exporting functions that are called in server.R and ui.R to make the package working

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(miRacumDQA)
+export(moduleAtempPlausibilityServer)
+export(moduleAtempPlausibilityUI)
+export(moduleConfigServer)
+export(moduleConfigUI)
+export(moduleDashboardServer)
+export(moduleDashboardUI)
+export(moduleDescriptiveServer)
+export(moduleDescriptiveUI)
+export(moduleMDRServer)
+export(moduleMDRUI)
+export(moduleRawdata1Server)
+export(moduleRawdata1UI)
+export(moduleReportServer)
+export(moduleReportUI)
+export(moduleUniquePlausibilityServer)
+export(moduleUniquePlausibilityUI)
+export(moduleVisualizationsServer)
+export(moduleVisualizationsUI)
+export(onStart)
 import(shiny)
 import(shinydashboard)
 importFrom(data.table,":=")

R/app_utils.R

@@ -14,6 +14,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title onStart
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#'
+#' @export
+#'
+# onStart
 # function to run on startup
 onStart <- function(session, rv, input, output){
   if (file.exists("./_settings/global_settings.JSON")){

R/moduleAtempPlausibility.R

@@ -14,7 +14,17 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# moduleVisualizationsServer
+#' @title moduleAtempPlausibilityServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
+# moduleAtempPlausibilityServer
 moduleAtempPlausibilityServer <- function(input, output, session, rv, input_re){
   observe({
     if (isFALSE(rv$target_getdata) && isFALSE(rv$source_getdata)){
@@ -303,7 +313,13 @@ moduleAtempPlausibilityServer <- function(input, output, session, rv, input_re){
   })
 }
 
-
+#' @title moduleAtempPlausibilityUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleAtempPlausibilityUI
 moduleAtempPlausibilityUI <- function(id){
   ns <- NS(id)
 

R/moduleConfig.R

@@ -14,6 +14,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleConfigServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleConfigServer
 moduleConfigServer <- function(input, output, session, rv, input_re){
   roots = c(home="/home/")
@@ -133,6 +143,12 @@ moduleConfigServer <- function(input, output, session, rv, input_re){
   })
 }
 
+#' @title moduleConfigUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
 # moduleConfigUI
 moduleConfigUI <- function(id){
   ns <- NS(id)

R/moduleDashboard.R

@@ -14,8 +14,28 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleDashboardServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleDashboardServer
 moduleDashboardServer <- function(input, output, session, rv, input_re){
+
+  # initialize some reactive stuff here
+  observe({
+    if (is.null(rv$dash_summary_source)){
+      rv$dash_summary_source <- summaryTable()
+    }
+    if (is.null(rv$dash_summary_target)){
+      rv$dash_summary_target <- summaryTable()
+    }
+  })
   output$dash_instruction <- renderText({
     paste0("Please configure and test your database connection in the settings tab.\nThen return here in order to load the data.")
   })
@@ -230,7 +250,12 @@ moduleDashboardServer <- function(input, output, session, rv, input_re){
 }
 
 
-
+#' @title moduleDashboardUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
 # moduleDashboardUI
 moduleDashboardUI <- function(id){
   ns <- NS(id)

R/moduleDescriptive.R

@@ -14,6 +14,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleDescriptiveServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleDescriptiveServer
 moduleDescriptiveServer <- function(input, output, session, rv, input_re){
 
@@ -298,6 +308,14 @@ moduleDescriptiveServer <- function(input, output, session, rv, input_re){
   })
 }
 
+
+#' @title moduleDescriptiveUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleDescriptiveUI
 moduleDescriptiveUI <- function(id){
   ns <- NS(id)
 

R/moduleMDR.R

@@ -14,6 +14,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleMDRServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleMDRServer
 moduleMDRServer <- function(input, output, session, rv, input_re){
 
@@ -60,6 +70,13 @@ moduleMDRServer <- function(input, output, session, rv, input_re){
 }
 
 
+#' @title moduleMDRUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleMDRUI
 moduleMDRUI <- function(id){
   ns <- NS(id)
 

R/moduleRawdata1.R

@@ -14,6 +14,16 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleRawdata1Server
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleRawdata1Server
 moduleRawdata1Server <- function(input, output, session, rv, input_re){
 
@@ -144,6 +154,14 @@ moduleRawdata1Server <- function(input, output, session, rv, input_re){
   })
 }
 
+
+#' @title moduleRawdata1UI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleRawdata1UI
 moduleRawdata1UI <- function(id){
   ns <- NS(id)
 

R/moduleReport.R

 # miRacumDQA - The MIRACUM consortium's data quality assessment tool.
 # Copyright (C) 2019 MIRACUM - Medical Informatics in Research and Medicine
-# 
+#
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-# 
+#
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleReportServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleReportServer
 moduleReportServer <- function(input, output, session, rv, input_re){
-  
+
   observe({
     req(rv$dqa_descriptive_results)
-    
+
     if (is.null(rv$report_created)){
       shiny::withProgress(
         message = paste0("Creating report ..."), value = 0, {
@@ -30,7 +40,7 @@ moduleReportServer <- function(input, output, session, rv, input_re){
           # copy header-folder to tempdir to make files available for the next command
           file.copy("./_utilities/RMD/_header", tempdir(), recursive=TRUE)
           rmarkdown::render(input=paste0(tempdir(), "/DQA_report.md"), output_file = paste0(tempdir(), "/DQA_report.pdf"), encoding = "UTF-8")
-          
+
           # debugging
           # setwd(paste0(getwd(), "/DQA_Tool/app"))
           # knitr::knit(input="./_utilities/RMD/DQA_report_debug.Rmd", output=paste0(tempdir(), "/DQA_report_debug.md"), encoding = "UTF-8")
@@ -38,12 +48,12 @@ moduleReportServer <- function(input, output, session, rv, input_re){
           # file.copy("./_utilities/RMD/_header", tempdir(), recursive=TRUE)
           # rmarkdown::render(input=paste0(tempdir(), "/DQA_report_debug.md"), output_file = paste0(tempdir(), "/DQA_report_debug.pdf"), encoding = "UTF-8")
         })
-      
+
       rv$report_created <- TRUE
     }
   })
-  
-  
+
+
   output$download_report <- downloadHandler(
     filename = function(){"DQA_report.pdf"},
     content = function(file){
@@ -53,17 +63,24 @@ moduleReportServer <- function(input, output, session, rv, input_re){
   )
 }
 
+#' @title moduleReportUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleReportUI
 moduleReportUI <- function(id){
   ns <- NS(id)
-  
+
   tagList(
     fluidRow(
       box(title = "Reporting",
-          downloadButton(ns("download_report"), "Download Report", style="white-space: normal; text-align:center; 
+          downloadButton(ns("download_report"), "Download Report", style="white-space: normal; text-align:center;
                                                                   padding: 9.5px 9.5px 9.5px 9.5px;
                                                                   margin: 6px 10px 6px 10px;"),
           width = 6
       )
     )
   )
-}
\ No newline at end of file
+}

R/moduleUniquePlausibility.R

@@ -14,12 +14,28 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleUniquePlausibilityServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleUniquePlausibilityServer
 moduleUniquePlausibilityServer <- function(input, output, session, rv, input_re){
 
 }
 
-
+#' @title moduleUniquePlausibilityUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleUniquePlausibilityUI
 moduleUniquePlausibilityUI <- function(id){
   ns <- NS(id)
 

R/moduleVisualizations.R

 # miRacumDQA - The MIRACUM consortium's data quality assessment tool.
 # Copyright (C) 2019 MIRACUM - Medical Informatics in Research and Medicine
-# 
+#
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-# 
+#
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+#' @title moduleVisualizationsServer
+#'
+#' @param input Shiny server input object
+#' @param output Shiny server output object
+#' @param session Shiny session object
+#' @param rv The global 'reactiveValues()' object, defined in server.R
+#' @param input_re The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})
+#'
+#' @export
+#'
 # moduleVisualizationsServer
 moduleVisualizationsServer <- function(input, output, session, rv, input_re){
-  
+
   output$visualizations_plot <- renderPlot({
     graphics::hist(rv$list_target$dt.ageindays_target[,get("encounter_subject_patient_age_days")])
   })
 }
 
-
+#' @title moduleVisualizationsUI
+#'
+#' @param id A character. The identifier of the shiny object
+#'
+#' @export
+#'
+# moduleVisualizationsUI
 moduleVisualizationsUI <- function(id){
   ns <- NS(id)
-  
+
   tagList(
     tagList(
       plotOutput(ns("visualizations_plot"))

docker/build_image.sh

@@ -3,8 +3,6 @@
 read -p "\nPlease enter your username to https://gitlab.miracum.org/: " gitusername
 read -s -p "\nPlease enter your password to https://gitlab.miracum.org/: " gitpassword
 
-echo $gitusername
-
 docker build --build-arg gitpassword=$gitpassword  --build-arg gitusername=$gitusername -f Dockerfile -t dqa-miracum .
 
 docker-compose up -d

inst/application/_utilities/MDR/mdr.csv

@@ -105,11 +105,11 @@ Item03;GESCHLECHT;FALL.CSV;csv;pl.item03_source;patient_gender;patient.gender;fa
 Patientennummer;PATIENTENNUMMER;FALL.CSV;csv;pl.item03_source;patient_identifier_value;patient.identifier.value;factor;"";;;0;"";"";"";"";"";""
 Fallnummer;KH_INTERNES_KENNZEICHEN;FALL.CSV;csv;pl.item04_source;encounter_identifier_value;encounter.identifier.value;factor;"";;;0;"";"";"";"";"";""
 ICD Code;ICD_Kode;ICD.CSV;csv;pl.item04_source;condition_code_coding_code;condition.code.coding.code;factor;"";;;0;"";"";"";"";"";""
-Item04;GESCHLECHT;FALL.CSV;csv;pl.item04_source;patient_gender;patient.gender;factor;"{""value_set"": ""w""}";;;1;Nur bei männlichen Patienten sind bösartige Neubildungen der männlichen Genitalorgane (ICD C60-C63) als Krankenhausdiagnose erlaubt.;ICD.CSV;FALL.CSV;KH_internes_Kennzeichen = KH_INTERNES_KENNZEICHEN;left outer;grepl(‘C6[0-3]’, ICD_Kode)
+Item04;GESCHLECHT;FALL.CSV;csv;pl.item04_source;patient_gender;patient.gender;factor;"{""value_set"": ""m""}";;;1;Nur bei männlichen Patienten sind bösartige Neubildungen der männlichen Genitalorgane (ICD C60-C63) als Krankenhausdiagnose erlaubt.;ICD.CSV;FALL.CSV;KH_internes_Kennzeichen = KH_INTERNES_KENNZEICHEN;left outer;grepl(‘C6[0-3]’, ICD_Kode)
 Patientennummer;PATIENTENNUMMER;FALL.CSV;csv;pl.item04_source;patient_identifier_value;patient.identifier.value;factor;"";;;0;"";"";"";"";"";""
 Aufnahmegrund;AUFNAHMEGRUND;FALL.CSV;csv;pl.item05_source;encounter_hospitalization_class;encounter.hospitalization.class;factor;"{""value_set"": ""01xx, 02xx, 03xx, 04xx, 05xx, 06xx, 08xx""}";;;0;"";"";"";"";"";""
 Fallnummer;KH_INTERNES_KENNZEICHEN;FALL.CSV;csv;pl.item05_source;encounter_identifier_value;encounter.identifier.value;factor;"";;;0;"";"";"";"";"";""
-Item05;GESCHLECHT;FALL.CSV;csv;pl.item05_source;patient_gender;patient.gender;factor;"";;;1;Nur bei weiblichen Patientinnen ist 'stationäre Entbindung' als Aufnahmegrund (05) erlaubt.;"";"";"";"";grepl(‘05xx’, AUFNAHMEGRUND)
+Item05;GESCHLECHT;FALL.CSV;csv;pl.item05_source;patient_gender;patient.gender;factor;"{""value_set"": ""w""}";;;1;Nur bei weiblichen Patientinnen ist 'stationäre Entbindung' als Aufnahmegrund (05) erlaubt.;"";"";"";"";grepl(‘05xx’, AUFNAHMEGRUND)
 Patientennummer;PATIENTENNUMMER;FALL.CSV;csv;pl.item05_source;patient_identifier_value;patient.identifier.value;factor;"";;;0;"";"";"";"";"";""
 Belegungstage in anderem Entgeltbereich;BELEGUNGSTAGE_IN_ANDEREM_ENTGELTBEREICH;FALL.CSV;csv;undefined;"";"";"";"";;;;"";"";"";"";"";""
 Beurlaubungstage (PSY);BEURLAUBUNGSTAGE_PSY;FALL.CSV;csv;undefined;"";"";"";"";;;;"";"";"";"";"";""
@@ -170,11 +170,11 @@ Item03;sex_cd;patient_dimension;i2b2;pl.item03_target;patient_gender;patient.gen
 Patientennummer;patient_num;observation_fact;i2b2;pl.item03_target;patient_identifier_value;patient.identifier.value;factor;"";;;0;"";"";"";"";"";""
 Fallnummer;encounter_num;observation_fact;i2b2;pl.item04_target;encounter_identifier_value;encounter.identifier.value;factor;"";;;0;"";"";"";"";"";""
 ICD Code;concept_cd;observation_fact;i2b2;pl.item04_target;condition_code_coding_code;condition.code.coding.code;factor;"";;;0;"";"";"";"";"";""
-Item04;sex_cd;patient_dimension;i2b2;pl.item04_target;patient_gender;patient.gender;factor;"{""value_set"": ""w""}";;;1;"";observation_fact;patient_dimension;patient_num = patient_num;left outer;concept_cd ~ 'ICD10:C6[0-3]'
+Item04;sex_cd;patient_dimension;i2b2;pl.item04_target;patient_gender;patient.gender;factor;"{""value_set"": ""m""}";;;1;"";observation_fact;patient_dimension;patient_num = patient_num;left outer;concept_cd ~ 'ICD10:C6[0-3]'
 Patientennummer;patient_num;observation_fact;i2b2;pl.item04_target;patient_identifier_value;patient.identifier.value;factor;"";;;0;"";"";"";"";"";""
 Aufnahmegrund;concept_cd;observation_fact;i2b2;pl.item05_target;encounter_hospitalization_class;encounter.hospitalization.class;factor;"{""value_set"": ""01xx, 02xx, 03xx, 04xx, 05xx, 06xx, 08xx""}";;;0;"";"";"";"";"";""
 Fallnummer;encounter_num;observation_fact;i2b2;pl.item05_target;encounter_identifier_value;encounter.identifier.value;factor;"";;;0;"";"";"";"";"";""
-Item05;sex_cd;patient_dimension;i2b2;pl.item05_target;patient_gender;patient.gender;factor;"";;;1;"";observation_fact;patient_dimension;patient_num = patient_num;left outer;concept_cd ~ 'AUFNGR:05'
+Item05;sex_cd;patient_dimension;i2b2;pl.item05_target;patient_gender;patient.gender;factor;"{""value_set"": ""w""}";;;1;"";observation_fact;patient_dimension;patient_num = patient_num;left outer;concept_cd ~ 'AUFNGR:05'
 Patientennummer;patient_num;observation_fact;i2b2;pl.item05_target;patient_identifier_value;patient.identifier.value;factor;"";;;0;"";"";"";"";"";""
 "";"";"";"";undefined;condition_bodySite;condition.bodySite;factor;"";;;;"";"";"";"";"";""
 "";"";"";"";undefined;procedure_bodySite;procedure.bodySite;factor;"";;;;"";"";"";"";"";""

inst/application/_utilities/MDR/value_set.R

@@ -91,8 +91,8 @@ mdr[name=="Item04" & source_system=="csv", value_set := '{"value_set": "m"}']
 mdr[name=="Item04" & source_system=="i2b2", value_set := '{"value_set": "m"}']
 
 # Item05
-mdr[name=="Item04" & source_system=="csv", value_set := '{"value_set": "w"}']
-mdr[name=="Item04" & source_system=="i2b2", value_set := '{"value_set": "w"}']
+mdr[name=="Item05" & source_system=="csv", value_set := '{"value_set": "w"}']
+mdr[name=="Item05" & source_system=="i2b2", value_set := '{"value_set": "w"}']
 
 # write mdr
 fwrite(mdr, paste0(getwd(), "/inst/application/_utilities/MDR/mdr.csv"), sep = ";")

inst/application/server.R

@@ -14,10 +14,10 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-shinyServer(function(input, output, session) {
+shiny::shinyServer(function(input, output, session) {
 
     # define reactive values here
-    rv <- reactiveValues(
+    rv <- shiny::reactiveValues(
         started = NULL,
         mdr = NULL,
         target_keys = NULL,
@@ -34,8 +34,8 @@ shinyServer(function(input, output, session) {
         data_objects = list(),
         list_source = NULL,
         list_target = NULL,
-        dash_summary_target = summaryTable(),
-        dash_summary_source = summaryTable()
+        dash_summary_target = NULL,
+        dash_summary_source = NULL
     )
 
 
@@ -43,8 +43,8 @@ shinyServer(function(input, output, session) {
     onStart(session, rv, input, output)
 
     # handle reset
-    observeEvent(input$reset, {
-        js$reset()
+    shiny::observeEvent(input$reset, {
+        shinyjs::js$reset()
     })
 
 
@@ -53,9 +53,9 @@ shinyServer(function(input, output, session) {
     # # tab_config
     # ########################
 
-    callModule(moduleConfigServer, "moduleConfig", rv, input_re=reactive({input}))
+    shiny::callModule(moduleConfigServer, "moduleConfig", rv, input_re=shiny::reactive({input}))
 
-    observe({
+    shiny::observe({
         if (!is.null(rv$target_getdata) && !is.null(rv$source_getdata)){
 
             # hide load data button
@@ -75,8 +75,8 @@ shinyServer(function(input, output, session) {
         }
     })
 
-    observe({
-        req(rv$report_created)
+    shiny::observe({
+        shiny::req(rv$report_created)
 
         # set end.time
         rv$end.time <- Sys.time()
@@ -89,18 +89,18 @@ shinyServer(function(input, output, session) {
         # gc()
 
         # render menu
-        output$menu <- renderMenu({
-            sidebarMenu(
-                menuItem("Review raw data", tabName = "tab_rawdata1", icon = icon("table")),
-                menuItem("Descriptive Results", tabName = "tab_descriptive", icon = icon("table")),
-                menuItem("Plausibility Checks", tabName = "tab_plausibility", icon = icon("check-circle"),
-                         menuSubItem("Atemporal Plausibility", tabName = "tab_atemp_plausibility"),
-                         menuSubItem("Uniqueness Plausibility", tabName = "tab_unique_plausibility")),
-                menuItem("Visualizations", tabName = "tab_visualizations", icon = icon("chart-line")),
-                menuItem("Reporting", tabName = "tab_report", icon = icon("file-alt"))
+        output$menu <- shinydashboard::renderMenu({
+            shinydashboard::sidebarMenu(
+                shinydashboard::menuItem("Review raw data", tabName = "tab_rawdata1", icon = icon("table")),
+                shinydashboard::menuItem("Descriptive Results", tabName = "tab_descriptive", icon = icon("table")),
+                shinydashboard::menuItem("Plausibility Checks", tabName = "tab_plausibility", icon = icon("check-circle"),
+                                         shinydashboard::menuSubItem("Atemporal Plausibility", tabName = "tab_atemp_plausibility"),
+                                         shinydashboard::menuSubItem("Uniqueness Plausibility", tabName = "tab_unique_plausibility")),
+                shinydashboard::menuItem("Visualizations", tabName = "tab_visualizations", icon = icon("chart-line")),
+                shinydashboard::menuItem("Reporting", tabName = "tab_report", icon = icon("file-alt"))
             )
         })
-        updateTabItems(session, "tabs", "tab_dashboard")
+        shinydashboard::updateTabItems(session, "tabs", "tab_dashboard")
 
         # for debugging purposes
         descriptive_results <<- rv$dqa_descriptive_results
@@ -113,38 +113,38 @@ shinyServer(function(input, output, session) {
     ########################
     # tab_dashboard
     ########################
-    callModule(moduleDashboardServer, "moduleDashboard", rv, input_re=reactive({input}))
+    shiny::callModule(moduleDashboardServer, "moduleDashboard", rv, input_re=reactive({input}))
 
 
     ########################
     # tab_rawdata1
     ########################
-    callModule(moduleRawdata1Server, "moduleRawdata1", rv, input_re=reactive({input}))
+    shiny::callModule(moduleRawdata1Server, "moduleRawdata1", rv, input_re=reactive({input}))
 
     ########################
     # tab_descriptive
     ########################
-    callModule(moduleDescriptiveServer, "moduleDescriptive", rv, input_re=reactive({input}))
+    shiny::callModule(moduleDescriptiveServer, "moduleDescriptive", rv, input_re=reactive({input}))
 
     ########################
     # tab_plausibility
     ########################
-    callModule(moduleAtempPlausibilityServer, "moduleAtempPlausibility", rv, input_re=reactive({input}))
-    callModule(moduleUniquePlausibilityServer, "moduleUniquePlausibility", rv, input_re=reactive({input}))
+    shiny::callModule(moduleAtempPlausibilityServer, "moduleAtempPlausibility", rv, input_re=reactive({input}))
+    shiny::callModule(moduleUniquePlausibilityServer, "moduleUniquePlausibility", rv, input_re=reactive({input}))
 
     ########################
     # tab_visualization
     ########################
-    callModule(moduleVisualizationsServer, "moduleVisulizations", rv, input_re=reactive({input}))
+    shiny::callModule(moduleVisualizationsServer, "moduleVisulizations", rv, input_re=reactive({input}))
 
     ########################
     # tab_report
     ########################
-    callModule(moduleReportServer, "moduleReport", rv, input_re=reactive({input}))
+    shiny::callModule(moduleReportServer, "moduleReport", rv, input_re=reactive({input}))
 
     ########################
     # tab_mdr
     ########################
-    callModule(moduleMDRServer, "moduleMDR", rv, input_re=reactive({input}))
+    shiny::callModule(moduleMDRServer, "moduleMDR", rv, input_re=reactive({input}))
 
 })

inst/application/ui.R

@@ -14,28 +14,28 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-shinyUI(dashboardPage(skin = "black",
+shiny::shinyUI(shinydashboard::dashboardPage(skin = "black",
 
                       # Application title
-                      dashboardHeader(title = "MIRACUM DQA Tool"),
+                      shinydashboard::dashboardHeader(title = "MIRACUM DQA Tool"),
 
-                      dashboardSidebar(
+                      shinydashboard::dashboardSidebar(
 
                         # Include shinyjs in the UI Sidebar
                         shinyjs::useShinyjs(),
                         shinyjs::extendShinyjs(script = "./_utilities/reset.js", functions = "reset"), # Add the js code to the page
 
                         #Sidebar Panel
-                        sidebarMenu(id = "tabs",
-                                    menuItem("Dashboard", tabName = "tab_dashboard", icon = icon("tachometer-alt")),
-                                    sidebarMenuOutput("menu"),
-                                    menuItem("Settings", tabName = "tab_config", icon = icon("cogs")),
-                                    menuItem("DQ MDR", tabName = "tab_mdr", icon = icon("database")),
-                                    tags$hr(),
-                                    actionButton("reset", "Reset DQA Tool")
+                        shinydashboard::sidebarMenu(id = "tabs",
+                                                    shinydashboard::menuItem("Dashboard", tabName = "tab_dashboard", icon = icon("tachometer-alt")),
+                                                    shinydashboard::sidebarMenuOutput("menu"),
+                                                    shinydashboard::menuItem("Settings", tabName = "tab_config", icon = icon("cogs")),
+                                                    shinydashboard::menuItem("DQ MDR", tabName = "tab_mdr", icon = icon("database")),
+                                    shiny::tags$hr(),
+                                    shiny::actionButton("reset", "Reset DQA Tool")
                         )),
 
-                      dashboardBody(
+                      shinydashboard::dashboardBody(
 
                         # Include shinyjs in the UI Body
                         shinyjs::useShinyjs(),
@@ -44,40 +44,40 @@ shinyUI(dashboardPage(skin = "black",
                         # https://stackoverflow.com/questions/25062422/restart-shiny-session
                         shinyjs::extendShinyjs(script = "./_utilities/reset.js", functions = "reset"), # Add the js code to the page
 
-                        tabItems(
-                          tabItem(tabName = "tab_dashboard",
+                        shinydashboard::tabItems(
+                          shinydashboard::tabItem(tabName = "tab_dashboard",
                                   moduleDashboardUI("moduleDashboard")
                           ),
 
-                          tabItem(tabName = "tab_config",
+                          shinydashboard::tabItem(tabName = "tab_config",
                                   moduleConfigUI("moduleConfig")
                           ),
 
-                          tabItem(tabName = "tab_rawdata1",
+                          shinydashboard::tabItem(tabName = "tab_rawdata1",
                                   moduleRawdata1UI("moduleRawdata1")
                           ),
 
-                          tabItem(tabName = "tab_descriptive",
+                          shinydashboard::tabItem(tabName = "tab_descriptive",
                                   moduleDescriptiveUI("moduleDescriptive")
                           ),
 
-                          tabItem(tabName = "tab_atemp_plausibility",
+                          shinydashboard::tabItem(tabName = "tab_atemp_plausibility",
                                   moduleAtempPlausibilityUI("moduleAtempPlausibility")
                           ),
 
-                          tabItem(tabName = "tab_unique_plausibility",
+                          shinydashboard::tabItem(tabName = "tab_unique_plausibility",
                                   moduleUniquePlausibilityUI("moduleUniquePlausibility")
                           ),
 
-                          tabItem(tabName = "tab_visualizations",
+                          shinydashboard::tabItem(tabName = "tab_visualizations",
                                   moduleVisualizationsUI("moduleVisulizations")
                           ),
 
-                          tabItem(tabName = "tab_report",
+                          shinydashboard::tabItem(tabName = "tab_report",
                                   moduleReportUI("moduleReport")
                           ),
 
-                          tabItem(tabName = "tab_mdr",
+                          shinydashboard::tabItem(tabName = "tab_mdr",
                                   moduleMDRUI("moduleMDR")
                           )
 

man/moduleAtempPlausibilityServer.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/moduleAtempPlausibility.R
+\name{moduleAtempPlausibilityServer}
+\alias{moduleAtempPlausibilityServer}
+\title{moduleAtempPlausibilityServer}
+\usage{
+moduleAtempPlausibilityServer(input, output, session, rv, input_re)
+}
+\arguments{
+\item{input}{Shiny server input object}
+
+\item{output}{Shiny server output object}
+
+\item{session}{Shiny session object}
+
+\item{rv}{The global 'reactiveValues()' object, defined in server.R}
+
+\item{input_re}{The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})}
+}
+\description{
+moduleAtempPlausibilityServer
+}

man/moduleAtempPlausibilityUI.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/moduleAtempPlausibility.R
+\name{moduleAtempPlausibilityUI}
+\alias{moduleAtempPlausibilityUI}
+\title{moduleAtempPlausibilityUI}
+\usage{
+moduleAtempPlausibilityUI(id)
+}
+\arguments{
+\item{id}{A character. The identifier of the shiny object}
+}
+\description{
+moduleAtempPlausibilityUI
+}

man/moduleConfigServer.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/moduleConfig.R
+\name{moduleConfigServer}
+\alias{moduleConfigServer}
+\title{moduleConfigServer}
+\usage{
+moduleConfigServer(input, output, session, rv, input_re)
+}
+\arguments{
+\item{input}{Shiny server input object}
+
+\item{output}{Shiny server output object}
+
+\item{session}{Shiny session object}
+
+\item{rv}{The global 'reactiveValues()' object, defined in server.R}
+
+\item{input_re}{The Shiny server input object, wrapped into a reactive expression: input_re = reactive({input})}
+}
+\description{
+moduleConfigServer
+}

man/moduleConfigUI.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/moduleConfig.R
+\name{moduleConfigUI}
+\alias{moduleConfigUI}
+\title{moduleConfigUI}
+\usage{
+moduleConfigUI(id)
+}
+\arguments{
+\item{id}{A character. The identifier of the shiny object}
+}
+\description{
+moduleConfigUI
+}