Documentation fixes

.github/workflows/r_codecov.yml

@@ -13,17 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    patch: off
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr, any::rcmdcheck, any::XML
+          extra-packages: covr
 
       - name: Test coverage
         run: covr::codecov()

NEWS.md

@@ -6,6 +6,10 @@
 
 - Part 1: Now also able to handle some more variations in Actigraph csv count file format #978, and automatically aggregates to lower resolution if short epoch size is longer than observed epoch size in actigraph count csv.
 
+- Part 5: Reverting decision to prohibit segmentDAYSPTcrit.part5 to be c(0, 0). The default remains unchanged and documentation now only emphasizes the downside of using c(0, 0). #980
+
+- Argument documentation: Fixing series of typos (thanks to Pieter-Jan Marent for pointing them out)
+
 - Part 5: Fix bug in recently added fucntionality for studying overlap between sibs and self-reported beahviours #989.
 
 # CHANGES IN GGIR VERSION 3.0-1

R/check_params.R

@@ -78,7 +78,7 @@ check_params = function(params_sleep = c(), params_metrics = c(),
     numeric_params = c("qlevels", "ilevels", "IVIS_windowsize_minutes", "IVIS_epochsize_seconds",
                        "IVIS.activity.metric", "IVIS_acc_threshold",
                        "qM5L5", "MX.ig.min.dur", "M5L5res", "winhr", "LUXthresholds", "LUX_cal_constant",
-                       "LUX_cal_exponent", "LUX_day_segments", "window.summary.size", "L5M5window")
+                       "LUX_cal_exponent", "LUX_day_segments", "L5M5window")
     boolean_params = c("cosinor", "part6CR", "part6HCA")
     character_params = c("qwindow_dateformat", "part6Window")
     check_class("247", params = params_247, parnames = numeric_params, parclass = "numeric")
@@ -433,23 +433,18 @@ check_params = function(params_sleep = c(), params_metrics = c(),
                      ", the default value has been assigned (i.e., 0.5) "), call. = FALSE)
     } else if (params_cleaning[["segmentWEARcrit.part5"]] < 0 | 
                params_cleaning[["segmentWEARcrit.part5"]] > 1) {
-      stop(paste0("Incorrect value of segmentWEARcrit.part5, this should be a",
-                  "fraction of the day between zero and one, please change."), 
+      stop(paste0("Incorrect value of segmentWEARcrit.part5, this should be a ",
+                  "fraction between zero and one, please change."), 
            call. = FALSE)
     }
     if (length(params_cleaning[["segmentDAYSPTcrit.part5"]]) != 2) {
       stop("\nArgument segmentDAYSPTcrit.part5 is expected to be a numeric vector of length 2", call. = FALSE)
     }
-    if (sum(params_cleaning[["segmentDAYSPTcrit.part5"]]) < 0.5 |
-        0 %in% params_cleaning[["segmentDAYSPTcrit.part5"]] == FALSE) {
-
-      stop(paste0("\nIf you used argument segmentDAYSPTcrit.part5 then make sure",
-                  " it includes one zero",
-                  " and one value of at least 0.5, see documentation for",
-                  " argument segmentDAYSPTcrit.part5. If you do not use",
-                  " argument segmentDAYSPTcrit.part5",
-                  " then delete it from your config.csv file (in your output folder)",
-                  " or delete the config.csv file itself."), call. = FALSE)
+    if (any(params_cleaning[["segmentDAYSPTcrit.part5"]] < 0) | 
+        any(params_cleaning[["segmentDAYSPTcrit.part5"]] > 1)) {
+      stop(paste0("Incorrect values of segmentDAYSPTcrit.part5, these should be a ",
+                  "fractions between zero and one, please change."), 
+           call. = FALSE)
     }
   }
 

R/createConfigFile.R

@@ -58,7 +58,7 @@ createConfigFile = function(config.parameters = c(), GGIRversion = "") {
                            "includedaycrit", "M5L5res", "winhr", "qwindow", "qlevels",
                            "ilevels", "mvpathreshold", "boutcriter", "ndayswindow",
                            "do.imp", "epochvalues2csv", "mvpadur",
-                           "window.summary.size", "dayborder", "closedbout",
+                           "dayborder", "closedbout",
                            "IVIS_windowsize_minutes", "IVIS_epochsize_seconds", "iglevels",
                            "IVIS.activity.metric", "TimeSegments2ZeroFile", "qM5L5", "do.part3.pdf") ==  TRUE) {
         out[i,3] = "Study design, Parameters descriptive analysis"

R/load_params.R

@@ -73,7 +73,7 @@ load_params = function(topic = c("sleep", "metrics", "rawdata",
                       MX.ig.min.dur = 10, M5L5res = 10, winhr = 5, iglevels = c(),
                       LUXthresholds = c(0, 100, 500, 1000, 3000, 5000, 10000),
                       LUX_cal_constant = c(), LUX_cal_exponent = c(), LUX_day_segments = c(),
-                      window.summary.size = 10, L5M5window = c(0, 24), cosinor = FALSE,
+                      L5M5window = c(0, 24), cosinor = FALSE,
                       part6CR = FALSE, part6HCA = FALSE,
                       part6Window = c("start", "end"))
   }