use GGIR parameter mode from config file, fixes #103

.Rbuildignore

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

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 
     correctly deprecated in the previous release
     \item Add 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)}{