Merge pull request #872 from wadpac/issue871_cleanup_part5

Clean up g.part5()

NAMESPACE

@@ -38,7 +38,8 @@ export(g.analyse, g.calibrate,
        detect_nonwear_clipping,
        ShellDoc2Vignette, parametersVignette,
        correctOlderMilestoneData,
-       convertEpochData, appendRecords, extractID)
+       convertEpochData, appendRecords, extractID,
+       g.part5_analyseSegment, g.part5_initialise_ts)
 importFrom("grDevices", "colors", "dev.off", "pdf","rainbow","rgb")
 importFrom("graphics", "abline", "axis", "par", "plot", "plot.new",
            "rect","axis.POSIXct", "barplot", "box", "legend",

R/g.part5_initialise_ts.R

@@ -0,0 +1,58 @@
+g.part5_initialise_ts = function(IMP, M, params_247, params_general) {
+
+  # extract key variables from the mile-stone data: time, acceleration and elevation angle
+  # note that this is imputed ACCELERATION because we use this for describing behaviour:
+  scale = ifelse(test = grepl("^Brond|^Neishabouri|^ZC", params_general[["acc.metric"]]), yes = 1, no = 1000)
+  # if (length(which(names(IMP$metashort) == "anglez")) == 0 & verbose == TRUE) {
+  #   cat("Warning: anglez not extracted. Please check that do.anglez == TRUE")
+  # }
+
+  if ("anglez" %in% names(IMP$metashort)) {
+    ts = data.frame(time = IMP$metashort[,1], ACC = IMP$metashort[,params_general[["acc.metric"]]] * scale,
+                    guider = rep("unknown", nrow(IMP$metashort)),
+                    angle = as.numeric(as.matrix(IMP$metashort[,which(names(IMP$metashort) == "anglez")])))
+  } else {
+    ts = data.frame(time = IMP$metashort[,1], ACC = IMP$metashort[,params_general[["acc.metric"]]] * scale,
+                    guider = rep("unknown", nrow(IMP$metashort)))
+  }
+  Nts = nrow(ts)
+  # add non-wear column
+  nonwear = IMP$rout[,5]
+  nonwear = rep(nonwear, each = (IMP$windowsizes[2]/IMP$windowsizes[1]))
+  if (length(nonwear) > Nts) {
+    nonwear = nonwear[1:Nts]
+  } else if (length(nonwear) < Nts) {
+    nonwear = c(nonwear, rep(0, (Nts - length(nonwear))))
+  }
+  ts$nonwear = 0 # initialise column
+  ts$nonwear = nonwear
+  lightpeak_available = "lightpeak" %in% colnames(M$metalong)
+  # Check if temperature and light are availble
+  if (lightpeak_available == TRUE) {
+    luz = M$metalong$lightpeak
+    if (length(params_247[["LUX_cal_constant"]]) > 0 &
+        length(params_247[["LUX_cal_exponent"]]) > 0) { # re-calibrate light
+      luz = params_247[["LUX_cal_constant"]] * exp(params_247[["LUX_cal_exponent"]] * luz)
+    }
+    handle_luz_extremes = g.part5.handle_lux_extremes(luz)
+    luz = handle_luz_extremes$lux
+    correction_log = handle_luz_extremes$correction_log
+    # repeate values to match resolution of other data
+    repeatvalues = function(x, windowsizes, Nts) {
+      x = rep(x, each = (windowsizes[2]/windowsizes[1]))
+      if (length(x) > Nts) {
+        x = x[1:Nts]
+      } else if (length(x) < Nts) {
+        x = c(x, rep(0, (Nts - length(x))))
+      }
+      return(x)
+    }
+    luz = repeatvalues(x = luz, windowsizes = IMP$windowsizes, Nts)
+    correction_log = repeatvalues(x = correction_log, windowsizes = IMP$windowsizes, Nts)
+    ts$lightpeak_imputationcode = ts$lightpeak = 0 # initialise column
+    ts$lightpeak = luz
+    ts$lightpeak_imputationcode = correction_log
+  }
+  return(ts)
+}
+

R/identify_level.R

@@ -108,5 +108,6 @@ identify_levels = function(ts, TRLi, TRMi, TRVi, ws3, params_phyact = c(), ...)
     CL = CL + 1
   }
   invisible(list(LEVELS = LEVELS, OLEVELS = OLEVELS, Lnames = Lnames, 
-                 bc.mvpa = bc.mvpa, bc.lig = bc.lig, bc.in = bc.in, ts = ts))
+                 bc.mvpa = bc.mvpa, bc.lig = bc.lig, bc.in = bc.in, ts = ts,
+                 threshold = c(TRLi, TRMi, TRVi)))
 }

man/g.part5_analyseSegment.Rd

@@ -0,0 +1,91 @@
+\name{g.part5_analyseSegment}
+\alias{g.part5_analyseSegment}
+\title{
+  Analyses the time series per time segment for part 5
+}
+\description{
+  Not intended for direct use by GGIR users, part of \link{g.part5}.
+}
+\usage{
+  g.part5_analyseSegment(indexlog, timeList, levelList,
+                                  segments,
+                                  segments_names,
+                                  dsummary, ds_names,
+                                  params_general, params_output,
+                                  params_sleep, params_247,
+                                  params_phyact,
+                                  sumSleep, sibDef,
+                                  fullFilename,
+                                  add_one_day_to_next_date,
+                                  lightpeak_available,
+                                  tail_expansion_log,
+                                  foldernamei)
+}
+\arguments{
+  \item{indexlog}{
+    List of objects related to indices of window, file, and segment that
+    are passed on from \link{g.part5} to aid selecting time segments or keeping track
+    of where in file the code is.
+  }
+  \item{timeList}{
+    List of objects related to time series passed on from \link{g.part5}.
+  }
+  \item{levelList}{
+    List of objects related to intensity levels passed on from \link{g.part5}. 
+  }
+  \item{segments}{
+    List produced by \link{g.part5}
+  }
+  \item{segments_names}{
+    Vector produced by \link{g.part5}
+  }
+  \item{dsummary}{
+    Matrix to hold all daysummary (and segment summary)
+  }
+  \item{ds_names}{
+    Character vector with column names of the dsummary matrix. The code collects
+    these separately in this vector and assigns them at the end.
+  }
+  \item{params_general}{
+    See \link{GGIR}
+  }
+  \item{params_output}{
+    See \link{GGIR}
+  }
+  \item{params_sleep}{
+    See \link{GGIR}
+  }
+  \item{params_247}{
+    See \link{GGIR}
+  }
+  \item{params_phyact}{
+    See \link{GGIR}
+  }
+  \item{sumSleep}{
+    Section of data.frame produced by \link{g.part4} passed on from \link{g.part5}.
+  }
+  \item{sibDef}{
+    Character to identify sib definition. 
+  }
+  \item{fullFilename}{
+    Character with full filename being processed
+  }
+  \item{add_one_day_to_next_date}{
+    Boolean to indicate whether one day should be added to next date
+  }
+  \item{lightpeak_available}{
+    Boolean to indicate whether light peak is available
+  }
+  \item{tail_expansion_log}{
+    Object generated in \link{g.part1} and passed on to \link{g.part5} when 
+    argument \code{recordingEndSleepHour} is used.
+  }
+  \item{foldernamei}{
+    Character with folder name in which the data file is stored.
+  }
+}
+\value{
+  List with objects: indexlog, timeList, and the matrix with the prelimenary results
+  and column names (dsummary and ds_names, see input arguments above)
+}
+\keyword{internal}

man/g.part5_initialise_ts.Rd

@@ -0,0 +1,29 @@
+\name{g.part5_initialise_ts}
+\alias{g.part5_initialise_ts}
+\title{
+  Initialise time series data from for part 5
+}
+\description{
+  Initialise time series dataframe ts, part of \link{g.part5}.
+}
+\usage{
+  g.part5_initialise_ts(IMP, M, params_247, params_general)
+}
+\arguments{
+  \item{IMP}{
+    Object derived from \link{g.part2}
+  }
+  \item{M}{
+    Object derived from \link{g.part1}.
+  }
+  \item{params_247}{
+    See \link{GGIR}
+  }
+  \item{params_general}{
+    See \link{GGIR} 
+  }
+}
+\value{
+  Data.frame ts
+}
+\keyword{internal}