Merge branch 'master' into issues_1082Date_1089NotWorn

wadpac · Jun 4, 2024 · f07718d · f07718d
2 parents 59f27a9 + ed9c373
commit f07718d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: GGIR
 Type: Package
 Title: Raw Accelerometer Data Analysis
-Version: 3.1-0
-Date: 2024-05-06
+Version: 3.1-1
+Date: 2024-06-04
 Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
                     email="[email protected]"),
              person("Jairo H","Migueles",role="aut",

diff --git a/NEWS.md b/NEWS.md
@@ -1,14 +1,21 @@
 # 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
-- Fixes reversion of reading `.csv.gz` files #1131.
+
+- Part 1: Fixes reversion of reading `.csv.gz` files #1131.
+
+- 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.
 
 - Visualreport: Improve handling of recordings where the accelerometer was not worn.
 
+- Part 4: 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.
+
 - Part 5: Fix incorrect calendar date when window starts 5 seconds before midnight, #1082
 
 # CHANGES IN GGIR VERSION 3.1-0

diff --git a/R/g.loadlog.R b/R/g.loadlog.R
@@ -7,6 +7,7 @@ g.loadlog = function(loglocation = c(), coln1 = c(), colid = c(),
   # Load sleep log data...
   S = data.table::fread(file = loglocation, stringsAsFactors = FALSE, data.table = FALSE,
                         check.names = TRUE, colClasses = "character")
+  S = Filter(function(x)!all(x == ""), S) # remove empty columns
   nnights = (ncol(S) - coln1 + 1) / 2
   cnt_time_notrecognise = 0
   advanced_sleeplog = length(grep(pattern = "date", x = colnames(S), ignore.case = TRUE)) > 0
@@ -216,7 +217,7 @@ g.loadlog = function(loglocation = c(), coln1 = c(), colid = c(),
     warning(paste0("\nWe see an odd number of timestamp columns",
                    " in the sleeplog. The last column will be ignored. If this is incorrect,",
                    " please check that argument coln1 is correctly specified if you use a basic sleeplog format and",
-                   " that all days have a date column if you use an advanced sleeplog format."))
+                   " that all days have a date column if you use an advanced sleeplog format."), call. = FALSE)
     nnights = floor(nnights)
   }
   nnights = nnights + deltadate + 1 # to account for the possibility of extra night at the beginning of recording

diff --git a/R/g.report.part4.R b/R/g.report.part4.R
@@ -194,6 +194,9 @@ 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

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,6 +1,17 @@
 .onAttach <- function(...) {
   if (!interactive()) return()
-  pkgs <- available.packages()
+  # stop interactive calling from `library(GGIR)`
+  repos = getOption("repos")
+  if ("@CRAN@" %in% repos) {
+    repos = utils::getCRANmirrors()
+    # choose cloud/first if option triggers `contrib.url`
+    # to call `chooseCRANmirror`
+    repos = repos$URL[1]
+    packageStartupMessage(
+      "No CRAN mirror set, so using ", repos,
+      " to check GGIR package version")
+  }
+  pkgs <- available.packages(repos = repos)
   cran_version <- package_version(pkgs[which(pkgs[,1] == "GGIR"),"Version"])
   local_version <- packageVersion("GGIR")
   behind_cran <- cran_version > local_version

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -83,7 +83,10 @@ navbar:
     right: [search, github, twitter]
 
 news:
+  cran_dates: TRUE
   releases:
+  - text: "Version 3.1-0"
+    href: https://www.accelting.com/updates/ggir-release-3-1-0/
   - text: "Version 3.0-0"
     href: https://www.accelting.com/updates/ggir-release-3-0-0/
   - text: "Version 2.9-0"

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/RELEASE_CYCLE.html b/docs/RELEASE_CYCLE.html
diff --git a/docs/articles/CutPoints.html b/docs/articles/CutPoints.html
diff --git a/docs/articles/ExternalFunction.html b/docs/articles/ExternalFunction.html