unlink(list.files(paste0("shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE))
+      unlink(list.files(paste0(r$this_wd,"/shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE))
       # Perform tests before running
-       if(!is.null(input$runLst)){
-         proj     <- r$proj_obj
+      if(!is.null(input$runLst)){
+        proj     <- r$proj_obj
         checkall <- unlist(sapply(input$runLst,function(x){
           chk    <- proj[[x]]$model
           chksrc <- try(source(chk,local=TRUE),silent=TRUE)
@@ -51,12 +51,12 @@ module_run_server <- function(id, r) {
           }
         }))
         if(length(checkall)>0){
-           myalert(paste("The following issues occured:",paste0(names(checkall),": ",checkall,collapse=", ")),type = "error")
+          myalert(paste("The following issues occured:",paste0(names(checkall),": ",checkall,collapse=", ")),type = "error")
         }else{
           myalert("model(s) submitted, wait for progress log to pop-up!",type = "succes")
           addcwres <- ifelse("Add CWRES to output"%in%input$addExtra,TRUE,FALSE)
           addnpde  <- ifelse("Add NPDE to output"%in%input$addExtra,TRUE,FALSE)
-          lapply(input$runLst,function(mods) run_nmx(mods, r$proj_obj, addcwres=addcwres,addnpde=addnpde))
+          lapply(input$runLst,function(mods) run_nmx(mods, r$proj_obj, addcwres=addcwres,addnpde=addnpde,projloc=r$this_wd))
         }
       }else{
         myalert("Please select models to run",type = "error")
@@ -65,14 +65,14 @@ module_run_server <- function(id, r) {
     # Get progress log
     runmodmonit <- reactivePoll(500, session,
       checkFunc = function() {
-        progf <- list.files("shinyMixR/temp",pattern="prog\\.txt$",full.names = TRUE)
+        progf <- list.files(paste0(r$this_wd,"/shinyMixR/temp"),pattern="prog\\.txt$",full.names = TRUE)
         if (length(progf)>0)
           max(file.info(progf)$mtime)
         else
           ""
       },
       valueFunc = function() {
-        progFn  <- list.files("shinyMixR/temp",pattern="prog\\.txt$",full.names = TRUE)
+        progFn  <- list.files(paste0(r$this_wd,"/shinyMixR/temp"),pattern="prog\\.txt$",full.names = TRUE)
         paste(unlist(lapply(progFn,function(x) c(paste0("\n ***************",x,"***************"),readLines(x, warn = FALSE)))),collapse="\n")
       }
     )
diff --git a/R/run_nmx.r b/R/run_nmx.r
index 11d71f5..e1b646a 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -32,7 +32,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
   # if(autoupdate) assign(dnm,get_proj(projloc=projloc))
   # Source model to obtain meta data (places meta object in env)
   sret <- try(source(proj[[mod]]$model,local=TRUE))
-  meta <- try(eval(parse(text=c("nlmixr(",readLines(proj[[mod]]$model),")$meta"))))
+  meta <- try(eval(parse(text=c("nlmixr2::nlmixr(",readLines(proj[[mod]]$model),")$meta"))))
   if(inherits(meta, "try-error") || inherits(sret, "try-error")){
     cat("Error in model syntax please check before running\n")
     if(ext) writeLines(meta, paste0(projloc,"/shinyMixR/temp/",mod,".prog.txt"))
@@ -59,7 +59,7 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
                  control=cntrll, 
                  saveres=saverds, 
                  modelname=mod,
-                 locproj=projloc,
+                 locproj=normalizePath(projloc,winslash = "/"),
                  addcwres=addcwres,
                  addnpde=addnpde)
 
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index a3dffe8..59f4dad 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -2,7 +2,6 @@
 #' Creates and run the interface
 #'
 #' @param wd character with the working directory
-#' @param dry_run logical, if TRUE, the function will not launch the app, but will only create the necessary files
 #' @param ... arguments passed to the shiny runApp function
 #' @importFrom shiny runApp HTML NS br checkboxGroupInput checkboxInput conditionalPanel
 #' div em eventReactive exportTestValues fluidRow hr icon
@@ -22,7 +21,7 @@
 #' \dontrun{
 #'  run_shinymixr(".")
 #' }
-run_shinymixr <- function(...){ # wd = getwd(), dry_run = FALSE,
+run_shinymixr <- function(wd = getwd(),...){ 
   
   #if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
   #if(!file.exists(paste0(wd,"/shinyMixR/app/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/app/shinyMixR/temp"),recursive=TRUE))
@@ -43,15 +42,19 @@ run_shinymixr <- function(...){ # wd = getwd(), dry_run = FALSE,
   # } else {
   #   shiny::runApp(paste0(wd,"/shinyMixR/app"),...)
   # }
-
-  if(!file.exists("shinyMixR/temp")) try(dir.create("shinyMixR/temp",recursive=TRUE))
-  proj_obj <- get_proj()
-  # Check and load nlmixr(2)
-  if ("nlmixr2" %in% rownames(installed.packages())){
-    library(nlmixr2)
-  } else {
-    cat("you need the 'nlmixr2' package to run models\n")
-  }
+  #owd <- getwd()
+  #if(normalizePath(owd)!=normalizePath(wd)) setwd(wd)
+  #cat("I am in ",getwd(),"\n")
+  #on.exit(setwd(owd))  
+  #if(!file.exists("shinyMixR/temp")) try(dir.create("shinyMixR/temp",recursive=TRUE))
+  if(!file.exists(paste0(wd,"/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/temp"),recursive=TRUE))
+  proj_obj <- get_proj(wd)
+  # Check and load nlmixr(2); set nlmixr2 as import so needed when package is loaded and this is also a CRAN warning
+  # if ("nlmixr2" %in% rownames(installed.packages())){
+  #   library(nlmixr2)
+  # } else {
+  #   cat("you need the 'nlmixr2' package to run models\n")
+  # }
 
   newtheme <- fresh::create_theme(
     theme = "darkly", # theme has no effect, at least within bs4Dash
@@ -110,8 +113,8 @@ run_shinymixr <- function(...){ # wd = getwd(), dry_run = FALSE,
        # Top-level reactive values
       r <- reactiveValues(active_tab = "",
                           model_updated = 0,
-                          proj_obj = get_proj(),
-                          this_wd = ".")
+                          proj_obj = get_proj(wd),
+                          this_wd = wd)
       
       observeEvent(input$tabs, r$active_tab <- input$tabs)
       
@@ -128,7 +131,5 @@ run_shinymixr <- function(...){ # wd = getwd(), dry_run = FALSE,
     },
     options = list(launch.browser=TRUE,...) # set general options here for running the app
   )
-  
-
-
+  #cat("I was in ",getwd(),"\n")
 }
diff --git a/R/utils.R b/R/utils.R
index db6efa3..86ba81d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -19,18 +19,18 @@ setup_shinymixr_test <- function(dir = "./tests/files", overwrite = TRUE, record
   }
 
   create_proj(dir, overwrite = overwrite)
-  run_shinymixr(wd = dir, dry_run = TRUE)
+  #run_shinymixr(wd = dir, dry_run = TRUE)
   
   if(incres){
     file.copy(system.file(c("other/run1.res.rds","other/run1.ressum.rds"),package="shinyMixR"),
-              paste0(dir,"/shinyMixR/app/shinyMixR"))
+              paste0(dir,"/shinyMixR"))
   }
   
   # create .Rprofile file to store settings
-  if (!file.exists(paste0(dir, "/.Rprofile"))) {
-    writeLines("options(shiny.testmode = TRUE)", 
-               con = paste0(dir, "/shinyMixR/app/.Rprofile"))
-  }
+  # if (!file.exists(paste0(dir, "/.Rprofile"))) {
+  #   writeLines("options(shiny.testmode = TRUE)", 
+  #              con = paste0(dir, "/shinyMixR/app/.Rprofile"))
+  # }
   
   if (record == TRUE) {
     shinytest2::record_test(paste0(dir, "/shinyMixR/app"))
diff --git a/inst/other/run_nmx.tmp b/inst/other/run_nmx.tmp
index 14f07a6..b60436f 100644
--- a/inst/other/run_nmx.tmp
+++ b/inst/other/run_nmx.tmp
@@ -21,7 +21,7 @@ if("{{subs}}"!=""){
 
 source("{{{modelloc}}}")
 setwd("{{{locproj}}}/shinyMixR/temp")
-modres <- try(nlmixr({{{modelname}}}, data=data_nlm, est="{{{est}}}",control={{{control}}},table=tableControl(cwres={{{addcwres}}}, npde={{{addnpde}}})))
+modres <- try(nlmixr2::nlmixr({{{modelname}}}, data=data_nlm, est="{{{est}}}",control={{{control}}},table=tableControl(cwres={{{addcwres}}}, npde={{{addnpde}}})))
 
 {{#saveres}}
 if(length(class(modres))>1 && !"try-error"%in%class(modres)){
diff --git a/man/run_shinymixr.Rd b/man/run_shinymixr.Rd
index 2147236..d78aef5 100644
--- a/man/run_shinymixr.Rd
+++ b/man/run_shinymixr.Rd
@@ -4,13 +4,11 @@
 \alias{run_shinymixr}
 \title{Creates and run the interface}
 \usage{
-run_shinymixr(wd = getwd(), dry_run = FALSE, ...)
+run_shinymixr(wd = getwd(), ...)
 }
 \arguments{
 \item{wd}{character with the working directory}
 
-\item{dry_run}{logical, if TRUE, the function will not launch the app, but will only create the necessary files}
-
 \item{...}{arguments passed to the shiny runApp function}
 }
 \value{
diff --git a/man/shinyMixR-package.Rd b/man/shinyMixR-package.Rd
index 3ee053c..c1a2009 100644
--- a/man/shinyMixR-package.Rd
+++ b/man/shinyMixR-package.Rd
@@ -20,6 +20,7 @@ Other contributors:
 \itemize{
   \item LAPP Consultants \email{info@lapp.nl} [funder, copyright holder]
   \item Matthew Fidler [contributor]
+  \item Veerle van Leemput [contributor]
 }
 
 }
diff --git a/tests/testthat.R b/tests/testthat.R
index bfa1583..4932974 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -3,6 +3,7 @@ options(chromote.timeout = 120)
 
 library(testthat)
 library(shinyMixR)
+library(nlmixr2)
 
 test_check("shinyMixR")
 # devtools::test() 
diff --git a/tests/testthat/test-shinymixr-01-model-run1.R b/tests/testthat/test-shinymixr-01-model-run1.R
index 390c7cb..97cfdb6 100644
--- a/tests/testthat/test-shinymixr-01-model-run1.R
+++ b/tests/testthat/test-shinymixr-01-model-run1.R
@@ -14,7 +14,8 @@ test_that("Shiny app runs model and returns parameters for run1", {
                                    record = FALSE)
   
   # Start driver for Shiny test
-  app <- AppDriver$new(app_dir = paste0(tempdir(),"/files/shinyMixR/app/"), 
+  shiny_app <- shinyMixR::run_shinymixr(paste0(tempdir(),"/files"))
+  app <- AppDriver$new(app_dir = shiny_app, 
                        name = "run1-model", 
                        seed = 123)
   
@@ -32,10 +33,10 @@ test_that("Shiny app runs model and returns parameters for run1", {
   
   # Test if run is done and 'correct' results have been created
   Sys.sleep(1)
-  rundone <- "run1.res.rds"%in%list.files(paste0(tempdir(),"/files/shinyMixR/app/shinyMixR"))
+  rundone <- "run1.res.rds"%in%list.files(paste0(tempdir(),"/files/shinyMixR"))
   expect_true(rundone)
   if(rundone){
-    runres <- readRDS(paste0(tempdir(),"/files/shinyMixR/app/shinyMixR/run1.res.rds"))
+    runres <- readRDS(paste0(tempdir(),"/files/shinyMixR/run1.res.rds"))
     expect_true(inherits(runres,"nlmixr2FitData"))
   }
   
diff --git a/tests/testthat/test-shinymixr-02-parameter-table.R b/tests/testthat/test-shinymixr-02-parameter-table.R
index ff78a0d..6be705f 100644
--- a/tests/testthat/test-shinymixr-02-parameter-table.R
+++ b/tests/testthat/test-shinymixr-02-parameter-table.R
@@ -11,7 +11,8 @@ test_that("Shiny app creates correct parameter table", {
                                    record = FALSE, incres = TRUE)
   
   # Start driver for Shiny test
-  app <- AppDriver$new(app_dir = paste0(tempdir(),"/files/shinyMixR/app/"), 
+  shiny_app <- shinyMixR::run_shinymixr(paste0(tempdir(),"/files"))
+  app <- AppDriver$new(app_dir = shiny_app, 
                        name = "run2-model", 
                        seed = 123)
   
diff --git a/tests/testthat/test-shinymixr-03-create-newmodel.R b/tests/testthat/test-shinymixr-03-create-newmodel.R
index 708d68e..31b9633 100644
--- a/tests/testthat/test-shinymixr-03-create-newmodel.R
+++ b/tests/testthat/test-shinymixr-03-create-newmodel.R
@@ -14,7 +14,8 @@ test_that("Shiny app correctly creates new model code", {
                                    incres = TRUE)
   
   # Start driver for Shiny test
-  app <- AppDriver$new(app_dir = paste0(temp_dir, "/files/shinyMixR/app/"), 
+  shiny_app <- shinyMixR::run_shinymixr(paste0(tempdir(),"/files"))
+  app <- AppDriver$new(app_dir = shiny_app, 
                        name = "run3-model", 
                        seed = 123)
   
@@ -32,10 +33,10 @@ test_that("Shiny app correctly creates new model code", {
   app$expect_values(input = "editor-newgo")
   
   # Check if new model is created and contains correct naming
-  modmade <- "run2.r" %in% list.files(paste0(temp_dir, "/files/shinyMixR/app/models"))
+  modmade <- "run2.r" %in% list.files(paste0(temp_dir, "/files/models"))
   expect_true(modmade)
   if(modmade){
-    modcont <- readLines(paste0(temp_dir, "/files/shinyMixR/app/models/run2.r"))
+    modcont <- readLines(paste0(temp_dir, "/files/models/run2.r"))
     expect_true(grepl("run2 <- function", modcont[1]))
   }
     
@@ -49,9 +50,10 @@ test_that("Shiny app correctly creates new model code", {
   expect_true(curvals$input$`editor-adapt_meta_ed-mdlimp`==1)
   app$click("editor-adapt_meta_ed-adpt")
   app$click(selector = ".swal2-confirm")
-  expect_true("run3.r"%in%list.files(paste0(tempdir(),"/files/shinyMixR/app/models")))
+  expect_true("run3.r"%in%list.files(paste0(tempdir(),"/files/models")))
   
   # Finally test if update inits works as expected (e.g. are initial changed, values itself tested outside shinytest)
+  app$set_inputs(`editor-editLst` = "run1")
   app$click("editor-updinit")
   Sys.sleep(1)
   app$set_inputs("editor-tosave" = c("run99.r"))

From f58b8f0bcd5e2bcd0d4d84a1d1c91ba1bddfafe8 Mon Sep 17 00:00:00 2001
From: Veerle van Leemput <info@hypebright.nl>
Date: Tue, 7 May 2024 16:28:25 +0200
Subject: [PATCH 40/41] fix: typo

---
 R/exploreplot.r | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/exploreplot.r b/R/exploreplot.r
index 72b9dc2..1358c38 100644
--- a/R/exploreplot.r
+++ b/R/exploreplot.r
@@ -67,9 +67,9 @@ exploreplot <- function(inputlist){
 	if(astats%in%c("mean","median")){
 	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=",astats,", geom='", ageom,"', ",argm,")")
 	}else if(astats=="mean (SD)"){
-	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=mean, funmin=function(x) mean(x) - sd(x), funmax=function(x) mean(x) + sd(x), geom='errorbar', width = 0.2, ",argm,")")
+	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=mean, fun.min=function(x) mean(x) - sd(x), fun.max=function(x) mean(x) + sd(x), geom='errorbar', width = 0.2, ",argm,")")
 	}else if(astats=="median (5-95th perc.)"){
-	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=median, funmin=function(x) quantile(x,0.05), funmax=function(x) quantile(x,0.95), geom='errorbar', width = 0.2, ",argm,")")
+	  lay  <- paste0("stat_summary","(aes(",aess,"), fun=median, fun.min=function(x) quantile(x,0.05), fun.max=function(x) quantile(x,0.95), geom='errorbar', width = 0.2, ",argm,")")
 	}else{
 	  lay  <- paste0("geom_",ageom,"(aes(",aess,"), ",argm,")")
 	}

From 84528e2e07e730dab51879e49cb306c2f21a8b76 Mon Sep 17 00:00:00 2001
From: RichardHooijmaijers <richardhooijmaijers@gmail.com>
Date: Tue, 14 May 2024 11:31:20 +0200
Subject: [PATCH 41/41] Cleaned code from unnecessary comments

---
 R/create_proj.r     |  4 ----
 R/get_proj.r        | 12 ------------
 R/gof_plot.r        |  3 ---
 R/module_edit.R     |  4 ----
 R/module_gof.R      |  2 --
 R/module_overview.R |  2 --
 R/module_partable.R |  3 ---
 R/module_reports.R  |  2 --
 R/run_nmx.r         |  3 ---
 R/run_shinymixr.r   | 31 -------------------------------
 R/utils.R           |  1 -
 11 files changed, 67 deletions(-)

diff --git a/R/create_proj.r b/R/create_proj.r
index 72acf68..639323e 100644
--- a/R/create_proj.r
+++ b/R/create_proj.r
@@ -17,10 +17,6 @@
 #' }
 create_proj <- function(loc=".", overwrite=FALSE){
   
-  # we want to create subfolders directly in loc, check run_app functionality to see changes there
-  # for this PR we can save the app in loc/shinyMixR/app, in the end we will not need this
-  # loc <- paste0(loc, "/shinyMixR/app")
-  
   if(!dir.exists(loc)) dir.create(loc, recursive = TRUE)
   
   # First create the folder structure
diff --git a/R/get_proj.r b/R/get_proj.r
index 64d6a3e..959c6c8 100644
--- a/R/get_proj.r
+++ b/R/get_proj.r
@@ -16,24 +16,19 @@
 get_proj <- function(projloc=".",geteval=TRUE){
   
   # Read in models and place in result objects
-  # dir.create(paste0(projloc,"/shinyMixR/app/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
-  # mdln    <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
   dir.create(paste0(projloc,"/shinyMixR"),showWarnings = FALSE,recursive = TRUE)
   mdln    <- normalizePath(list.files(paste0(projloc,"/models"),pattern="run[[:digit:]]*\\.[r|R]",full.names = TRUE))
   mdlnb   <- sub("\\.[r|R]","",basename(mdln))
-  #sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR/app/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
   sumres  <- normalizePath(list.files(paste0(projloc,"/shinyMixR"),pattern="run[[:digit:]]*\\.ressum\\.rds",full.names = TRUE))
   sumresi <- file.info(sumres)
   summdli <- file.info(mdln)
   
   # read in data folder (only in case objects are not yet present)
-  #datf  <- list.files(paste0(projloc,"/shinyMixR/app/data"))
   datf  <- list.files(paste0(projloc,"/data"))
   grepd <- " |^[[:digit:]]|\\!|\\#|\\$|\\%|\\&|\\'|\\(|\\)|\\-|\\;|\\=|\\@|\\[|\\]|\\^\\`\\{\\|\\}"
   if(any(grepl(grepd,datf))) warning("Data files with special characters found, take into acount that models that use these can crash")
 
   # Read in models and results
-  #if(!file.exists(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))){
   if(!file.exists(paste0(projloc,"/shinyMixR/project.rds"))){
     mdls <- lapply(mdln,list)
     names(mdls) <- sub("\\.[r|R]","",basename(mdln))
@@ -42,7 +37,6 @@ get_proj <- function(projloc=".",geteval=TRUE){
     }else{
       for(i in 1:length(mdln)){
         names(mdls[[i]]) <- "model"
-        #if(geteval) mdls[[i]]$modeleval <- try(eval(parse(text=c("nlmixrUI(",readLines(mdln[i]),")"))))
         mdls[[i]]$modeleval <- list()
         if(geteval) mdls[[i]]$modeleval$meta <- try(get_meta(mdln[i]))
       }
@@ -50,11 +44,9 @@ get_proj <- function(projloc=".",geteval=TRUE){
     for(i in sumres) mdls[[sub("\\.ressum\\.rds","",basename(i))]]$results <- readRDS(i)
     mdls$meta <- list(lastrefresh=Sys.time())
   }else{
-    #mdls   <- readRDS(paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
     mdls   <- readRDS(paste0(projloc,"/shinyMixR/project.rds"))
     # for the list with models, check if new models are available or old models are deleted
     # and if models are updated after last refresh:
-    # inproj <- unlist(sapply(mdls[names(mdls)[names(mdls)!="meta"]],"[",1))
     inproj <- names(mdls)[names(mdls)!="meta"]
     todel  <- setdiff(tolower(inproj),tolower(mdlnb))
     toadd  <- setdiff(tolower(mdlnb),tolower(inproj))
@@ -66,7 +58,6 @@ get_proj <- function(projloc=".",geteval=TRUE){
       names(mdls2) <- toadd
       for(i in 1:length(mdls2)){
         names(mdls2[[i]]) <- "model"
-        #if(geteval) mdls2[[i]]$modeleval <- try(eval(parse(text=c("nlmixrUI(",readLines(mdln[which(mdlnb%in%toadd)][i]),")"))))
         if(geteval) mdls2[[i]]$modeleval$meta <- try(get_meta(mdln[which(mdlnb%in%toadd)][i]))
       }
       mdls <- c(mdls,mdls2)
@@ -75,7 +66,6 @@ get_proj <- function(projloc=".",geteval=TRUE){
     if(geteval){
       for(i in mdln){
         if(summdli$mtime[row.names(summdli)==i] > mdls$meta$lastrefresh)
-          #mdls[[sub("\\.[r|R]","",basename(i))]]$modeleval <- try(eval(parse(text=c("nlmixrUI(",readLines(i),")"))))
           mdls[[sub("\\.[r|R]","",basename(i))]]$modeleval$meta <- try(get_meta(i))
       }
     }
@@ -89,9 +79,7 @@ get_proj <- function(projloc=".",geteval=TRUE){
   chk       <- data.frame(mdl=sub("\\.[r|R]","",basename(mdln)),mdlsv=summdli$mtime,stringsAsFactors = FALSE)
   chk$ressv <- sumresi$mtime[match(chk$mdl,sub("\\.ressum\\.rds","",basename(sumres)))]
   chk       <- chk[which(chk$mdlsv>chk$ressv),]
-  #if(nrow(chk)>0) noret <- apply(chk,1,function(x) cat("Be aware that model is saved after results for",x['mdl'],"\n"))
 
-  #saveRDS(mdls,file=paste0(projloc,"/shinyMixR/app/shinyMixR/project.rds"))
   saveRDS(mdls,file=paste0(projloc,"/shinyMixR/project.rds"))
   return(mdls)
 }
diff --git a/R/gof_plot.r b/R/gof_plot.r
index 9d850d6..f4975cc 100644
--- a/R/gof_plot.r
+++ b/R/gof_plot.r
@@ -87,13 +87,10 @@ gof_plot <- function(dfrm,type="xpose",mdlnm=NULL,colby=NULL,ptype="all",outnm=N
     return(pl)
   }else{
     if(is.null(mdlnm)) stop("in case output should be saved, mdlnm should be given")
-    #titl <- cowplot::ggdraw() + cowplot::draw_label(mdlnm, fontface = 'bold', x = 0,hjust = 0) + theme(plot.margin = margin(0, 0, 0, 7))
     dir.create(paste0(projloc,"/analysis/",mdlnm),showWarnings=FALSE)
     if(grepl("\\.tex$",outnm)){
-      #R3port::ltx_plot(cowplot::plot_grid(titl,pl,rel_heights = c(0.1, 1),ncol=1),out=paste0(projloc,"/analysis/",mdlnm,"/",basename(outnm)),title="GOF plots",...)
       R3port::ltx_plot(pl,out=paste0(projloc,"/analysis/",mdlnm,"/",basename(outnm)),title="GOF plots",...)
     }else if(grepl("\\.html$",outnm)){
-      #R3port::html_plot(cowplot::plot_grid(titl,pl,rel_heights = c(0.1, 1),ncol=1),out=paste0(projloc,"/analysis/",mdlnm,"/",basename(outnm)),title="GOF plots",...)
       R3port::html_plot(pl,out=paste0(projloc,"/analysis/",mdlnm,"/",basename(outnm)),title="GOF plots",...)
     }
   }
diff --git a/R/module_edit.R b/R/module_edit.R
index 318d1d9..bcf2e86 100644
--- a/R/module_edit.R
+++ b/R/module_edit.R
@@ -111,14 +111,10 @@ module_edit_server <- function(id, r, settings) {
     observeEvent(input$updinit,{showModal(initmodal())},ignoreInit = TRUE)
     observeEvent(input$goupdate,{
       if(isTruthy(input$finest) && isTruthy(input$tosave)){
-        #res <- try(update_inits(input$editor,paste0("shinyMixr/",input$finest,".res.rds"),paste0("models/",input$tosave)))
-        #cat("getting stuff from",paste0(r$this_wd,"/models/",input$finest,".r"),"with results from",paste0(r$this_wd,"/shinyMixr/",input$finest,".res.rds"), 
-        #    "to model",paste0(r$this_wd,"/models/",input$tosave))
         res <- try(update_inits(readLines(paste0(r$this_wd,"/models/",input$finest,".r")),
                                 paste0(r$this_wd,"/shinyMixr/",input$finest,".res.rds"),
                                 paste0(r$this_wd,"/models/",input$tosave)))
         if("try-error"%in%class(res)){
-          #myalert("Could not update initials",type = "error")
           myalert(res,type = "error")
         }else{
           r$proj_obj <- get_proj(r$this_wd)
diff --git a/R/module_gof.R b/R/module_gof.R
index 1a76989..fd40b8d 100644
--- a/R/module_gof.R
+++ b/R/module_gof.R
@@ -24,8 +24,6 @@ module_gof_ui <- function(id, proj_obj) {
         numericInput(ns("plheight"), "plot height:", 800)
         
       ),
-      # When using a box, the content overflows, also a box does not provide a lot of functionality in this case
-      # box(width=9, title = "Output",status="lightblue",solidHeader=TRUE,plotOutput(ns("gof_plot")),height="80vh") #,width="80%" ,height="100%"
       column(9,plotOutput(ns("gof_plot")))
     )
   )
diff --git a/R/module_overview.R b/R/module_overview.R
index 9a8a816..f526a63 100644
--- a/R/module_overview.R
+++ b/R/module_overview.R
@@ -11,11 +11,9 @@ module_overview_ui <- function(id) {
   tagList(
     div(id='buttondiv', class='btn-group',
       actionButton(ns("overview_refr"), "Refresh",icon=icon("arrows-rotate")),
-      #actionButton(ns("overview_adpt"), "Adapt model notes",icon=icon("list")),
       module_metadata_ui(ns("adapt_meta_ov"),"overview"),
       module_scripts_ui(ns("runscripts")),
       module_reports_ui(ns("reports")),
-      #module_metadata_ui(ns("dummy"),"save"),
       actionButton(ns("hlr"), "Results",icon=icon("file-lines")),
       actionButton(ns("del"), "Delete model(s)",icon=icon("trash"))
     ),br(),br(),
diff --git a/R/module_partable.R b/R/module_partable.R
index 1b4adcf..8a2ca75 100644
--- a/R/module_partable.R
+++ b/R/module_partable.R
@@ -46,12 +46,9 @@ module_pt_server <- function(id, r) {
     parTable <- function(inp, projloc, saveit = FALSE){
       obj <- get_proj(projloc = projloc)
       if(!saveit) {
-        #print(obj)
-        #print(inp$EstLst)
         par_table(obj,models=inp$EstLst,bsv=inp$bsv,shrink=inp$shrink,backt=inp$backt,formatting=TRUE)
       } else {
         savnm  <- ifelse(inp$typePars=="PDF",paste0(inp$namePars,".tex"),paste0(inp$namePars,".html"))
-        #print(savnm)
         par_table(obj,models=inp$EstLst,outnm=savnm,show=inp$showPars,projloc=projloc,bsv=inp$bsv,shrink=inp$shrink,backt=inp$backt,formatting=ifelse(inp$typePars=="PDF",FALSE,TRUE))
       }
     }
diff --git a/R/module_reports.R b/R/module_reports.R
index a7e5e12..6408456 100644
--- a/R/module_reports.R
+++ b/R/module_reports.R
@@ -23,7 +23,6 @@ module_reports_server <- function(id) {
       ns <- session$ns
       modalDialog(title="Reports",easyClose = TRUE,size="l",fade=FALSE,
           fluidRow(
-            #column(6,selectInput(ns("models"),"Model(s)",basename(models()),multiple=FALSE,size=15,selectize=FALSE,width='100%')),
             column(6,selectInput(ns("models"),"Model(s)",list.dirs("analysis",recursive=FALSE,full.names=FALSE),multiple=FALSE,size=15,selectize=FALSE,width='100%')),
             column(6,selectInput(ns("results"),"Result(s)","",multiple=TRUE,size=15,selectize=FALSE,width='100%'))
           ),
@@ -76,7 +75,6 @@ module_reports_server <- function(id) {
           }
         }
       }else{
-        #shinyWidgets::sendSweetAlert(session = session, title="Report",text = "Select folder and results for report" ,type = "error")
         myalert("Select folder and results for report",type = "error")
       }
     })  
diff --git a/R/run_nmx.r b/R/run_nmx.r
index e1b646a..0914598 100644
--- a/R/run_nmx.r
+++ b/R/run_nmx.r
@@ -71,8 +71,6 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
     }else{
       system(paste0(R.home("bin"), "/Rscript \"", tscr,  "\" > \"",projloc,"/shinyMixR/temp/",mod,".prog.txt\" 2>&1"),wait=FALSE)
     }
-    
-    # if(autoupdate) assign(dnm,proj,pos = .GlobalEnv)
   }else{
     # Handle subsetting (data is loaded in global environment by get_proj function)
     if(!is.null(meta$subs) && meta$subs!="") data_nlm <- subset(get(meta$data),eval(parse(text=(meta$subs)))) else data_nlm <- get(meta$data)
@@ -87,7 +85,6 @@ run_nmx <- function(mod,proj=proj,ext=TRUE,saverds=TRUE,autoupdate=TRUE,projloc=
       saveRDS(ressum,file=paste0(projloc,"/shinyMixR/",mod,".ressum.rds"))
     }
     proj[[mod]]$results <- ressum
-    # assign(dnm,proj,pos = .GlobalEnv)
     return(modres)
   }
 }
diff --git a/R/run_shinymixr.r b/R/run_shinymixr.r
index 59f4dad..396ccab 100644
--- a/R/run_shinymixr.r
+++ b/R/run_shinymixr.r
@@ -23,38 +23,8 @@
 #' }
 run_shinymixr <- function(wd = getwd(),...){ 
   
-  #if(!file.exists(paste0(wd,"/shinyMixR/app/www"))) try(dir.create(paste0(wd,"/shinyMixR/app/www"),recursive = TRUE))
-  #if(!file.exists(paste0(wd,"/shinyMixR/app/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/app/shinyMixR/temp"),recursive=TRUE))
-  #if(!file.exists(paste0(wd,"/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/temp"),recursive=TRUE))
-  
-  #try(file.copy(system.file("dashboard","app.R",package="shinyMixR"),          paste0(wd,"/shinyMixR/app/app.R"),overwrite = TRUE),silent = TRUE)
-  #try(file.copy(system.file("dashboard","www/logoshinyMixR.png",package="shinyMixR"), paste0(wd,"/shinyMixR/app/www/logoshinyMixR.png")),silent = TRUE)
-  
-  # Set the working directory so the project can be found
-  #adpt <- readLines(system.file("dashboard", "app.R", package = "shinyMixR"))
-  #adpt <- c(paste0("setwd(\"", normalizePath(wd, winslash = "/"), "\")"), adpt)
-  #writeLines(adpt, paste0(wd,"/shinyMixR/app/app.R"))
-  
-  # Clean up stuff before running the app (check if feasible or not)
-  #try(unlink(list.files(paste0(wd,"/shinyMixR/temp"),pattern=".*prog\\.txt$",full.names = TRUE)))
-  # if (dry_run == TRUE) {
-  #   return()
-  # } else {
-  #   shiny::runApp(paste0(wd,"/shinyMixR/app"),...)
-  # }
-  #owd <- getwd()
-  #if(normalizePath(owd)!=normalizePath(wd)) setwd(wd)
-  #cat("I am in ",getwd(),"\n")
-  #on.exit(setwd(owd))  
-  #if(!file.exists("shinyMixR/temp")) try(dir.create("shinyMixR/temp",recursive=TRUE))
   if(!file.exists(paste0(wd,"/shinyMixR/temp")))    try(dir.create(paste0(wd,"/shinyMixR/temp"),recursive=TRUE))
   proj_obj <- get_proj(wd)
-  # Check and load nlmixr(2); set nlmixr2 as import so needed when package is loaded and this is also a CRAN warning
-  # if ("nlmixr2" %in% rownames(installed.packages())){
-  #   library(nlmixr2)
-  # } else {
-  #   cat("you need the 'nlmixr2' package to run models\n")
-  # }
 
   newtheme <- fresh::create_theme(
     theme = "darkly", # theme has no effect, at least within bs4Dash
@@ -131,5 +101,4 @@ run_shinymixr <- function(wd = getwd(),...){
     },
     options = list(launch.browser=TRUE,...) # set general options here for running the app
   )
-  #cat("I was in ",getwd(),"\n")
 }
diff --git a/R/utils.R b/R/utils.R
index 86ba81d..dd9ffd7 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -19,7 +19,6 @@ setup_shinymixr_test <- function(dir = "./tests/files", overwrite = TRUE, record
   }
 
   create_proj(dir, overwrite = overwrite)
-  #run_shinymixr(wd = dir, dry_run = TRUE)
   
   if(incres){
     file.copy(system.file(c("other/run1.res.rds","other/run1.ressum.rds"),package="shinyMixR"),