Refactoring

DESCRIPTION

@@ -1,46 +1,50 @@
-Package: shinybrapps
 Type: Package
+Package: shinybrapps
 Title: ShinyBrAPPs
 Version: 27.8
 Authors@R: c(
-  person("Jean-François", "Rami", email = "[email protected]", role = c("aut", "ctb", "cre")),
-  person("Alice", "Boizet", email = "[email protected]", role = c("aut", "ctb")),
-  person("Mariano", "Crimi", email = "[email protected]", role = c("aut", "ctb")),
-  person("Léo", "Valette", email = "[email protected]", role = c("aut"))
+    person("Jean-François", "Rami", email = "[email protected]", role = c("aut", "ctb", "cre")),
+    person("Alice", "Boizet", email = "[email protected]", role = c("aut", "ctb")),
+    person("Mariano", "Crimi", email = "[email protected]", role = c("aut", "ctb")),
+    person("Léo", "Valette", email = "[email protected]", role = c("aut"))
   )
-Description: ShinyBrAPPs 
-    Shiny apps integrated to the Breeding Management System
+Maintainer: Leo Valette <[email protected]>
+Description: ShinyBrAPPs Shiny apps integrated to the Breeding Management
+    System.
 License: GPL (>= 3)
-Encoding: UTF-8
-LazyData: true
 Depends:
-    shiny,
-    shinyjs,
-    data.table,
-    ggplot2,
-    plotly,
+    R (>= 2.10),
+    data.table
+Imports: 
+    brapir,
+    brapirv2,
+    bslib,
     DT,
-    gridExtra,
-    magrittr,
-    RColorBrewer,
     e1071,
-    statgenSTA,
-    statgenGxE,
-    brapirv1,
-    brapirv2,
-    SpATS,
-    shinyWidgets,
-    shinybusy,
-    shinyBS,
-    varhandle,
+    ggnewscale,
+    ggplot2,
     ggpubr,
-    ggExtra,
+    gridExtra,
+    gtools,
+    htmltools,
+    httr,
+    jsonlite,
     leaflet,
-    rclipboard,
+    metan,
     openxlsx,
+    plotly,
+    rclipboard,
+    rmarkdown,
+    scales,
+    shiny,
     shinycssloaders,
-    gtools,
-    ggnewscale,
-    metan,
-    R (>= 2.10)
-RoxygenNote: 7.1.1
+    shinyjs,
+    shinyWidgets,
+    statgenGxE,
+    statgenSTA,
+    stringmagic,
+    tidyr,
+    varhandle
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,3 +1,52 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(get_env_data)
+export(groupModal)
+export(group_selector)
+export(make_study_metadata)
+export(mod_banner_server)
+export(mod_banner_ui)
+export(mod_dataquality_server)
+export(mod_dataquality_ui)
+export(mod_get_extradata_server)
+export(mod_get_extradata_ui)
+export(mod_get_studydata_server)
+export(mod_get_studydata_ui)
+export(mod_groups_sidebar_server)
+export(mod_groups_sidebar_ui)
+export(mod_gxe_server)
+export(mod_gxe_ui)
+export(mod_model_server)
+export(mod_model_ui)
+export(mod_scatterplot_server)
+export(mod_scatterplot_ui)
+export(mod_trialdataxplor_server)
+export(mod_trialdataxplor_ui)
+export(parse_api_url)
+export(run_decision)
+export(run_stabrapp)
+export(run_test)
+export(run_trialdataxplor)
+export(select_from_layout)
+export(shortest_interval)
+import(brapirv2)
 import(bslib)
-import(statgenGxE)
+import(data.table)
+import(ggplot2)
+import(leaflet)
+import(plotly)
+import(shiny)
+import(shinyWidgets)
+import(shinyjs)
+import(statgenGxE)
+import(statgenSTA)
+importFrom(DT,JS)
+importFrom(DT,dataTableProxy)
+importFrom(DT,datatable)
+importFrom(DT,formatRound)
+importFrom(DT,formatStyle)
+importFrom(DT,renderDT)
+importFrom(ggpubr,get_legend)
+importFrom(gridExtra,arrangeGrob)
+importFrom(statgenSTA,createTD)
+importFrom(varhandle,check.numeric)

R/custom_input_genotype_groups.R

@@ -114,7 +114,7 @@ function copyToClipboard(id, names) {
         clearInterval(temp);
       }, 2000 );
   } else {
-    console.info( "document.execCommand went wrong…" )
+    console.info("document.execCommand went wrong…")
   }
 
   document.body.removeChild(dummy);

R/module_banner.R

@@ -5,7 +5,7 @@ mod_banner_ui <- function(id){
 }
 
 #' @export
-mod_banner_server <- function(id, rv){
+mod_banner_server <- function(id, rv, appname){
   moduleServer(
     id,
     function(input, output, session){
@@ -17,7 +17,7 @@ mod_banner_server <- function(id, rv){
                   style="border-radius: 6px;
                 width:129px;
                 height:34px;
-                margin-right:10px"),paste(rv$appname," - Study: ", paste(rv$data[,unique(trialName)], collapse = ", ")),
+                margin-right:10px"),paste(appname," - Study: ", paste(rv$data[,unique(trialName)], collapse = ", ")),
           style="font: 500 20px/32px Roboto,Helvetica Neue,sans-serif;display: flex;justify-content: center;position: relative; z-index: 30;",
           div(style="margin-left: auto;",
               dropdown(
@@ -32,7 +32,7 @@ mod_banner_server <- function(id, rv){
                 #circle = FALSE,
                 #downloadBttn(ns("dwnld1"),label = "As csv", style = "minimal", size="xs"),
                 downloadButton(ns("dwnld1"),label = "As csv file"),
-                if (rv$appname!="BMS trial data explorer") downloadButton(ns("dwnld2"),label = "As TD object")
+                if (appname!="BMS trial data explorer") downloadButton(ns("dwnld2"),label = "As TD object")
               ))),
         style = "padding: 2px 0 2px 10px;
                     width:100%;
@@ -51,14 +51,14 @@ mod_banner_server <- function(id, rv){
           paste("data-", Sys.Date(), ".csv", sep="")
         },
         content = function(file) {
-          if (rv$appname=="DSBrAPP"){
-            write.csv(rv$data_plot, file, row.names = F)
+          if (appname=="DSBrAPP"){
+            write.csv(rv$extradata, file, row.names = F)
           } else {
-            if (rv$appname=="STABrAPP"){
+            if (appname=="STABrAPP"){
               write.csv(rv$data, file, row.names = F)
             } else {
-              if (rv$appname=="BMS trial data explorer"){
-                write.csv(rv$data_dq[,-c("facetrows", "facetcols"), with=F], file, row.names = F)
+              if (appname=="BMS trial data explorer"){
+                write.csv(rv$data[,-c("facetrows", "facetcols"), with=F], file, row.names = F)
               }
             }
           }
@@ -69,16 +69,16 @@ mod_banner_server <- function(id, rv){
           paste("data-", Sys.Date(), ".Rdata", sep="")
         },
         content = function(file) {
-          if (rv$appname=="DSBrAPP"){
-            write.csv(rv$data_plot, file, row.names = F)
+          if (appname=="DSBrAPP"){
+            write.csv(rv$data, file, row.names = F)
             if (is.null(rv$TD)){
               showNotification("You must select a Trait and a Variable to use as Environment Name to form the TD object", type = "error", duration = notification_duration)
             } else {
               TD <- rv$TD
               save(TD, file = file)
             }
           } else {
-            if (rv$appname=="STABrAPP"){
+            if (appname=="STABrAPP"){
               if (is.null(rv$TD)){
                 showNotification("Please fit a model first", type = "error", duration = notification_duration)
               } else {