From cc12bf832949ca5201a6f4249fa5b1ecf8829eb9 Mon Sep 17 00:00:00 2001
From: l-k- <alenka0000@hotmail.com>
Date: Wed, 13 Dec 2023 01:25:16 -0500
Subject: [PATCH] Enable g.calibrate to handle temperature data from ad-hoc csv
 file

---
 NEWS.md         |  2 ++
 R/g.calibrate.R | 19 ++++++++++---------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 0c0097049..9812ab8bc 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,6 +8,8 @@
 
 - Part 5: Fix bug in recently added fucntionality for studying overlap between sibs and self-reported beahviours #989.
 
+- Part 1: Fix bug in adhoc-csv format calibration process as it could not extract temperature column #991
+
 # CHANGES IN GGIR VERSION 3.0-1
 
 - Part 2: Added option to provide a csv file with start and end dates when accelerometer is expected to be worn #943
diff --git a/R/g.calibrate.R b/R/g.calibrate.R
index 96353164a..f6888696c 100644
--- a/R/g.calibrate.R
+++ b/R/g.calibrate.R
@@ -141,11 +141,17 @@ g.calibrate = function(datafile, params_rawdata = c(),
           data = P$data
         }
       } else if (dformat == FORMAT$AD_HOC_CSV) {
-        if (length(params_rawdata[["rmc.col.time"]]) > 0 && mon == MONITOR$AD_HOC) {
+        if ("timestamp" %in% colnames(P$data)) {
           columns_to_use = 2:4
         } else {
           columns_to_use = 1:3
         }
+        if ("temperature" %in% colnames(P$data)) {
+          columns_to_use = c(columns_to_use, which(colnames(P$data) == "temperature"))
+          use.temp = TRUE
+        } else {
+          use.temp = FALSE
+        }
         data = P$data[, columns_to_use]
       } else if (dformat == FORMAT$GT3X) {
         data = as.matrix(P[,2:4])
@@ -193,13 +199,8 @@ g.calibrate = function(datafile, params_rawdata = c(),
           } else if (mon == MONITOR$MOVISENS) {
             Gx = data[,1]; Gy = data[,2]; Gz = data[,3]
             use.temp = TRUE
-          } else if (mon == MONITOR$AD_HOC && dformat == FORMAT$AD_HOC_CSV && length(params_rawdata[["rmc.col.temp"]]) > 0) { # ad-hoc format csv with temperature
-            Gx = as.numeric(data[,1]); Gy = as.numeric(data[,2]); Gz = as.numeric(data[,3])
-            temperature = as.numeric(data[, params_rawdata[["rmc.col.temp"]]])
-            use.temp = TRUE
-          } else if (mon == MONITOR$AD_HOC && dformat == FORMAT$AD_HOC_CSV && length(params_rawdata[["rmc.col.temp"]]) == 0) { # ad-hoc format csv without temperature
+          } else if (dformat == FORMAT$AD_HOC_CSV) {
             Gx = as.numeric(data[,1]); Gy = as.numeric(data[,2]); Gz = as.numeric(data[,3])
-            use.temp = FALSE
           } else if (dformat == FORMAT$CSV && mon != MONITOR$AXIVITY) { # csv and not AX (so, GENEAcitv)
             data2 = matrix(NA,nrow(data),3)
             if (ncol(data) == 3) extra = 0
@@ -220,8 +221,8 @@ g.calibrate = function(datafile, params_rawdata = c(),
           } else if (mon == MONITOR$AXIVITY && dformat == FORMAT$CWA) {
             temperaturecolumn = 5
             temperature = as.numeric(data[,temperaturecolumn])
-          } else if (mon == MONITOR$AD_HOC && use.temp == TRUE) {
-            temperaturecolumn = params_rawdata[["rmc.col.temp"]]
+          } else if (dformat == FORMAT$AD_HOC_CSV && use.temp == TRUE) {
+            temperaturecolumn = 4
             temperature = as.numeric(data[,temperaturecolumn])
           } else if (mon == MONITOR$ACTIGRAPH) {
             use.temp = FALSE