remove count aggregation (will do it in GGIR) and by that simplify re…

…ad functionality #68,

R/readActiGraphCount.R

@@ -1,4 +1,4 @@
-readActiGraphCount = function(filename = NULL, desiredEpochSize = NULL,
+readActiGraphCount = function(filename = NULL,
                             timeformat = "%m/%d/%Y %H:%M:%S", tz = "", timeformatName = "timeformat") {
   # In GGIR set timeformatName to extEpochData_timeformat
   deviceSerialNumber = NULL
@@ -168,18 +168,7 @@ readActiGraphCount = function(filename = NULL, desiredEpochSize = NULL,
   checkTimeFormat(timestamp_POSIX = timestamp_POSIX, rawValue = timestamp[1],
                   timeformat = timeformat,
                   timeformatName = timeformatName)
-
-
-  # 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 = matAggregate(D, step)
-      epSizeShort = epSizeShort * step
-    }
-    checkEpochMatch(desiredEpochSize, epSizeShort)
-  }
+
   invisible(list(data = D, epochSize = epSizeShort,
                  startTime = timestamp_POSIX,
                  deviceSerialNumber = deviceSerialNumber))

R/readActicalCount.R

@@ -1,4 +1,4 @@
-readActicalCount = function(filename = NULL, desiredEpochSize = NULL,
+readActicalCount = function(filename = NULL,
                             timeformat = "%m/%d/%Y %H:%M:%S", tz = "",
                             timeformatName = "timeformat") {
   # In GGIR set timeformatName to extEpochData_timeformat
@@ -51,16 +51,7 @@ readActicalCount = function(filename = NULL, desiredEpochSize = NULL,
   D = D[, -which(colnames(D) %in% c("date", "time"))]
   D = as.matrix(D, drop = FALSE)
   if (quote == "") D = apply(D, 2, as.numeric)
-  # 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 = matAggregate(D, step)
-      epSizeShort = epSizeShort * step
-    }
-    checkEpochMatch(desiredEpochSize, epSizeShort)
-  }
+
   invisible(list(data = D, epochSize = epSizeShort,
                  startTime = timestamp_POSIX))
 }

R/readActiwatchCount.R

@@ -1,4 +1,4 @@
-readActiwatchCount = function(filename = NULL, desiredEpochSize = NULL,
+readActiwatchCount = function(filename = NULL,
                             timeformat = "%m/%d/%Y %H:%M:%S", tz = "",
                             timeformatName = "timeformat") {
   # In GGIR set timeformatName to extEpochData_timeformat
@@ -86,17 +86,7 @@ readActiwatchCount = function(filename = NULL, desiredEpochSize = NULL,
 
   }
   D = as.matrix(D, drop = FALSE)
-  if (quote == "") D = apply(D, 2, as.numeric)  
-  # 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 = matAggregate(D, step)
-      epSizeShort = epSizeShort * step
-    }
-    checkEpochMatch(desiredEpochSize, epSizeShort)
-  }
+  if (quote == "") D = apply(D, 2, as.numeric)
   invisible(list(data = D, epochSize = epSizeShort,
                  startTime = timestamp_POSIX))
 }

R/utils_for_countdata.R

@@ -25,17 +25,6 @@ checkTimeFormat = function(timestamp_POSIX, rawValue = " ?? ", timeformat = " ??
   }
 }
 
-checkEpochMatch = function(desiredEpochSize, epSizeShort) {
-  # Check whether desired and derived epoch size match
-  if (!is.null(desiredEpochSize) && epSizeShort != desiredEpochSize) {
-    stop(paste0("\nThe short epoch size as specified by the user (",
-                desiredEpochSize, " seconds) does NOT match the short",
-                " epoch size we see in the data (", epSizeShort,
-                " seconds). Please correct."), call. = FALSE)
-  }
-  return()
-}
-
 detectQuote = function(fn, index) {
   # data.table::fread has argument quote.
   # On some computers the quotes in the files are
@@ -62,24 +51,7 @@ getExtension <- function(filename){
   return(ex[-1])
 }
 
-matAggregate = function(mat, step) {
-  # Aggregate matrix mat by taking over step number of rows
-  # as sum unless column names is sleep or nonwear in that case 
-  # we take the rounded mean.
-  mat = rbind(rep(0, ncol(mat)), mat)
-  cumsum2 = function(x) {
-    x = cumsum(ifelse(is.na(x), 0, x)) + x*0
-    return(x)
-  }
-  mat = apply(mat, 2, cumsum2)
-  mat = mat[seq(1, nrow(mat), by = step), , drop = FALSE]
-  mat = apply(mat, 2, diff)
-  # Correct non incremental variables
-  for (niv in c("sleep", "nonwear")) {
-    if (niv %in% colnames(D)) D[, niv] = round(D[, niv] / step)
-  }
-  return(mat)
-}
+
 
 findStartData = function(filename, quote, startindex) {
   # Function used to find start of time series in Actiwatch and Actical data

man/readActiGraphCount.Rd

@@ -7,18 +7,14 @@
   Reads ActiGraph Count data file. Currently a variety of csv format are facilitated.
 }
 \usage{
-  readActiGraphCount(filename = NULL, desiredEpochSize = NULL,
+  readActiGraphCount(filename = NULL,
                             timeformat = "\%m/\%d/\%Y \%H:\%M:\%S", tz = "",
                             timeformatName = "timeformat")
 }
 \arguments{
   \item{filename}{
     filename (required)
   }
-  \item{desiredEpochSize}{
-    Numeric, desired epoch size in seconds. If set aggregate data by summation to
-    this epochsize.
-  }
   \item{timeformat}{
     Character, timestemp format.
   }

man/readActicalCount.Rd

@@ -7,18 +7,14 @@
   Reads Actical Count data file.
 }
 \usage{
-  readActicalCount(filename = NULL, desiredEpochSize = NULL,
+  readActicalCount(filename = NULL,
                             timeformat = "\%m/\%d/\%Y \%H:\%M:\%S", tz = "",
                             timeformatName = "timeformat")
 }
 \arguments{
   \item{filename}{
     filename (required)
   }
-  \item{desiredEpochSize}{
-    Numeric, desired epoch size in seconds. If set aggregate data by summation to
-    this epochsize.
-  }
   \item{timeformat}{
     Character, timestemp format.
   }

man/readActiwatchCount.Rd

@@ -7,18 +7,14 @@
   Reads Actiwatch Count data file. Currently a variety of csv format are facilitated.
 }
 \usage{
-  readActiwatchCount(filename = NULL, desiredEpochSize = NULL,
+  readActiwatchCount(filename = NULL,
                             timeformat = "\%m/\%d/\%Y \%H:\%M:\%S", tz = "",
                             timeformatName = "timeformat")
 }
 \arguments{
   \item{filename}{
     filename (required)
   }
-  \item{desiredEpochSize}{
-    Numeric, desired epoch size in seconds. If set aggregate data by summation to
-    this epochsize.
-  }
   \item{timeformat}{
     Character, timestemp format.
   }

tests/testthat/test_readActiGraphCount.R

@@ -2,16 +2,7 @@ library(GGIRread)
 context("read ActiGraph csv files")
 test_that("ActiGraph61 is correctly read", {
   file = system.file("testfiles/ActiGraph61.csv", package = "GGIRread")
-  D = readActiGraphCount(filename = file, desiredEpochSize = 10, timeformat = "%m/%d/%Y %H:%M:%S", tz =  "")
-  expect_equal(D$deviceSerialNumber, "MOS2D16160581")
-  expect_equal(D$epochSize, 10)
-  expect_equal(format(D$startTime), "2016-08-15 21:35:00")
-  expect_equal(nrow(D$data), 495)
-  expect_equal(ncol(D$data), 5)
-  expect_equal(sum(D$data[, c("y", "x", "z", "vm")]), 63952.33)
-  expect_equal(sum(D$data[, c("steps")]), 253)
-
-  D = readActiGraphCount(filename = file, desiredEpochSize = 5, timeformat = "%m/%d/%Y %H:%M:%S", tz =  "")
+  D = readActiGraphCount(filename = file, timeformat = "%m/%d/%Y %H:%M:%S", tz =  "")
   expect_equal(D$deviceSerialNumber, "MOS2D16160581")
   expect_equal(D$epochSize, 5)
   expect_equal(format(D$startTime), "2016-08-15 21:35:00")
@@ -23,55 +14,31 @@ test_that("ActiGraph61 is correctly read", {
 
 test_that("ActiGraph31 is correctly read", {
   file = system.file("testfiles/ActiGraph13.csv", package = "GGIRread")
-  D = readActiGraphCount(filename = file, desiredEpochSize = 15, timeformat = "%m/%d/%Y %H:%M:%S", tz =  "")
+  D = readActiGraphCount(filename = file, timeformat = "%m/%d/%Y %H:%M:%S", tz =  "")
   expect_equal(D$deviceSerialNumber, "CLE2A2123456")
   expect_equal(D$epochSize, 15)
   expect_equal(format(D$startTime), "2013-08-26 09:00:00")
   expect_equal(nrow(D$data), 990)
   expect_equal(ncol(D$data), 5)
   expect_equal(sum(D$data[, c("y", "x", "z", "vm")]), 272870.6, tol = 0.1)
   expect_equal(sum(D$data[, c("steps")]), 1118)
-
-  D = readActiGraphCount(filename = file, desiredEpochSize = 30, timeformat = "%m/%d/%Y %H:%M:%S", tz =  "")
-  expect_equal(D$deviceSerialNumber, "CLE2A2123456")
-  expect_equal(D$epochSize, 30)
-  expect_equal(format(D$startTime), "2013-08-26 09:00:00")
-  expect_equal(nrow(D$data), 495)
-  expect_equal(ncol(D$data), 5)
-  expect_equal(sum(D$data[, c("y", "x", "z", "vm")]), 272870.6, tol = 0.1)
-  expect_equal(sum(D$data[, c("steps")]), 1118)
-
 })
 
 test_that("ActiGraph13_timestamps_headers.csv is correctly read", {
   file = system.file("testfiles/ActiGraph13_timestamps_headers.csv", package = "GGIRread")
-  D = readActiGraphCount(filename = file, desiredEpochSize = 1, timeformat = "%d-%m-%Y %H:%M:%S", tz =  "")
+  D = readActiGraphCount(filename = file, timeformat = "%d-%m-%Y %H:%M:%S", tz =  "")
   expect_equal(D$deviceSerialNumber, "TAS1D48140206")
   expect_equal(D$epochSize, 1)
   expect_equal(format(D$startTime), "2017-12-09 15:00:00")
   expect_equal(nrow(D$data), 1000)
   expect_equal(ncol(D$data), 5)
   expect_equal(sum(D$data[, c("y", "x", "z", "vm")]), 255707.4, tol = 0.1)
   expect_equal(sum(D$data[, c("steps")]), 442)
-
-  D = readActiGraphCount(filename = file, desiredEpochSize = 5, timeformat = "%d-%m-%Y %H:%M:%S", tz =  "")
-  expect_equal(D$deviceSerialNumber, "TAS1D48140206")
-  expect_equal(D$epochSize, 5)
-  expect_equal(format(D$startTime), "2017-12-09 15:00:00")
-  expect_equal(nrow(D$data), 200)
-  expect_equal(ncol(D$data), 5)
-  expect_equal(sum(D$data[, c("y", "x", "z", "vm")]), 255707.4, tol = 0.1)
-  expect_equal(sum(D$data[, c("steps")]), 442)
 })
 
 test_that("Actiwatch csv error correctly", {
   file = system.file("testfiles/ActiGraph13_timestamps_headers.csv", package = "GGIRread")
   expect_error(readActiGraphCount(filename = file,
-                                  desiredEpochSize = 5,
                                   timeformat = "%m/%d/%Y %H:%M:%S"),
                regexp = "Time format*")
-  expect_error(readActiGraphCount(filename = file,
-                                  desiredEpochSize = 0.5,
-                                  timeformat = "%d-%m-%Y %H:%M:%S"),
-               regexp = "The short*")
 })

tests/testthat/test_readActicalCount.R

@@ -2,30 +2,17 @@ library(GGIRread)
 context("read Actical files")
 test_that("Actical csv is correctly read", {
   file = system.file("testfiles/Actical.csv", package = "GGIRread")
-  D = readActicalCount(filename = file, desiredEpochSize = 60, timeformat = "%d-%b-%y %H:%M", tz =  "")
+  D = readActicalCount(filename = file, timeformat = "%d-%b-%y %H:%M", tz =  "")
   expect_equal(D$epochSize, 60)
   expect_equal(format(D$startTime), "2021-05-13")
   expect_equal(nrow(D$data), 501)
   expect_equal(ncol(D$data), 2)
   expect_equal(sum(D$data, na.rm = TRUE), 8436)
-
-  D = readActicalCount(filename = file, desiredEpochSize = 120, timeformat = "%d-%b-%y %H:%M", tz =  "")
-  expect_equal(D$epochSize, 120)
-  expect_equal(format(D$startTime), "2021-05-13")
-  expect_equal(nrow(D$data), 250)
-  expect_equal(ncol(D$data), 2)
-  expect_equal(sum(D$data, na.rm = TRUE), 8436)
 })
 
 test_that("Actical csv error correctly", {
   file = system.file("testfiles/Actical.csv", package = "GGIRread")
   expect_error(readActicalCount(filename = file, 
-                                desiredEpochSize = 60,
                                 timeformat = "%d/%m/%Y %H:%M", tz =  ""),
                regexp = "Time format*")
-
-  expect_error(readActicalCount(filename = file,
-                                desiredEpochSize = 5,
-                                timeformat = "%d-%b-%y %H:%M", tz =  ""),
-               regexp = "The short*")
 })

tests/testthat/test_readActiwatchCount.R

@@ -2,63 +2,39 @@ library(GGIRread)
 context("read Actiwatch files")
 test_that("Actiwatch csv is correctly read", {
   file = system.file("testfiles/Actiwatch.csv", package = "GGIRread")
-  D = readActiwatchCount(filename = file, desiredEpochSize = 15, timeformat = "%d/%m/%Y %H:%M:%S", tz =  "")
+  D = readActiwatchCount(filename = file, timeformat = "%d/%m/%Y %H:%M:%S", tz =  "")
   expect_equal(D$epochSize, 15)
   expect_equal(format(D$startTime), "2019-11-23 06:00:00")
   expect_equal(nrow(D$data), 860)
   expect_equal(ncol(D$data), 3)
   expect_equal(sum(D$data[, "counts"], na.rm = TRUE), 4589)
   expect_equal(sum(D$data[, "sleep"], na.rm = TRUE), 55)
   expect_equal(sum(D$data[, "nonwear"], na.rm = TRUE), 797)
-
-  D = readActiwatchCount(filename = file, desiredEpochSize = 30, timeformat = "%d/%m/%Y %H:%M:%S", tz =  "")
-  expect_equal(D$epochSize, 30)
-  expect_equal(format(D$startTime), "2019-11-23 06:00:00")
-  expect_equal(nrow(D$data), 430)
-  expect_equal(ncol(D$data), 3)
-  expect_equal(sum(D$data[, "counts"], na.rm = TRUE), 4569)
-  expect_equal(sum(D$data[, "sleep"], na.rm = TRUE), 54)
-  expect_equal(sum(D$data[, "nonwear"], na.rm = TRUE), 797)
 })
 test_that("Actiwatch awd is correctly read", {
   file = system.file("testfiles/Actiwatch.AWD", package = "GGIRread")
-  D = readActiwatchCount(filename = file, desiredEpochSize = 60, timeformat = "%d-%b-%Y %H:%M:%S", tz =  "")
+  D = readActiwatchCount(filename = file, timeformat = "%d-%b-%Y %H:%M:%S", tz =  "")
   expect_equal(D$epochSize, 60)
   expect_equal(format(D$startTime), "2009-10-01 17:00:00")
   expect_equal(nrow(D$data), 329)
   expect_equal(ncol(D$data), 2)
   expect_equal(sum(D$data[, "counts"], na.rm = TRUE), 108864)
   expect_equal(sum(D$data[, "light"], na.rm = TRUE), 0)
-
-  D = readActiwatchCount(filename = file, desiredEpochSize = 300, timeformat =  "%d-%b-%Y %H:%M:%S", tz =  "")
-  expect_equal(D$epochSize, 300)
-  expect_equal(format(D$startTime), "2009-10-01 17:00:00")
-  expect_equal(nrow(D$data), 65)
-  expect_equal(ncol(D$data), 2)
-  expect_equal(sum(D$data[, "counts"], na.rm = TRUE), 108713)
-  expect_equal(sum(D$data[, "light"], na.rm = TRUE), 0)
 })
 
 test_that("Actiwatch awd error correctly", {
   file = system.file("testfiles/Actiwatch.AWD", package = "GGIRread")
   expect_error(readActiwatchCount(filename = file,
-                                  desiredEpochSize = 60,
                                   timeformat = "%d-%m-%Y %H:%M:%S"),
                regexp = "Time format*")
 
-  expect_error(readActiwatchCount(filename = file,
-                                  desiredEpochSize = 5,
-                                  timeformat = "%d-%b-%Y %H:%M:%S"),
-               regexp = "The short*")
-
   expect_error(readActiwatchCount(filename = "",
-                                  desiredEpochSize = 60,
                                   timeformat = "%d-%b-%Y %H:%M:%S"),
                regexp = "Cannot")
 
 })
 
-test_that("checkTimeFormat also detect implausible year", {
+test_that("checkTimeFormat also detects implausible year", {
   rawValue = "6/28/21 10:10:10"
   timeformat = "%m/%d/%y %H:%M:%S"
   timestamp_POSIX = as.POSIXlt("6/28/21 10:10:10", format = "%m/%d/%Y %H:%M:%S")