re-insert option to control HDCZA internal thresholds, but let them d…

…efault to the thresholds used in the paper.

R/HASPT.R

@@ -1,5 +1,5 @@
 HASPT = function(angle, sptblocksize = 30, spt_max_gap = 60, ws3 = 5,
-                 HASPT.algo="HDCZA", HDCZA_threshold = 0.2, invalid,
+                 HASPT.algo="HDCZA", HDCZA_threshold = c(), invalid,
                  HASPT.ignore.invalid=FALSE, activity = NULL) {
   tib.threshold = SPTE_start = SPTE_end = part3_guider = c()
   # internal functions ---------
@@ -25,7 +25,10 @@ HASPT = function(angle, sptblocksize = 30, spt_max_gap = 60, ws3 = 5,
 
       x = zoo::rollapply(angle, width = k1, FUN = medabsdi, fill = 0) # 5 minute rolling median of the absolute difference
       if (is.null(HDCZA_threshold)) {
-        threshold = quantile(x, probs = 0.1) * 15
+        HDCZA_threshold = c(10, 15)
+      }
+      if (length(HDCZA_threshold) == 2) {
+        threshold = quantile(x, probs = HDCZA_threshold[1] / 100) * HDCZA_threshold[2]
         if (threshold < 0.13) {
           threshold = 0.13
         } else if (threshold > 0.50) {

man/GGIR.Rd

@@ -1159,7 +1159,9 @@ GGIR(mode = 1:5,
         et al. 2018 Scientific Report (doi: 10.1038/s41598-018-31266-z). However,
         doing so has not been supported by research yet and is only intended to
         facilitate methodological research, so we advise sticking with the default in
-        line with the publication.
+        line with the publication. Further, if HDCZA_threshold is set to a numeric vector of
+        length 2, e.g. c(10, 15), that will be used as percentile and 
+        multiplier for the above mentioned 6th step.
       }
 
       \item{HASPT.ignore.invalid}{