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Enable g.calibrate to handle temperature data from ad-hoc csv file #992

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Enable g.calibrate to handle temperature data from ad-hoc csv file #992

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2 changes: 2 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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14 changes: 4 additions & 10 deletions R/g.calibrate.R
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Expand Up @@ -141,12 +141,7 @@
data = P$data
}
} else if (dformat == FORMAT$AD_HOC_CSV) {
if (length(params_rawdata[["rmc.col.time"]]) > 0 && mon == MONITOR$AD_HOC) {
columns_to_use = 2:4
} else {
columns_to_use = 1:3
}
data = P$data[, columns_to_use]
data = P$data[, c(params_rawdata[["rmc.col.acc"]], params_rawdata[["rmc.col.temp"]])]

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@l-k- l-k- Dec 13, 2023 •
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I think this might actually be incorrect?

We get P$data from read.myacc.csv, and there it gets populated with columns c("timestamp","accx","accy","accz","temperature"), in that exact order. You can see it here:
https://github.com/wadpac/GGIR/blob/master/R/read.myacc.csv.R#L172-L179

So it doesn't matter where the acceleration and temperature columns were located in the original csv file. P$data$temperature is always 4th or 5th column (depending on whether there is a timestamp column), no matter what params_rawdata[["rmc.col.temp"]] value was. And acceleration columns are always either 1:3 or 2:4, no matter what params_rawdata[["rmc.col.acc"]] values were.

It was just a coincidence that our test file had rmc.col.acc = 2:4, rmc.col.temp = 5, like what read.myacc.csv produces.

I'll send an alternative PR in a bit.

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Thanks for spotting that Lena, I will now close this PR.

} else if (dformat == FORMAT$GT3X) {
data = as.matrix(P[,2:4])
}
Expand Down Expand Up @@ -195,7 +190,6 @@
use.temp = TRUE
} else if (mon == MONITOR$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
Gx = as.numeric(data[,1]); Gy = as.numeric(data[,2]); Gz = as.numeric(data[,3])
Expand All @@ -205,11 +199,10 @@
if (ncol(data) == 3) extra = 0
if (ncol(data) >= 4) extra = 1
for (jij in 1:3) {
data2[,jij] = data[,(jij+extra)]
data2[, jij] = data[, (jij + extra)]
}
Gx = data[,1]; Gy = data[,2]; Gz = data[,3]
}

if (mon == MONITOR$GENEACTIV) {
if ("temperature" %in% colnames(data)) {
temperaturecolumn = which(colnames(data) == "temperature") #GGIRread
Expand All @@ -221,7 +214,8 @@
temperaturecolumn = 5
temperature = as.numeric(data[,temperaturecolumn])
} else if (mon == MONITOR$AD_HOC && use.temp == TRUE) {
temperaturecolumn = params_rawdata[["rmc.col.temp"]]
temperaturecolumn = which(names(data) == "temperature")
if (length(temperaturecolumn) == 0) temperaturecolumn = 4

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temperature = as.numeric(data[,temperaturecolumn])
} else if (mon == MONITOR$ACTIGRAPH) {
use.temp = FALSE
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