fixes #53

wadpac · Dec 1, 2023 · 44fa412 · 44fa412
1 parent 0694fd1
commit 44fa412
Show file tree

Hide file tree

Showing 4 changed files with 17 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,9 +16,9 @@ Description: For processesing accelerometer data generated in the mechanical sha
 URL: https://github.com/wadpac/mechanicalshakerexperiments
 License: Apache License version 2.0 | file LICENSE
 Suggests: testthat, covr, knitr, rmarkdown
-Imports: gdata, doParallel, foreach, GENEAread, GGIR, GGIRread, read.gt3x, data.table, lubridate, signal, zoo, ggplot2, ggpubr, pracma, readxl, viridis
+Imports: doParallel, foreach, GENEAread, GGIR, GGIRread, read.gt3x, data.table, lubridate, signal, zoo, ggplot2, ggpubr, pracma, readxl, viridis
 Depends: stats, utils, R (>= 3.5.0)
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Encoding: UTF-8
diff --git a/NAMESPACE b/NAMESPACE
@@ -25,7 +25,6 @@ importFrom(GGIR,g.downsample)
 importFrom(GGIRread,readAxivity)
 importFrom(GGIRread,resample)
 importFrom(data.table,fread)
-importFrom(gdata,read.xls)
 importFrom(ggplot2,scale_x_discrete)
 importFrom(graphics,abline)
 importFrom(graphics,plot)

diff --git a/R/getwindows.R b/R/getwindows.R
@@ -8,7 +8,6 @@
 #' @param data Data object
 #' @param experimentfile .xlsx file with protocol description, defaults to file stored inside the code
 #' @return List of data.frames with the accelerometer time series where each list item represents 1 recording
-#' @importFrom gdata read.xls
 #' @export
 
 
@@ -17,12 +16,24 @@ getwindows <- function(brand, experiment, path, data, experimentfile = c()) {
   if (length(experimentfile) == 0) {
     experimentfile = system.file("datadescription/data_description.xlsx", package = "mechanicalshakerexperiments")[1]
   }
-  description <- gdata::read.xls(experimentfile, header = TRUE)
+  tz = "Europe/Amsterdam"
+  description <- as.data.frame(readxl::read_excel(path = experimentfile, col_types = "text"))
+  for (jj in 7:8) {
+    description[, jj] = suppressWarnings(format(x = as.POSIXct(as.numeric(description[, jj]) * (60*60*24),
+                                                               origin = "1899-12-30",
+                                                               tz = tz),
+                                                format = "%H:%M:%S"))
+  }
+  description[, 2] = suppressWarnings(format(x = as.POSIXct(as.numeric(description[, 2]) * (60*60*24),
+                                                            origin = "1899-12-30",
+                                                            tz = tz), 
+                                             format = "%Y-%m-%d"))
+
   description <- description[which(description$experiment == experiment),]
   # Calculate indices for the windows to select
   start_time <- c()
   end_time <- c()
-  tz = "Europe/Amsterdam"
+
   if (experiment == "box") {
     start <- strftime(toString(paste(description$date[1], description$start_time[1]), sep = " "), format = "%Y-%m-%d %H:%M:%OS2", tz = tz)
     start_time <- start
@@ -58,7 +69,6 @@ getwindows <- function(brand, experiment, path, data, experimentfile = c()) {
   selected_data <- data.frame()
   #Select the windows
   cat("file ")
-  tz = "Europe/Amsterdam"
   for(pp in 1:length(data)) { # pp is file number?
     cat(paste0(" ",pp))
     if (brand %in% c("Axivity", "GENEActiv")) {

diff --git a/R/loaddata.R b/R/loaddata.R
@@ -87,7 +87,6 @@ loaddata <- function(path, brand, experiment, windows = TRUE, experimentfile, ac
   cl <- parallel::makeCluster(Ncores) #not to overload your computer
   doParallel::registerDoParallel(cl)
   i = NULL
-
   `%myinfix%` = foreach::`%dopar%`
   parallelLoad <- function(file_path, file_list, brand, experiment, windows, path) {
     foreach::foreach(i = 1:length(file_list), .packages = c("read.gt3x", "GGIRread", "GENEAread"),
@@ -214,7 +213,7 @@ loaddata <- function(path, brand, experiment, windows = TRUE, experimentfile, ac
                        }
                        if (brand %in% c("Axivity", "GENEActiv") == FALSE) {
                          rawdata = rawdata[which(rawdata$time >= start & rawdata$time <= end),]
-                       }else {
+                       } else {
                          if (brand == "GENEActiv") {
                            rawdata$data.out = rawdata$data.out[which(rawdata$data.out$time >= start & rawdata$data.out$time <= end),]
                          } else if (brand == "Axivity") {