Merge branch 'issue1148_wear_percentage_part5' into issues_1082Date_1…

…089NotWorn

.Rbuildignore

@@ -9,8 +9,9 @@ RELEASE_CYCLE.md
 ^CRAN-SUBMISSION$
 ^_pkgdown\.yml$
 ^docs$
+^docs
 ^pkgdown$
-^vignettes/chapter.*\\.Rmd$
+^vignettes/chapter*
 ^dev-functions$
 .zenodo.json
 ^doc$

.github/pull_request_template.md

@@ -1,7 +1,7 @@
 <!-- Describe your PR here -->
 
 <!-- Please, make sure the following items are checked -->
-Checklist before merging:
+### Checklist before merging:
 
 - [ ] Existing tests still work (check by running the test suite, e.g. from RStudio).
 - [ ] Added tests (if you added functionality) or fixed existing test (if you fixed a bug).
@@ -15,14 +15,14 @@ Checklist before merging:
 - [ ] Added your name to the contributors lists in the `DESCRIPTION` file, if you think you made a significant contribution.
 - [ ] GGIR parameters were added/removed. If yes, please also complete checklist below.
 
-If NEW GGIR parameter(s) were added then these NEW parameter(s) are :
+**If NEW GGIR parameter(s) were added then these NEW parameter(s) are:**
 - [ ] documented in `man/GGIR.Rd`
 - [ ] included with a default in `R/load_params.R`
 - [ ] included with value class check in `R/check_params.R`
 - [ ] included in table of `vignettes/GGIRParameters.Rmd` with references to the GGIR parts the parameter is used in.
 - [ ] mentioned in NEWS.Rd as NEW parameter
 
-If GGIR parameter(s) were deprecated these parameter(s) are:
+**If GGIR parameter(s) were deprecated these parameter(s) are:**
 - [ ] documented as deprecated in `man/GGIR.Rd`
 - [ ] removed from `R/load_params.R`
 - [ ] removed from `R/check_params.R`

NEWS.md

@@ -1,3 +1,11 @@
+# CHANGES IN GGIR VERSION 3.1-2
+
+- Report part 5: fix bug that was introduced on 2024-Feb-19 in the calculation of wear percentage #1148
+
+- Part 3 and 4: Revise NotWorn algorithm to work with both count and raw data with varying degrees of nonwear.
+
+- Visualreport: Improve handling of recordings where the accelerometer was not worn.
+
 # CHANGES IN GGIR VERSION 3.1-1
 
 - Part 2: Corrected calculation of LXhr and MXhr which had one hour offset when timing was after midnight, #1117
@@ -6,15 +14,13 @@
 
 - Loading GGIR: Stops interactive calling of `chooseCRANmirror` on `.onAttach` if interactive and CRAN mirror not set #1141.
 
-- Part 4: Corrected documentation for parameter relyonguider.
-
-- Part 3 and 4: Revise NotWorn algorithm to work with both count and raw data with varying degrees of nonwear.
+- Part 4:
 
-- Visualreport: Improve handling of recordings where the accelerometer was not worn.
+  - Corrected documentation for parameter relyonguider.
 
-- Part 4: Ignore empty sleeplog columns, which are sometimes accidentally created the user. GGIR can now handle these. #1138
+  - Ignore empty sleeplog columns, which are sometimes accidentally created the user. GGIR can now handle these. #1138
 
-- Part 4 report: Bug fixed causing night_part4 column to not be used #1142.
+  - report: Bug fixed causing night_part4 column to not be used #1142.
 
 - Part 5: Fix incorrect calendar date when window starts 5 seconds before midnight, #1082
 

R/g.report.part4.R

@@ -75,6 +75,7 @@ g.report.part4 = function(datadir = c(), metadatadir = c(), loglocation = c(),
       out = as.matrix(nightsummary)
     }
     nightsummary2 = as.data.frame(do.call(rbind, lapply(fnames.ms4, myfun)), stringsAsFactors = FALSE)
+    nightsummary2$night = as.numeric(gsub(" ", "", nightsummary2$night))
     # ====================================== 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 = ""))) {
@@ -131,7 +132,6 @@ g.report.part4 = function(datadir = c(), metadatadir = c(), loglocation = c(),
         }
       }
       # merge in variable
-      nightsummary2$night = as.numeric(gsub(" ", "", nightsummary2$night))
       outputp5$night = as.numeric(outputp5$night)
       nightsummary2 = base::merge(nightsummary2, outputp5, by = c("ID", "night"), all.x = TRUE)
       if (remove_oldID == TRUE) {
@@ -194,9 +194,6 @@ g.report.part4 = function(datadir = c(), metadatadir = c(), loglocation = c(),
           if (length(data_cleaning_file) > 0) {
             DaCleanFile = data.table::fread(data_cleaning_file, data.table = FALSE)
             if ("night_part4" %in% colnames(DaCleanFile)) {
-              if (inherits(x = nightsummary$night, "character")) {
-                nightsummary$night = as.numeric(gsub(pattern = " ", replacement = "", x = nightsummary$night))
-              }
               days2exclude = which(nightsummary$ID %in% DaCleanFile$ID & nightsummary$night %in% DaCleanFile$night_part4)
               if (length(days2exclude) == 0 & inherits(x = nightsummary$ID, "character")) {
                 # Try again by now attempt to read ID as numeric

R/g.report.part5.R

@@ -50,7 +50,7 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
       x$wear_min_day_spt = (1 - (x$nonwear_perc_day_spt / 100)) * x$dur_day_spt_min #valid minute during waking hours
 
       x$wear_min_day = (1 - (x$nonwear_perc_day / 100)) * x$dur_day_min #valid minute during waking hours
-      x$wear_perc_day = 100 - (x$nonwear_perc_day / 100) #wear percentage during waking hours
+      x$wear_perc_day = 100 - x$nonwear_perc_day #wear percentage during waking hours
 
       minimumValidMinutesMM = 0 # default
       if (length(params_cleaning[["includedaycrit"]]) == 2) {