Merge pull request #1158 from wadpac/issues1155_chunksize_1154_adhoccsv

Reduce constraints on value of chunksize and make sure time gap imputation cal also run for adhoc csv
wadpac · Jun 24, 2024 · 756e1f3 · 756e1f3
2 parents db8a657 + 0cf0c8e
commit 756e1f3
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Showing 6 changed files with 20 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: GGIR
 Type: Package
 Title: Raw Accelerometer Data Analysis
-Version: 3.1-1
-Date: 2024-06-04
+Version: 3.1-2
+Date: 2024-06-26
 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
@@ -4,6 +4,10 @@
 
 - Report part 5: fix bug that was introduced on 2024-Feb-19 in the calculation of wear percentage #1148
 
+- Part 1: Enable timegap imputation for ad-hoc csv data. #1154
+
+- Part 1: Reduce constraints on value for parameter chunksize #1155.
+
 - Report part 5: Rename variable sleep_efficiency to sleep_efficiency_after_onset, #1157
 
 - Vignette: Migrated many sections from main CRAN vignette to wadpac.github.io/GGIR/

diff --git a/R/check_params.R b/R/check_params.R
@@ -75,8 +75,7 @@ check_params = function(params_sleep = c(), params_metrics = c(),
     check_class("Raw data", params = params_rawdata, parnames = boolean_params, parclass = "boolean")
     check_class("Raw data", params = params_rawdata, parnames = character_params, parclass = "character")
 
-    if (params_rawdata[["chunksize"]] > 1.5) params_rawdata[["chunksize"]] = 1.5
-    if (params_rawdata[["chunksize"]] < 0.2) params_rawdata[["chunksize"]] = 0.2
+    if (params_rawdata[["chunksize"]] < 0.05) params_rawdata[["chunksize"]] = 0.05
   }
   if (length(params_247) > 0) {
     # iglevels and qwindow can be numeric or character, so not tested

diff --git a/R/g.getmeta.R b/R/g.getmeta.R
@@ -219,15 +219,17 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
         }
       }
 
-      if (params_rawdata[["imputeTimegaps"]] && (dformat == FORMAT$CSV || dformat == FORMAT$GT3X)) {
+      if (params_rawdata[["imputeTimegaps"]] && (dformat == FORMAT$CSV ||
+                                                 dformat == FORMAT$AD_HOC_CSV ||
+                                                 dformat == FORMAT$GT3X)) {
         P = g.imputeTimegaps(data, sf = sf, k = 0.25,
                              PreviousLastValue = PreviousLastValue,
                              PreviousLastTime = PreviousLastTime,
                              epochsize = c(ws3, ws2))
         data = P$x
         PreviousLastValue = data[nrow(data), c("x", "y", "z")]
         if ("time" %in% colnames(data)) {
-          PreviousLastTime = as.POSIXct(data$time[nrow(data)])
+          PreviousLastTime = as.POSIXct(data$time[nrow(data)], origin = "1970-1-1")
         } else {
           PreviousLastTime = NULL
         }

diff --git a/R/g.imputeTimegaps.R b/R/g.imputeTimegaps.R
@@ -79,6 +79,10 @@ g.imputeTimegaps = function(x, sf, k=0.25, impute = TRUE,
     }
     # refill if first value is not consecutive from last value in previous chunk
     if (!is.null(PreviousLastTime)) {
+      if (!inherits(x = PreviousLastTime, what = "numeric") &&
+          inherits(x = x$time[1], what = "numeric")) {
+        PreviousLastTime = as.numeric(PreviousLastTime)
+      }
       first_deltatime = diff(c(PreviousLastTime, x$time[1]))
       if (!is.numeric(first_deltatime)) {  # in csv axivity, the time is directly read as numeric (seconds)
         units(first_deltatime) = "secs"

diff --git a/man/GGIR.Rd b/man/GGIR.Rd
@@ -355,12 +355,15 @@ GGIR(mode = 1:5,
 
       \item{chunksize}{
         Numeric (default = 1).
-        Value between 0.2 and 1 to specify the size of chunks to be
+        Value to specify the size of chunks to be
         loaded as a fraction of an approximately 12 hour period for auto-calibration
         procedure and as fraction of 24 hour period for the metric calculation, e.g., 
         0.5 equals 6 and 12 hour chunks, respectively. 
         For machines with less than 4Gb of RAM memory or with < 2GB memory per process
-        when using \code{do.parallel = TRUE} a value below 1 is recommended.}
+        when using \code{do.parallel = TRUE} a value below 1 is recommended.
+        The value is constrained by GGIR to not be lower than 0.05. Please note that
+        setting 0.05 will not produce output when 3rd value of parameter windowsizes
+        is 3600.}
 
       \item{dynrange}{
         Numeric (default = NULL).