part6_threshold_combi now uses first value of lig, mod and vig thresh…

…olds if not specified
wadpac · Oct 15, 2024 · 2e3e8ae · 2e3e8ae
1 parent 9a968c2
commit 2e3e8ae
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Showing 4 changed files with 9 additions and 8 deletions.
diff --git a/R/check_params.R b/R/check_params.R
@@ -313,9 +313,9 @@ check_params = function(params_sleep = c(), params_metrics = c(),
       params_phyact[["mvpadur"]] = c(1,5,10)
       warning("\nmvpadur needs to be a vector with length three, value now reset to default c(1, 5, 10)", call. = FALSE)
     }
-    if (length(params_phyact[["threshold.lig"]]) == 1 &&
+    if ((length(params_phyact[["threshold.lig"]]) == 1 &&
         length(params_phyact[["threshold.mod"]]) == 1 &&
-        length(params_phyact[["threshold.vig"]]) == 1) {
+        length(params_phyact[["threshold.vig"]]) == 1) | is.null(params_phyact[["part6_threshold_combi"]])) {
       params_phyact[["part6_threshold_combi"]] = paste(params_phyact[["threshold.lig"]],
                                                        params_phyact[["threshold.mod"]],
                                                        params_phyact[["threshold.vig"]], sep = "_")

diff --git a/R/g.plot5.R b/R/g.plot5.R
@@ -902,9 +902,8 @@ g.plot5 = function(metadatadir = c(), dofirstpage = FALSE, viewingwindow = 1,
                   ((daycount - 1) / NGPP) == (round((daycount - 1) / NGPP))) {
                 mtext(paste0("Filename: ", fnames_ms1_stripped[sel]),
                       side = 3, line = 0, outer = TRUE, font = 2, cex = 0.6)
-                mtext(text = paste0("Warning: This GGIR report will be deprecated,",
-                                    " please start using the new ",
-                                    "visualreport as now stored in the same folder."),
+                mtext(text = paste0("Warning: This GGIR report is not intended to be used for data quality assessment and is a legacy of a quick attempt in 2015 to have something to show to a study participant,",
+                                    " To visually quality check your data see file names starting with Time_report_ "),
                       side = 3, line = 1, outer = TRUE, font = 2, cex = 0.7
                 )
               }

diff --git a/R/load_params.R b/R/load_params.R
@@ -88,7 +88,7 @@ load_params = function(topic = c("sleep", "metrics", "rawdata",
                          threshold.mod = 100, threshold.vig = 400,
                          boutdur.mvpa = c(1,5,10), boutdur.in = c(10,20,30),
                          boutdur.lig = c(1,5,10), frag.metrics = c(),
-                         part6_threshold_combi = "40_100_400")
+                         part6_threshold_combi = NULL)
   }
   if ("cleaning" %in% topic) {
     params_cleaning = list(includedaycrit = 16, ndayswindow = 7,

diff --git a/man/GGIR.Rd b/man/GGIR.Rd
@@ -1067,8 +1067,10 @@ GGIR(mode = 1:5,
         See package vignette for description of fragmentation metrics.}
 
       \item{part6_threshold_combi}{
-        Character (default = "40_100_120") to indicate the threshold combination derived in
-        part 5 to be used for part 6
+        Character (default = NULL) to indicate the threshold combination derived in
+        part 5 to be used for part 6. For example, "40_100_120". If left in default value
+        GGIR will use the first threshold value from parameters \code{threshold.lig},
+        \code{threshold.mod}, and \code{threshold.vig}.
       }
     }
   }