Use GGIR parameter mode as specified by GUI user

.Rbuildignore

@@ -7,3 +7,4 @@ CONTRIBUTING.md
 INSTRUCTIONS_TOOL_MAINTAINERS.md
 UCloud_files
 HabitusGUIbookmark.RData
+codecov.yml

.github/workflows/r_new.yml

@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

DESCRIPTION

@@ -2,15 +2,15 @@ Package: HabitusGUI
 Title: R Shiny App for Processing Behavioural Data
 Description: Shiny app to ease processing behavioural data with research software such as GGIR, hbGPS,and hbGIS.
 Version: 0.3.2
-Date: 2024-03-24
+Date: 2024-03-25
 Authors@R: 
     c(person(given = "Vincent",
            family = "van Hees",
            role = c("aut", "cre"),
            email = "[email protected]"))
 License: Apache License version 2.0 | file LICENSE
 Imports: shiny, shinyFiles, GGIR, bslib, methods, jsonlite, DT, 
-    magrittr, shinyjs, callr, hbGPS, hbGIS
+    magrittr, shinyjs, callr, hbGPS, hbGIS, data.table
 Remotes: habitus-eu/hbGPS, habitus-eu/hbGIS
 LazyData: true
 Suggests: testthat, covr, rmarkdown

NAMESPACE

@@ -18,6 +18,7 @@ import(hbGPS)
 import(shiny)
 import(shinyFiles)
 importFrom(callr,r_bg)
+importFrom(data.table,fread)
 importFrom(hbGIS,hbGIS)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)

R/GGIRshiny.R

@@ -7,12 +7,35 @@
 #' @return no object is returned, only a new file is created in the output directory
 #' @import GGIR
 #' @importFrom utils write.table
+#' @importFrom data.table fread
 #' @export
 #' 
 
 GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c()) {
   if (length(sleepdiary) == 0) sleepdiary = c()
-  if (length(configfile) == 0) configfile = c()
+  if (length(configfile) == 0) {
+    configfile = c()
+    modeIS = ""
+  } else {
+    configfile = "D:/Dropbox/Work/sharedfolder/DATA/Habitus/GPSprocessing/JosefMarch2024/config_GGIR_counts.csv"
+    # extract mode from config file
+    config = data.table::fread(file = configfile, data.table = FALSE)
+    modeChar = config$value[which(config$argument == "mode")]
+    # check that mode is nothing more than a numeric vector
+    checkMode = suppressWarnings(as.numeric(gsub(x = modeChar, pattern = "c|[(]|[)]|:|,", replacement = "")))
+    if (is.numeric(checkMode) == FALSE) {
+      stop("\nUnexpected value for parameter mode")
+    } else {
+      modeNum = eval(parse(text = modeChar)) 
+    }
+    if (min(modeNum) > 0 && max(modeNum) <= 6) {
+      # use mode value from config file if values are plausible
+      modeIS = paste0(", mode = ", modeChar)
+    } else {
+      # do not use mode value and let GGIR use its default
+      modeIS = ""
+    }
+  }
 
   # create R script with the code to run the data analysis via a command line call
   # in this way turning off or restarting the app will not kill the data analysis
@@ -25,10 +48,10 @@ GGIRshiny = function(rawaccdir, outputdir, sleepdiary = c(), configfile = c()) {
                "if (length(args) == 4) {",
                "GGIR::GGIR(datadir = args[1], outputdir = args[2], ",
                "configfile = args[3], loglocation = args[4],",
-               "do.parallel = TRUE)",
+               "do.parallel = TRUE", modeIS,")",
                "} else {",
                "GGIR::GGIR(datadir = args[1], outputdir = args[2], ",
-               "configfile = args[3], do.parallel = TRUE)",
+               "configfile = args[3], do.parallel = TRUE", modeIS,")",
                "}"),
              fileConn)
   close(fileConn)

inst/NEWS.Rd

@@ -1,12 +1,13 @@
 \name{NEWS}
 \title{News for Package \pkg{HabitusGUI}}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
-\section{Changes in version 0.3.2 (GitHub-only-release date: 20-03-2024)}{
+\section{Changes in version 0.3.2 (GitHub-only-release date: 25-03-2024)}{
   \itemize{
     \item Changed default for save_ms5rawlevels in template config.csv to TRUE
-    \item Fix issue with old activityCounts dependency that we was not 
+    \item Fix issue with old activityCounts dependency that was not 
     correctly deprecated in the previous release
-    \item Add hbGIS parameter documentation for use inside the GUI
+    \item Added hbGIS parameter documentation for use inside the GUI
+    \item Now uses GGIR parameter mode as set by user and do not fall back on GGIR default, fixes #103
   }
 }
 \section{Changes in version 0.3.1 (GitHub-only-release date: 22-01-2024)}{