migrate utils functions to their own function files #68

R/checkTimeFormat.R

@@ -0,0 +1,22 @@
+checkTimeFormat = function(timestamp_POSIX, rawValue = " ?? ", timeformat = " ?? ",
+                           timeformatName = NULL) {
+  # If timestamp_POSIX is NA gieve error message to inform user that something went wrong.
+  if (is.na(timestamp_POSIX)) {
+    stop(paste0("\nTime format in data ", rawValue, 
+                " does not match with time format ", timeformat,
+                " as specified by argument ", timeformatName,
+                ", please correct.\n"), call. = FALSE)
+  } else {
+    year = as.numeric(format(timestamp_POSIX, format = "%Y"))
+    if (year < 1980 || year > 2500) {
+      # Assumption that after 2500 no new ActiGraph data will be collected!
+      stop(paste0("\nTimestamp recognised as ", format(timestamp_POSIX), 
+                  " with year identified as ", year,
+                  ". This does not seem to be correct. Raw timestamp value is stored as ",
+                  rawValue, ". please change specification of ",
+                  "argument ", timeformatName, " (currently ",
+                  timeformat, ") to ensure correct interpretation of timestamp.\n"),
+           call. = FALSE)
+    }
+  }
+}

R/detectQuote.R

@@ -0,0 +1,18 @@
+detectQuote = function(filename, skip) {
+  # data.table::fread has argument quote.
+  # On some computers the quotes in the files are
+  # not recognised, to catch this first try to check whether this is the case:
+  quote = "\""
+  Dtest = NULL
+  try(expr = {Dtest = data.table::fread(input = filename,
+                                        header = FALSE, sep = ",", skip = skip,
+                                        nrows = 20, quote = quote)}, silent = TRUE)
+  if (length(Dtest) == 0) {
+    quote = ""
+  } else {
+    if (nrow(Dtest) <= 1) {
+      quote = "" 
+    }
+  }
+  return(quote)
+}

R/findStartData.R

@@ -0,0 +1,32 @@
+findStartData = function(filename, quote, startindex) {
+  # Function used to find start of time series in Actiwatch and Actical data
+  # ! Assumptions that timeseries start before line 1000
+  while (startindex > 0) {
+    testraw = data.table::fread(input = filename,
+                                header = FALSE, sep = ",", skip = startindex,
+                                nrows = 2, data.table = FALSE, quote = quote)
+    if (length(testraw) > 0) {
+      if (nrow(testraw) == 2) {
+        if (testraw$V1[2] == testraw$V1[1] + 1) {
+          break
+        }
+      }
+    }
+    startindex = startindex - 100
+  }
+  # ! Assumption that first column are the epoch numbers
+  delta = 1 - testraw$V1[1]
+  startindex = startindex + delta
+  startFound = FALSE
+  while (startFound == FALSE) {
+    Dtest = data.table::fread(input = filename, sep = ",", skip = startindex, quote = quote, nrows = 1)
+    if (Dtest$V1[1] == 1) {
+      startFound = TRUE
+    } else {
+      # This happens when file is has an empty row between each measurement point is stored
+      startindex = startindex - 1
+      if (startindex < 1) stop("Could not find start of recording", call. = FALSE)
+    }
+  }
+  return(startindex)
+}

R/getExtension.R

@@ -0,0 +1,9 @@
+getExtension <- function(filename){ 
+  # Extract file extension
+  ex <- unlist(strsplit(basename(filename), split = "[.]"))
+  if (length(ex) < 2) stop(paste0("Cannot recognise extension from '", filename, "' as filename, please check"), call. = FALSE)
+  return(ex[-1])
+}
+
+
+

R/readActicalCount.R

@@ -7,7 +7,7 @@ readActicalCount = function(filename = NULL,
   if (length(configtz) == 0) configtz = desiredtz
   # ! Assumptions that timeseries start before line 1000
   startindex = 300
-  quote = detectQuote(fn = filename, index = startindex)
+  quote = detectQuote(filename = filename, skip = startindex)
   startindex = findStartData(filename, quote, startindex)
   # -1 because Actical starts at epoch 0 while function looks for epoch 1
   startindex = startindex - 1 

R/readActiwatchCount.R

@@ -14,7 +14,7 @@ readActiwatchCount = function(filename = NULL,
     #=========================================================
     # ! Assumptions that timeseries start before line 1000
     startindex = 1000
-    quote = detectQuote(fn = filename, index = startindex)
+    quote = detectQuote(filename = filename, skip = startindex)
     index = findStartData(filename, quote, startindex)
     D = data.table::fread(input = filename, sep = ",", skip = index, quote = quote, data.table = FALSE)
     # ! Assumption that column names are present 2 lines prior to timeseries
@@ -55,7 +55,7 @@ readActiwatchCount = function(filename = NULL,
     # ! Assumption that first data row equals the first row with 3 columns
     index = 0
 
-    quote = detectQuote(fn = filename, index = 50)
+    quote = detectQuote(filename = filename, skip = 50)
     NC = 1
     while (NC >= 3) {
       testraw = data.table::fread(input = filename,

man/checkTimeFormat.Rd

@@ -0,0 +1,36 @@
+\name{checkTimeFormat}
+\alias{checkTimeFormat}
+\title{
+  Check timestamp format
+}
+\description{
+  Helper function used internally. Generate informative error message if timestamp
+  could not be recognisede.
+}
+\usage{
+  checkTimeFormat(timestamp_POSIX, rawValue = " ?? ", timeformat = " ?? ",
+                           timeformatName = NULL)
+}
+\arguments{
+  \item{timestamp_POSIX}{
+    POSIX object with timestamp
+  }
+  \item{rawValue}{
+    Timestamp value as encounterd in the data before processing
+  }
+  \item{timeformat}{
+    Timestap format used for converting timestamp
+  }
+  \item{timeformatName}{
+    Character with the argument name to specify the timeformat.
+    If used as dependency of GGIR then this argument name will be different.
+  }
+}
+\value{
+  No output value is generated, only an error message if timestamp could not be
+  recognised.
+}
+\keyword{internal}
+\author{
+  Vincent T van Hees <v.vanhees@accelting.com>
+}

man/detectQuote.Rd

@@ -0,0 +1,27 @@
+\name{detectQuote}
+\alias{detectQuote}
+\title{
+  Detect quote
+}
+\description{
+  Helper function used internally, used to find out what value should
+  be used for argument quote in function fread.
+}
+\usage{
+  detectQuote(filename, skip)
+}
+\arguments{
+  \item{filename}{
+    Character
+  }
+  \item{skip}{
+    skip
+  }
+}
+\value{
+  Character with quote object to be used for fread
+}
+\keyword{internal}
+\author{
+  Vincent T van Hees <v.vanhees@accelting.com>
+}

man/findStartData.Rd

@@ -0,0 +1,31 @@
+\name{findStartData}
+\alias{findStartData}
+\title{
+  Find start of data inside text file.
+}
+\description{
+  Helper function used internally. Finds variables start of the data in 
+  Actiwatch and Actical data.
+}
+\usage{
+  findStartData(filename, quote, startindex)
+}
+\arguments{
+  \item{filename}{
+    Character
+  }
+  \item{quote}{
+    Quote as extracted with \link{detectQuote}
+  }
+  \item{startindex}{
+    Start index where to start searching. For Actical we start at 300 while
+    for Actiwatch we start at 1000.
+  }
+}
+\value{
+  Start index
+}
+\keyword{internal}
+\author{
+  Vincent T van Hees <v.vanhees@accelting.com>
+}

man/getExtension.Rd

@@ -0,0 +1,23 @@
+\name{getExtension}
+\alias{getExtension}
+\title{
+  Get File Extension
+}
+\description{
+  Helper function used internally to get file extension.
+}
+\usage{
+  getExtension(filename)
+}
+\arguments{
+  \item{filename}{
+    Character
+  }
+}
+\value{
+  Character with file extension
+}
+\keyword{internal}
+\author{
+  Vincent T van Hees <v.vanhees@accelting.com>
+}