migrate function for reading ActiGraph csv from GGIR to GGIRread #68

DESCRIPTION

@@ -22,7 +22,7 @@ URL: https://github.com/wadpac/GGIRread/
 BugReports: https://github.com/wadpac/GGIRread/issues
 License: Apache License (== 2.0)
 Suggests: testthat
-Imports: matlab, bitops, Rcpp (>= 0.12.10)
+Imports: matlab, bitops, Rcpp (>= 0.12.10), data.table
 Depends: stats, utils, R (>= 3.5.0)
 NeedsCompilation: yes
 LinkingTo: Rcpp

NAMESPACE

@@ -1,5 +1,9 @@
-export(readGenea, readAxivity, readGENEActiv, GENEActivReader, resample, readWav)
+export(readGenea, readAxivity, readGENEActiv, 
+       GENEActivReader, resample, readWav, 
+       readActiGraphCount)
 useDynLib(GGIRread, .registration = TRUE)
 importFrom(Rcpp, sourceCpp)
+importFrom(data.table, fread)
 importFrom("utils", "setTxtProgressBar", "txtProgressBar")
-importFrom("utils", "read.csv")
+importFrom("utils", "read.csv")
+importFrom("utils", "available.packages")

NEWS.md

@@ -2,6 +2,7 @@
 
 - Added a `NEWS.md` file to track changes to the package.
 - Stops interactive calling of `chooseCRANmirror` on `.onAttach` if interactive and CRAN mirror not set GGIR #1141.
+- Migrate read function for ActiGraph count data (csv) to GGIRread #68.
 
 # Changes in version 1.0.1 (release date:03-06-2024)
 

R/readActiGraphCount.R

@@ -0,0 +1,176 @@
+readActiGraphCount = function(filename = file, desiredEpochSize = NULL,
+                            timeformat = "%m/%d/%Y %H:%M:%S", tz = "") {
+  deviceSerialNumber = NULL
+  # Test if file has header by reading first ten rows
+  # and checking whether it contains the word
+  # serial number.
+  headerAvailable = FALSE
+  header = data.table::fread(
+    input = filename,
+    header = FALSE,
+    nrows = 10,
+    data.table = FALSE,
+    sep = ","
+  )
+  if (nrow(header) < 10) {
+    stop(paste0("File ", filename, " cannot be processed because it has less than ten rows"))
+  }
+  splitHeader = function(x) {
+    tmp = unlist(strsplit(x, " "))
+    item = gsub(
+      pattern = ":| ",
+      replacement = "",
+      x = paste0(tmp[1:(length(tmp) - 1)], collapse = "")
+    )
+    df = data.frame(item = tolower(item), value = tmp[length(tmp)])
+    return(df)
+  }
+  fileHeader = NULL
+  for (hh in header[2:9,1]) {
+    fileHeader = rbind(fileHeader, splitHeader(hh))
+  }
+  if (any(grepl("serialnumber", fileHeader$item))) headerAvailable = TRUE
+
+  # Depending on whether header is present assign number of rows to skip:
+  if (headerAvailable == TRUE) {
+    skip = 10
+  } else {
+    tmp = data.table::fread(input = filename,
+                            header = FALSE,
+                            data.table = FALSE,
+                            skip = 0,
+                            nrows = 1)
+    if (any(grepl("data|scoring", tmp[1,]))) {
+      skip = 1
+    } else {
+      skip = 0
+    }
+  }
+
+  # Check if file was exported with column names:
+  colnames = FALSE
+  colnames_test = data.table::fread(input = filename,
+                                    header = FALSE,
+                                    data.table = FALSE,
+                                    skip = skip,
+                                    nrows = 1)
+  if (any(grepl("Axis|vector magnitude|vm", colnames_test[1,], ignore.case = TRUE))) {
+    colnames = TRUE
+  }
+  # Increment skip if column names are present
+  Dtest = data.table::fread(input = filename,
+                            header = colnames,
+                            data.table = FALSE,
+                            skip = skip, nrows = 1)
+  if (length(grep(pattern = "time|date", x = Dtest[1, 1], ignore.case = TRUE)) > 0) {
+    skip = skip + 1
+  }
+  # Read all data from file
+  D = data.table::fread(input = filename,
+                        header = colnames,
+                        data.table = FALSE,
+                        skip = skip)
+
+  # Ignore time and date column if present
+  D = D[, grep(pattern = "time|date", x = Dtest[1, ], ignore.case = TRUE, invert = TRUE), drop = FALSE]
+  D = D[, grep(pattern = "time|date", x = colnames(Dtest), ignore.case = TRUE, invert = TRUE), drop = FALSE]
+  if (inherits(x = D[1,1], what = "POSIXt")) {
+    D = D[, -1, drop = FALSE]
+  }
+  # Identify columns with count data
+  acccol = vmcol = NA
+  if (colnames == TRUE) {
+    acccol = grep("axis|activity", colnames(D), ignore.case = TRUE)
+    vmcol = grep("vector magnitude|vm", colnames(D), ignore.case = TRUE)
+  } else {
+    # Then assume first 3 columns are axis1, axis2, axis3 if ncol(D) >= 3
+    # First column is VM if ncol(D) < 3
+    # Note that in ActiLife software the user can select
+    # the columns to export (e.g, it could be "Axis1", "Vector Magnitude", "Steps")
+    # which may mean that our assumptions here are not necessarily true.
+    if (ncol(D) >= 3) {
+      acccol = 1:3
+    } else {
+      vmcol = 1
+    }
+  }
+  # Assign colnames and formatting
+  if (is.na(acccol[1]) == FALSE) { 
+    colnames(D)[acccol] = c("y", "x", "z") # ActiGraph always stores y axis first
+  }
+  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("vm")
+  }
+  keep = c(acccol, vmcol)[!is.na(c(acccol, vmcol))]
+  D = D[, keep, drop = FALSE]
+  if (ncol(D) == 3 & is.na(vmcol)) {
+    D$vm = sqrt(D[,1]^2 + D[,2]^2 + D[,3]^2)
+  }
+  # Extract information from header, if present
+  if (headerAvailable == TRUE) {
+    deviceSerialNumber = fileHeader$value[grep(pattern = "serialnumber", x = fileHeader$item)]
+    epochSize = fileHeader$value[grep(pattern = "epochperiod|cycleperiod", x = fileHeader$item)]
+    epSizeShort = sum(as.numeric(unlist(strsplit(epochSize, ":"))) * c(3600, 60, 1))
+    starttime = fileHeader$value[grep(pattern = "starttime", x = fileHeader$item)]
+    startdate = fileHeader$value[grep(pattern = "startdate", x = fileHeader$item)]
+    timestamp = paste0(startdate, " ", starttime)
+    timestamp_POSIX = as.POSIXlt(timestamp, tz = tz,
+                                 format = timeformat)
+  } else if (headerAvailable == FALSE) {
+    # Extract date/timestamp from first values of column
+    tmp = data.table::fread(input = filename,
+                            header = colnames,
+                            data.table = FALSE,
+                            skip = skip,
+                            nrows = 2)
+    if (colnames == TRUE) {
+      datecol = grep("date", colnames(tmp), ignore.case = TRUE)
+      timecol = grep("time|epoch", colnames(tmp), ignore.case = TRUE)
+      time = tmp[, timecol]
+      date = tmp[, datecol]
+
+      starttime = time[1]
+      starttime = date[1]
+      timestamp = paste0(date, " ", time)
+      format = timeformat
+      timestamp_POSIX = as.POSIXlt(timestamp, tz = tz, format = format)
+      if (all(is.na(timestamp_POSIX))) {
+        stop(paste0("\nTimestamps are not available in the file, neither has",
+                    " it a header to extract the timestamps from. Therefore, the file",
+                    " cannot be processed.\n"))
+      }
+      epochSize = difftime(timestamp_POSIX[2], timestamp_POSIX[1], 
+                           units = "secs")
+      epSizeShort = as.numeric(epochSize)
+      timestamp_POSIX = timestamp_POSIX[1] # startTime
+    }
+  }
+  # Check timestamp is meaningful
+  if (all(is.na(timestamp_POSIX))) {
+    stop(paste0("\nTime format in data ", timestamp, " does not match with time format ",
+                timeformat,
+                " as specified by argument extEpochData_timeformat, please correct.\n"))
+  }
+  # If requested, aggregate data to lower resolution to match desired 
+  # epoch size in argument windowsizes
+  if (!is.null(desiredEpochSize)) {
+    if (desiredEpochSize > epSizeShort) {
+      step = desiredEpochSize %/% epSizeShort
+      D = rbind(rep(0, ncol(D)), D)
+      D = apply(D, 2, cumsum)
+      D = D[seq(1, nrow(D), by = step), , drop = FALSE]
+      D = apply(D, 2, diff)
+      epSizeShort = epSizeShort * step
+    }
+    if (epSizeShort != desiredEpochSize) {
+      stop(paste0("\nThe short epoch size as specified by the user as the first value of argument windowsizes (",
+                  desiredEpochSize,
+                  " seconds) does NOT match the short epoch size we see in the data (", epSizeShort),
+           " seconds). Please correct.", call. = FALSE)
+    }
+  }
+  invisible(list(data = D, epochSize = epSizeShort,
+                 startTime = timestamp_POSIX,
+                 deviceSerialNumber = deviceSerialNumber))
+}