Merge branch 'master' of https://github.com/wadpac/GGIR

NEWS.md

@@ -9,6 +9,9 @@
 - Part 5: Fix bug in addition of first wake-up time if not present #1179
 
 - Part 2: Correctly skip MXLX calculation when it cannot be calculated, which caused error when trying to use the output. Fixes #1180
+
+- Part 1: Add parameter nonwear_range_threshold to control range threshold for nonwear detection,
+this used to be a constant. And default changed to 50mg. #1172
 
 # CHANGES IN GGIR VERSION 3.1-2
 

R/check_params.R

@@ -59,7 +59,8 @@ check_params = function(params_sleep = c(), params_metrics = c(),
                        "rmc.col.acc", "interpolationType",
                        "rmc.firstrow.acc", "rmc.firstrow.header", "rmc.header.length",
                        "rmc.col.temp", "rmc.col.time",
-                       "rmc.sf", "rmc.col.wear", "rmc.noise", "frequency_tol", "rmc.scalefactor.acc")
+                       "rmc.sf", "rmc.col.wear", "rmc.noise", "frequency_tol",
+                       "rmc.scalefactor.acc", "nonwear_range_threshold")
     boolean_params = c("printsummary", "do.cal", "rmc.unsignedbit", "rmc.check4timegaps", "rmc.doresample",
                        "imputeTimegaps")
     character_params = c("backup.cal.coef", "rmc.dec", "rmc.unit.acc",

R/g.getmeta.R

@@ -126,13 +126,10 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
   deviceSerialNumber = hvars$deviceSerialNumber
 
   # get now-wear, clip, and blocksize parameters (thresholds)
-  ncb_params = get_nw_clip_block_params(chunksize = params_rawdata[["chunksize"]],
-                                        dynrange = params_rawdata[["dynrange"]],
-                                        monc = mon, dformat = dformat,
+  ncb_params = get_nw_clip_block_params(monc = mon, dformat = dformat,
                                         deviceSerialNumber = deviceSerialNumber,
-                                        rmc.noise = params_rawdata[["rmc.noise"]],
                                         sf = sf,
-                                        rmc.dynamic_range = params_rawdata[["rmc.dynamic_range"]])
+                                        params_rawdata = params_rawdata)
   clipthres = ncb_params$clipthres
   blocksize = ncb_params$blocksize
   sdcriter = ncb_params$sdcriter

R/get_nw_clip_block_params.R

@@ -1,14 +1,14 @@
-get_nw_clip_block_params = function(chunksize, dynrange, monc, dformat, deviceSerialNumber = "", rmc.noise=c(), sf,
-                                    rmc.dynamic_range) {
-  blocksize = round(14512 * (sf/50) * chunksize)
-  if (monc == MONITOR$GENEA) blocksize = round(21467 * (sf/80)  * chunksize)
+get_nw_clip_block_params = function(monc, dformat, deviceSerialNumber = "", sf,
+                                    params_rawdata) {
+  blocksize = round(14512 * (sf/50) * params_rawdata[["chunksize"]])
+  if (monc == MONITOR$GENEA) blocksize = round(21467 * (sf/80)  * params_rawdata[["chunksize"]])
   if (monc == MONITOR$ACTIGRAPH && dformat == FORMAT$CSV) blocksize = round(blocksize)#round(blocksize/5)
-  if (monc == MONITOR$ACTIGRAPH && dformat == FORMAT$GT3X) blocksize = (24 * 3600) * chunksize
+  if (monc == MONITOR$ACTIGRAPH && dformat == FORMAT$GT3X) blocksize = (24 * 3600) * params_rawdata[["chunksize"]]
   if (monc == MONITOR$AXIVITY && dformat == FORMAT$CWA) {
     if (utils::packageVersion("GGIRread") >= "0.3.1") {
       # 24-hour block.
       # CWA data blocks can have 40, 80 or 120 samples each; we'll take 80 as the average number.
-      blocksize = round(24 * 3600 * sf / 80 * chunksize)      
+      blocksize = round(24 * 3600 * sf / 80 * params_rawdata[["chunksize"]])      
     } else {
       blocksize = round(blocksize * 1.0043)
     }
@@ -17,7 +17,7 @@ get_nw_clip_block_params = function(chunksize, dynrange, monc, dformat, deviceSe
   if (monc == MONITOR$MOVISENS) blocksize = sf * 60 * 1440
   if (monc == MONITOR$VERISENSE && dformat == FORMAT$CSV) blocksize = round(blocksize)
 
-
+  dynrange = params_rawdata[["dynrange"]]
   if (monc == MONITOR$ACTIGRAPH) {
     # If Actigraph then try to specify dynamic range based on Actigraph model
     if (length(grep(pattern = "CLE", x = deviceSerialNumber)) == 1) {
@@ -38,20 +38,20 @@ get_nw_clip_block_params = function(chunksize, dynrange, monc, dformat, deviceSe
     if (monc == MONITOR$MOVISENS) {
       clipthres = 15.5 # hard coded assumption that dynamic range is 16g
     } else if (monc == MONITOR$AD_HOC) {
-      clipthres = rmc.dynamic_range
+      clipthres = params_rawdata[["rmc.dynamic_range"]]
     }
   }
   # Nonwear threshold: non-wear criteria are monitor-specific
-  racriter = 0.15 # very likely irrelevant parameters, but leave in for consistency
+  racriter = params_rawdata[["nonwear_range_threshold"]] / 1000
   sdcriter = 0.013
   #if (monc == MONITOR$GENEA) { sdcriter = 0.003;  racriter = 0.05 }
   if (monc == MONITOR$VERISENSE) {
     racriter = 0.20
   } else if (monc == MONITOR$AD_HOC) {
-    if (length(rmc.noise) == 0) {
+    if (length(params_rawdata[["rmc.noise"]]) == 0) {
       stop("Argument rmc.noise not specified, please specify expected noise level in g-units")
     }
-    sdcriter = rmc.noise * 1.2
+    sdcriter = params_rawdata[["rmc.noise"]] * 1.2
   }
   invisible(list(clipthres=clipthres, blocksize=blocksize, sdcriter=sdcriter, racriter=racriter))
 }

R/load_params.R

@@ -61,7 +61,7 @@ load_params = function(topic = c("sleep", "metrics", "rawdata",
       rmc.desiredtz = NULL, rmc.configtz = NULL,  rmc.sf = c(),
       rmc.headername.sf = c(), rmc.headername.sn = c(),
       rmc.headername.recordingid = c(), rmc.header.structure = c(),
-      rmc.check4timegaps = FALSE,  rmc.noise = 13,
+      rmc.check4timegaps = FALSE,  rmc.noise = 13, nonwear_range_threshold = 50,
       rmc.col.wear = c(), rmc.doresample = FALSE,
       interpolationType = 1,
       imputeTimegaps = TRUE, frequency_tol = 0.1, rmc.scalefactor.acc = 1)

man/GGIR.Rd

@@ -513,7 +513,8 @@ GGIR(mode = 1:5,
 
       \item{rmc.noise}{
         Numeric (default = 13).
-        Noise level of acceleration signal in m\emph{g}-units, used when working ad-hoc .csv data formats
+        Noise level of acceleration signal in m\emph{g}-units, used when working 
+        ad-hoc .csv data formats
         using \link{read.myacc.csv}. The \link{read.myacc.csv} does not take rmc.noise as argument,
         but when interacting with \link{GGIR} or \link{g.part1} rmc.noise is used.}
         
@@ -530,6 +531,11 @@ GGIR(mode = 1:5,
         by lack of movement with gravitational oriationed guessed from most recent
         valid data block. Only applicable to Axivity .cwa data.
       }
+      \item{nonwear_range_threshold}{
+        Numeric (default 150) used to define maximum value range per axis for non-wear
+        detection, used in combination with brand specific standard deviation per
+        axis.
+      }
       
     }
   }

man/get_nw_clip_block_params.Rd

@@ -9,16 +9,10 @@
   Not designed for direct use by user.
 }
 \usage{
-  get_nw_clip_block_params(chunksize, dynrange, monc, dformat, deviceSerialNumber,
-    rmc.noise=c(), sf, rmc.dynamic_range)
+  get_nw_clip_block_params(monc, dformat, deviceSerialNumber = "", sf,
+                            params_rawdata)
 }
 \arguments{
-  \item{chunksize}{
-    See \link{g.calibrate}
-  }
-  \item{dynrange}{
-    See \link{g.getmeta}
-  }
   \item{monc}{
     See \link{g.inspectfile}
   }
@@ -28,17 +22,11 @@
   \item{deviceSerialNumber}{
     As produced by \link{g.extractheadervars}
   }
-  \item{rmc.noise}{
-    Noise level of acceleration signal in _g_-units, used when working ad-hoc .csv data formats
-    using \link{read.myacc.csv}. The \link{read.myacc.csv} does not take rmc.noise as argument,
-    but when interacting with \link{GGIR} or \link{g.part1} rmc.noise is used.
-    There, rmc.noise is taken from the params_rawdata object if not explicitly specified by user.
-  }
-   \item{sf}{
+  \item{sf}{
     Numeric, sample frequency in Hertz
   }
-  \item{rmc.dynamic_range}{
-    Optional, please see \link{read.myacc.csv}
+  \item{params_rawdata}{
+    See \link{GGIR}
   }
 }
 \keyword{internal}

tests/testthat/test_load_check_params.R

@@ -13,7 +13,7 @@ test_that("load_params can load parameters", {
   expect_equal(length(params), 8)
   expect_equal(length(params$params_sleep), 22)
   expect_equal(length(params$params_metrics), 41)
-  expect_equal(length(params$params_rawdata), 38)
+  expect_equal(length(params$params_rawdata), 39)
   expect_equal(length(params$params_247), 22)
   expect_equal(length(params$params_cleaning), 24)
   expect_equal(length(params$params_phyact), 14)