Merge pull request #995 from wadpac/issue991_v3_tempcolumn_adhoccsv_c…

…alibration Extension to PR 993
wadpac · Dec 13, 2023 · 4e33a63 · 4e33a63
2 parents 55f233b + ee9d3df
commit 4e33a63
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 17 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -14,7 +14,7 @@
 
 - Part 5: Fix bug in recently added functionality for studying overlap between sibs and self-reported behaviours #989.
 
-- Part 1: Fix bug in adhoc-csv format calibration process as it could not extract temperature column #991
+- Part 1:Enable use of temperature data in adhoc-csv format throughout GGIR #991
 
 - Part 1: Fix bug that caused a mismatch between IDs and filenames in part 1 when movisens participant folders did not contain the acc.bin file #994.
 

diff --git a/R/convertEpochData.R b/R/convertEpochData.R
@@ -258,7 +258,7 @@ convertEpochData = function(datadir = c(), metadatadir = c(),
         }
         if (is.na(vmcol[1]) == FALSE) { 
           D = as.matrix(D, drop = FALSE) # convert to matrix as data.frame will auto-collapse to vector
-          colnames(D)[vmcol] = c("NeishabouriCount_vm")
+          colnames(D)[vmcol] = c("NeishabouriCount_x")
         }
         keep = c(acccol, vmcol)[!is.na(c(acccol, vmcol))]
         D = D[, keep, drop = FALSE]

diff --git a/R/g.getmeta.R b/R/g.getmeta.R
@@ -202,9 +202,9 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
     QClog = NULL
     if (temp.available == FALSE) {
       metalong = matrix(" ", ((nev/(sf*ws2)) + 100), 4) #generating output matrix for 15 minutes summaries
-    } else if (temp.available == TRUE && mon != MONITOR$MOVISENS) {
+    } else if (temp.available == TRUE && mon != MONITOR$MOVISENS && mon != MONITOR$AD_HOC) {
       metalong = matrix(" ", ((nev/(sf*ws2)) + 100), 7) #generating output matrix for 15 minutes summaries
-    } else if (temp.available == TRUE && mon == MONITOR$MOVISENS) {
+    } else if (temp.available == TRUE && (mon == MONITOR$MOVISENS || mon == MONITOR$AD_HOC)) {
       metalong = matrix(" ", ((nev/(sf*ws2)) + 100), 5) #generating output matrix for 15 minutes summaries
     }
     #===============================================
@@ -364,10 +364,10 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
           (mon == MONITOR$AXIVITY && dformat == FORMAT$CSV) ||
           (mon == MONITOR$AD_HOC && use.temp == FALSE)) {
         metricnames_long = c("timestamp","nonwearscore","clippingscore","en")
-      } else if (mon == MONITOR$GENEACTIV || (mon == MONITOR$AXIVITY && dformat == FORMAT$CWA) ||
-                 (mon == MONITOR$AD_HOC & use.temp == TRUE)) {
+      } else if (mon == MONITOR$GENEACTIV || (mon == MONITOR$AXIVITY && dformat == FORMAT$CWA)) {
         metricnames_long = c("timestamp","nonwearscore","clippingscore","lightmean","lightpeak","temperaturemean","EN")
-      } else if (mon == MONITOR$MOVISENS) {
+      } else if (mon == MONITOR$MOVISENS || (mon == MONITOR$AD_HOC & use.temp == TRUE)) { 
+        # at the moment read.myacc.csv does not facilitate extracting light data, so only temperature is used
         metricnames_long = c("timestamp","nonwearscore","clippingscore","temperaturemean","EN")
       }
       rm(SWMT)
@@ -424,7 +424,7 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
           } else if (mon == MONITOR$MOVISENS) {
             temperaturecolumn = 4
           } else if (mon == MONITOR$AD_HOC) {
-            temperaturecolumn = params_rawdata[["rmc.col.temp"]]
+            temperaturecolumn = which(colnames(data) == "temperature")
           }
           if (mon != MONITOR$AD_HOC && mon != MONITOR$MOVISENS) {
             light = as.numeric(data[, lightcolumn])
@@ -435,7 +435,6 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
           }
           temperature = as.numeric(data[, temperaturecolumn])
         }
-
         # Initialization of variables
         data_scaled = FALSE
         if (mon == MONITOR$ACTIGRAPH && dformat == FORMAT$GT3X) {
@@ -485,12 +484,6 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
               data = apply(data, 2,as.numeric)
             }
           }
-          if (ncol(data) >= 4 & mon == MONITOR$AD_HOC) {
-            columns_to_use = params_rawdata[["rmc.col.acc"]]
-          } else {
-            columns_to_use = 1:3
-          }
-          data = data[,columns_to_use]
           suppressWarnings(storage.mode(data) <- "numeric")
           if ((mon == MONITOR$ACTIGRAPH || mon == MONITOR$AD_HOC || mon == MONITOR$VERISENSE) && use.temp == FALSE) {
             data = scale(data,center = -offset, scale = 1/scale)  #rescale data
@@ -610,7 +603,7 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
         metalong[count2:((count2 - 1) + length(NWav)),col_mli] = NWav; col_mli = col_mli + 1
         metalong[(count2):((count2 - 1) + length(NWav)),col_mli] = CWav; col_mli = col_mli + 1
         if (mon == MONITOR$GENEACTIV || (mon == MONITOR$AXIVITY && dformat == FORMAT$CWA) || 
-            mon == MONITOR$MOVISENS) { # going from sample to ws2
+            mon == MONITOR$MOVISENS || (mon == MONITOR$AD_HOC && length(params_rawdata[["rmc.col.temp"]]) != 0)) { # going from sample to ws2
           if (mon == MONITOR$GENEACTIV || mon == MONITOR$AXIVITY) {
             #light (running mean)
             lightc = cumsum(c(0,light))
@@ -646,7 +639,7 @@ g.getmeta = function(datafile, params_metrics = c(), params_rawdata = c(),
           col_mli = col_mli + 1
           metalong[(count2):((count2 - 1) + length(NWav)), col_mli] = round(temperatureb, digits = n_decimal_places)
           col_mli = col_mli + 1
-        } else if (mon == MONITOR$MOVISENS) {
+        } else if (mon == MONITOR$MOVISENS || (mon == MONITOR$AD_HOC && length(params_rawdata[["rmc.col.temp"]]) != 0)) {
           metalong[(count2):((count2 - 1) + length(NWav)), col_mli] = round(temperatureb, digits = n_decimal_places)
           col_mli = col_mli + 1
         }