Merge branch 'master' into issue653_step_updated_withmaster

wadpac · Oct 1, 2024 · 8d34347 · 8d34347
2 parents 241be6c + 7a402c7
commit 8d34347
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diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,14 @@
 # CHANGES IN GGIR VERSION 3.1-?
 
+- Part 5: Fixed minor bug in g.part5.addfirstwake causing the first wake is not correctly added when
+no SIBs are detected from the beginning of the recording until the first detected night. #1198
+
 - Part 5: Add parameters require_complete_lastnight_part5 to control whether last window is included if last night is incomplete. #1196
 
+- General: GGIR version look-up in .onattach() no longer crashes when computer is offline, fixes #1203.
+
+- Reports: The calendar_date and filename columns in reports have been standardized, as %Y-%m-%d and the input accelerometer file name, respectively. #1197
+
 # CHANGES IN GGIR VERSION 3.1-4
 
 - Part 3: Update threshold used for HorAngle to 60 degree, and auto-setting HASPT.ignore.invalid to NA when NotWorn guider is used. #1186

diff --git a/R/GGIR.R b/R/GGIR.R
@@ -369,7 +369,7 @@ GGIR = function(mode = 1:5, datadir = c(), outputdir = c(),
       g.report.part2(metadatadir = metadatadir, f0 = f0, f1 = f1,
                      maxdur = params_cleaning[["maxdur"]],
                      store.long = store.long, params_output,
-                     verbose = verbose)
+                     verbose = verbose, desiredtz = params_general[["desiredtz"]])
     }
   }
   if (length(which(do.report == 4)) > 0) {

diff --git a/R/g.part5.R b/R/g.part5.R
@@ -170,6 +170,7 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
         # convert to character/numeric if stored as factor in metashort and metalong
         M$metashort = correctOlderMilestoneData(M$metashort)
         M$metalong = correctOlderMilestoneData(M$metalong)
+        filename = filename_dir
         # load output g.part3
         longitudinal_axis = NULL # initialise var that is part of ms3.out
         load(paste0(metadatadir, "/meta/ms3.out/", fnames.ms3[i]))
@@ -601,6 +602,7 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                                            ID = ID,
                                            params_output = params_output,
                                            params_247 = params_247,
+                                           filename = filename,
                                            timewindow = timewindowi)
                   }
                 }

diff --git a/R/g.part5.addfirstwake.R b/R/g.part5.addfirstwake.R
@@ -73,7 +73,9 @@ g.part5.addfirstwake = function(ts, summarysleep, nightsi, sleeplog, ID,
     if (is.na(wake_night1_index)) wake_night1_index = 0
     if (wake_night1_index < firstwake & wake_night1_index > 1 &
         (wake_night1_index - 1) > nightsi[1]) {
-      newWakeIndex = max(which(ts$sibdetection[1:(wake_night1_index - 1)] == 1))
+      newWakeIndex = c()
+      firstSIBs = which(ts$sibdetection[1:(wake_night1_index - 1)] == 1)
+      if (length(firstSIBs) > 0) newWakeIndex = max(firstSIBs)
       if (length(newWakeIndex) == 0) {
         newWakeIndex = wake_night1_index - 1
       }
@@ -94,4 +96,4 @@ g.part5.addfirstwake = function(ts, summarysleep, nightsi, sleeplog, ID,
     }
   }
   return(ts)
-}
+}
diff --git a/R/g.part5.savetimeseries.R b/R/g.part5.savetimeseries.R
@@ -3,8 +3,9 @@ g.part5.savetimeseries = function(ts, LEVELS, desiredtz, rawlevels_fname,
                                   includedaycrit.part5 = 2/3, ID = NULL,
                                   params_output,
                                   params_247 = NULL,
+                                  filename = "",
                                   timewindow = NULL) {
-  
+
   ms5rawlevels = data.frame(date_time = ts$time, class_id = LEVELS,
                             # class_name = rep("",Nts),
                             stringsAsFactors = FALSE)
@@ -104,7 +105,7 @@ g.part5.savetimeseries = function(ts, LEVELS, desiredtz, rawlevels_fname,
       mdat$timestamp = as.POSIXct(mdat$timenum, origin = "1970-01-01",tz = desiredtz)
       rawlevels_fname = gsub(pattern = ".csv", replacement = ".RData", x = rawlevels_fname)
       fname = unique(rawlevels_fname[grep("*RData$", rawlevels_fname)])
-      save(mdat, file = fname)
+      save(mdat, filename, file = fname)
     }
     #===============================
     rm(mdat)

diff --git a/R/g.part6.R b/R/g.part6.R
@@ -116,6 +116,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
       } else {
         mdat = data.table::fread(file = paste0(metadatadir, "/meta/ms5.outraw/", 
                                                params_phyact[["part6_threshold_combi"]],  "/", fnames.ms5raw[i]), data.table = FALSE)
+        filename = fnames.ms5raw[i]
       }
       nfeatures = 50
       summary = matrix(NA, nfeatures, 1)
@@ -188,7 +189,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
       summary[fi] = format(starttime)
       s_names[fi] = "starttime"
       fi = fi + 1
-      summary[fi] = gsub(pattern = "[.]RData|[.]csv", replacement = "", x = fnames.ms5raw[i])
+      summary[fi] = gsub(pattern = "[.]RData$|[.]csv$", replacement = "", x = filename)
       s_names[fi] = "filename"
       fi = fi + 1
       summary[fi] = ifelse(test = nrow(ts) == 1,
@@ -281,9 +282,9 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
         }
         output_part6$GGIRversion = GGIRversion
         save(output_part6, GGIRversion, file = paste0(metadatadir, ms6.out, "/",
-                                         gsub(pattern = "[.]csv|[.]RData",
-                                              replacement = "",
-                                              x = fnames.ms5raw[i]), ".RData"))
+                                                      gsub(pattern = "[.]csv|[.]RData",
+                                                           replacement = "",
+                                                           x = fnames.ms5raw[i]), ".RData"))
       }
       rm(output_part6, summary)
     }

diff --git a/R/g.report.part2.R b/R/g.report.part2.R
@@ -1,5 +1,6 @@
 g.report.part2 = function(metadatadir = c(), f0 = c(), f1 = c(), maxdur = 0,
-                          store.long = FALSE, params_output, myfun = c(), verbose = TRUE) {
+                          store.long = FALSE, params_output, myfun = c(), verbose = TRUE,
+                          desiredtz = "") {
   ms2.out = "/meta/ms2.out"
   if (file.exists(paste0(metadatadir,ms2.out))) {
     if (length(dir(paste0(metadatadir,ms2.out))) == 0) {
@@ -278,7 +279,14 @@ g.report.part2 = function(metadatadir = c(), f0 = c(), f1 = c(), maxdur = 0,
     if (length(SUMMARY) > 0 & length(daySUMMARY) > 0) {
       SUMMARY_clean = tidyup_df(SUMMARY)
       daySUMMARY_clean = tidyup_df(daySUMMARY)
-
+      daySUMMARY_clean$start_time = daySUMMARY_clean$calendar_date
+      # reorder to have starttime next to calendar_date
+      old_vars = which(colnames(daySUMMARY_clean) != "start_time")
+      new_var = which(colnames(daySUMMARY_clean) == "start_time")
+      daySUMMARY_clean = daySUMMARY_clean[, c(old_vars[1:3], new_var, old_vars[4:length(old_vars)])]
+      # format calendar dates
+      dd = iso8601chartime2POSIX(daySUMMARY_clean$calendar_date, tz = desiredtz) 
+      daySUMMARY_clean$calendar_date = format(dd, format = "%Y-%m-%d")
       #===============================================================================
       # store final matrices again
       data.table::fwrite(x = SUMMARY_clean, file = paste0(metadatadir, "/results/part2_summary.csv"),

diff --git a/R/g.report.part4.R b/R/g.report.part4.R
@@ -76,6 +76,9 @@ g.report.part4 = function(datadir = c(), metadatadir = c(), loglocation = c(),
     }
     nightsummary2 = as.data.frame(do.call(rbind, lapply(fnames.ms4, myfun)), stringsAsFactors = FALSE)
     nightsummary2$night = as.numeric(gsub(" ", "", nightsummary2$night))
+    nightsummary2$calendar_date = as.Date(nightsummary2$calendar_date, format = "%d/%m/%Y")
+    nightsummary2$calendar_date = format(nightsummary2$calendar_date, format = "%Y-%m-%d")
+    nightsummary2$filename = gsub(".RData$", "", nightsummary2$filename)
     # ====================================== Add non-wearing during SPT from part 5, if it is availabe:
     ms5.out = "/meta/ms5.out"
     if (file.exists(paste(metadatadir, ms5.out, sep = ""))) {

diff --git a/R/g.report.part5.R b/R/g.report.part5.R
@@ -200,6 +200,9 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
       outputfinal = outputfinal[,-cut]
     }
 
+    # revise filename
+    outputfinal$filename = gsub(".RData$", "", outputfinal$filename)
+
     # order data.frame
     outputfinal$window_number = as.numeric(gsub(" ", "", outputfinal$window_number))
     outputfinal = outputfinal[order(outputfinal$filename, outputfinal$window_number, outputfinal$window), ]

diff --git a/R/zzz.R b/R/zzz.R
@@ -13,6 +13,7 @@
   }
   pkgs <- available.packages(repos = repos)
   cran_version <- package_version(pkgs[which(pkgs[,1] == "GGIR"),"Version"])
+  if (length(cran_version) == 0) return() # handle no internet connection
   local_version <- packageVersion("GGIR")
   behind_cran <- cran_version > local_version
   if (interactive()) {

diff --git a/man/g.part5.savetimeseries.Rd b/man/g.part5.savetimeseries.Rd
@@ -13,6 +13,7 @@
                               includedaycrit.part5 = 2/3,
                               ID = NULL, params_output,
                               params_247 = NULL,
+                              filename = "",
                               timewindow = NULL)
 }
 \arguments{
@@ -26,7 +27,7 @@
      See \link{GGIR}.
   }
   \item{rawlevels_fname}{
-    Path to the file where the output should be stored
+    Path to the file where the output (time series) should be stored
   }
   \item{DaCleanFile}{
     Content of data_cleaning_file as documented in \link{g.report.part5}.
@@ -49,6 +50,10 @@
   \item{params_247}{
     See \link{GGIR}
   }
+  \item{filename}{
+    Character (default = "") indicating the name of the accelerometer data file 
+    that was used as input. This name will be stored inside the time series output file.
+  }
   \item{timewindow}{
     See \link{GGIR}
   }
@@ -60,4 +65,4 @@
 \keyword{internal}
 \author{
   Vincent T van Hees <v.vanhees@accelting.com>
-}
+}
diff --git a/man/g.report.part2.Rd b/man/g.report.part2.Rd
@@ -9,7 +9,8 @@
 }
 \usage{
   g.report.part2(metadatadir = c(), f0 = c(), f1 = c(), maxdur = 0,
-  store.long = FALSE, params_output, myfun = c(), verbose = TRUE)
+                  store.long = FALSE, params_output, myfun = c(), 
+                  verbose = TRUE, desiredtz = "")
 }
 \arguments{
   \item{metadatadir}{
@@ -44,6 +45,9 @@
   \item{verbose}{
     See details in \link{GGIR}.
   }
+  \item{desiredtz}{
+    See details in \link{GGIR}.
+  }
 }
 \value{
 Function does not produce data, but only writes reports

diff --git a/tests/testthat/test_part6.R b/tests/testthat/test_part6.R
@@ -21,14 +21,17 @@ test_that("Part 6 with household co-analysis", {
   data(data.ts)
   mdat = data.ts
   mdat$timenum = mdat$timenum - (5 * 60) 
-  save(mdat, file = paste0(dn, "/800-900-001_left wrist.RData"))
+  filename = "800-900-001_left wrist.bin"
+  save(mdat, filename, file = paste0(dn, "/800-900-001_left wrist.RData"))
   mdat$timenum = mdat$timenum + (7 * 60)
-  save(mdat, file = paste0(dn, "/800-900-002_left wrist.RData"))
+  filename = "800-900-002_left wrist.bin"
+  save(mdat, filename, file = paste0(dn, "/800-900-002_left wrist.RData"))
   mdat$timenum = mdat$timenum + (14 * 60)
-  save(mdat, file = paste0(dn, "/800-900-003_left wrist.RData"))
+  filename = "800-900-003_left wrist.bin"
+  save(mdat, filename, file = paste0(dn, "/800-900-003_left wrist.RData"))
 
   # Run household co-analysis  
-  # Update parameters to align with datset
+  # Update parameters to align with dataset
   params_general = load_params(topic = "general")$params_general
   params_general[["desiredtz"]] = "America/Curacao"
   params_phyact = load_params(topic = "phyact")$params_phyact