Merge pull request #19 from bhelsel/development

agcounts 0.6.4

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: agcounts
 Type: Package
 Title: R Package for Extracting Actigraphy Counts from Accelerometer Data
-Version: 0.6.2
+Version: 0.6.4
 Authors@R: c(
     person(c("Brian", "C."), "Helsel", email = "[email protected]",
         role = c("aut", "cre")),
@@ -12,7 +12,7 @@ Description: This R Package reads the X, Y, and Z axes in a GT3X accelerometer f
     The link to the article (https://www.researchsquare.com/article/rs-1370418/v1) and Python implementation of this code (https://github.com/actigraph/agcounts).
 Depends:
     R (>= 3.5.0)
-License: MIT + file LICENSE
+License: file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3

LICENSE

@@ -1,2 +1,3 @@
-YEAR: 2022
-COPYRIGHT HOLDER: agcounts authors
+Copyright © 2022 University of Kansas. All rights reserved.
+
+Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

NEWS.md

@@ -1,3 +1,10 @@
+# agcounts 0.6.4
+* Updated the agcounts license with KU Copyright and Creative Commons (CC BY-NC-SA 4.0).
+* Changed the parsers to reflect the Python and R package names.
+* Created more flexibility for adding a Shiny app theme.
+* Extending the `.last_complete_epoch` function after discovering a file that did not find a complete epoch.
+
+
 # agcounts 0.6.3
 * Improved test coverage including tests for the Shiny Server
 * Removed the Shiny App from the inst folder to only make it a callable app using `agShinyDeployApp`

R/agcounts.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title agcounts: R Package for Extracting Actigraphy Counts from Accelerometer Data.
 #'
 #' @description This R Package reads the X, Y, and Z axes in a GT3X accelerometer file

R/agcountsShinyApp.R

@@ -1,11 +1,14 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title agShinyDeployApp
 #' @description This function deploys the agcounts Shiny app.
 #' @return No data or values are returned.
 #' @details This function deploys the agcounts Shiny app for data visualization
 #' and exploration. It also provides an opportunity to compare ActiGraph counts
 #' generated from the agcounts package with those from ActiGraph's .agd files.
-#' @param shinyTheme Change the theme of the shiny app using the \code{\link[bslib]{bs_theme}} function, Default: 'spacelab'
-#' @param ... arguments passed to \code{\link[shiny]{shinyApp}}
+#' @param ... arguments passed to \code{\link[bslib]{bs_theme}}
 #' @seealso
 #'  \code{\link[shiny]{fluidPage}}, \code{\link[shiny]{titlePanel}}, \code{\link[shiny]{reexports}}, \code{\link[shiny]{shinyApp}}
 #'  \code{\link[bslib]{bs_theme}}
@@ -21,9 +24,9 @@
 #' @importFrom dplyr mutate group_by summarise select mutate_at
 #' @importFrom stats sd
 
-agShinyDeployApp <-function(shinyTheme = "spacelab", ...){
+agShinyDeployApp <-function(...){
   ui <- shiny::fluidPage(
-    theme = bslib::bs_theme(bootswatch = shinyTheme),
+    theme = bslib::bs_theme(...),
     shiny::titlePanel("agcounts: An R Package to Calculate ActiGraph Counts"),
     shiny::h3("Import and Visualize Raw Acceleration Data"),
     rawDataModuleUI("rawDataModule"),
@@ -39,7 +42,7 @@ agShinyDeployApp <-function(shinyTheme = "spacelab", ...){
     compareCountsModuleServer("compareCountsModule", filteredData)
   }
 
-  shiny::shinyApp(ui, server, ...)
+  shiny::shinyApp(ui, server)
 }
 
 #' @title .agPlotTheme

R/agread.R

@@ -1,14 +1,18 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title Read in raw acceleration data
-#' @description This generic function reads in calibrated raw acceleration data
-#'     from the python module pygt3x or the R GGIR package or uncalibrated data
-#'     from the read.gt3x package.
+#' @description This function reads in raw acceleration data
+#'     with the pygt3x Python package, the read.gt3x R package with GGIR autocalibration, or the read.gt3x R package.
 #' @param path Path name to the GT3X file or the dataset with columns time, X, Y, and Z axis
 #' @param verbose Print the read method, Default: FALSE.
-#' @param parser The parser to use when reading in the data. Parser values include pygt3x, ggir, and uncalibrated readers
+#' @param parser The parser to use when reading in the data. Parser values include pygt3x, GGIR, and read.gt3x options.
 #' @param tz the desired timezone, Default: \code{UTC}
 #' @param ... Additional arguments to pass into the agread function
-#' @return Returns the calibrated or uncalibrated raw acceleration data
-#' @details This function reads in calibrated raw acceleration data from GGIR or pygt3x.
+#' @return Returns the raw acceleration data
+#' @details This function reads in raw acceleration data
+#'     with the pygt3x Python package, the read.gt3x R package with GGIR autocalibration, or the read.gt3x R package.
 #' @examples
 #' \dontrun{
 #'    agread(system.file("extdata/example.gt3x", package = "agcounts"), parser = "pygt3x")
@@ -22,22 +26,22 @@
 #' @importFrom GGIR g.calibrate
 #' @importFrom read.gt3x read.gt3x
 
-agread <- function(path, parser = c("pygt3x", "ggir", "uncalibrated"), tz = "UTC", verbose = FALSE, ...){
+agread <- function(path, parser = c("pygt3x", "GGIR", "read.gt3x"), tz = "UTC", verbose = FALSE, ...){
   parser = match.arg(parser)
 
   if(parser == "pygt3x" & !reticulate::py_module_available("pygt3x")) {
     message('Python module "pygt3x" is not found. Switching parser to GGIR.')
-    parser <- "ggir"
+    parser <- "GGIR"
   }
   switch(parser,
          "pygt3x" = .pygt3xReader(path = path, verbose = verbose, ...),
-         "ggir" = .ggirReader(path = path, verbose = verbose, ...),
-         "uncalibrated" = .uncalibratedReader(path = path, verbose = verbose, ...),
+         "GGIR" = .ggirReader(path = path, verbose = verbose, ...),
+         "read.gt3x" = .gt3xReader(path = path, verbose = verbose, ...),
          stop("No method exists yet for ", sQuote(parser), call. = FALSE)
          )
 }
 
-.pygt3xReader <- function(path, parser = c("pygt3x", "ggir", "gt3x"), tz = "UTC", verbose = FALSE, ...){
+.pygt3xReader <- function(path, tz = "UTC", verbose = FALSE, ...){
   reader <- NULL
   if(!reticulate::py_module_available("pygt3x")) stop('Python module "pygt3x" not found.')
   if(verbose) print("Reading and calibrating data with pygt3x.")
@@ -62,17 +66,17 @@ agread <- function(path, parser = c("pygt3x", "ggir", "uncalibrated"), tz = "UTC
   raw
 }
 
-.ggirReader <- function(path, parser = c("pygt3x", "ggir", "gt3x"), tz = "UTC", verbose = FALSE, ...){
+.ggirReader <- function(path, tz = "UTC", verbose = FALSE, ...){
   if(verbose) print("Reading data with read.gt3x and calibrating with GGIR.")
   C <- GGIR::g.calibrate(datafile = path, use.temp = FALSE, printsummary = FALSE)
   raw <- read.gt3x::read.gt3x(path, asDataFrame = TRUE, imputeZeroes = TRUE)
   raw[, 2:4] <- scale(raw[, 2:4], center = -C$offset, scale = 1/C$scale)
-  if(C$nhoursused==0) message("\n There is not enough data to perform the GGIR calibration method. Returning uncalibrated data.")
+  if(C$nhoursused==0) message("\n There is not enough data to perform the GGIR autocalibration method. Returning data as read by read.gt3x.")
   raw
 }
 
-.uncalibratedReader <- function(path, parser = c("pygt3x", "ggir", "gt3x"), tz = "UTC", verbose = FALSE, ...){
-  if(verbose) print("Reading uncalibrated with read.gt3x.")
+.gt3xReader <- function(path, tz = "UTC", verbose = FALSE, ...){
+  if(verbose) print("Reading data with read.gt3x.")
   raw <- read.gt3x::read.gt3x(path, asDataFrame = TRUE, imputeZeroes = TRUE)
   raw
 }
@@ -114,7 +118,7 @@ agcalibrate <- function(raw, verbose = FALSE, tz = "UTC", ...){
   raw[which(is.na(raw[, 3])), 3] <- 0
   raw[which(is.na(raw[, 4])), 4] <- 0
   raw[, c("X", "Y", "Z")] <- scale(raw[, c("X", "Y", "Z")], center = -C$offset, scale = 1/C$scale)
-  if(C$nhoursused==0) message("\n There is not enough data to perform the GGIR calibration method. Returning uncalibrated data.")
+  if(C$nhoursused==0) message("\n There is not enough data to perform the GGIR calibration method. Returning data as read by read.gt3x.")
   raw
 }
 

R/calculate_counts.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title calculate_counts
 #' @description Calculate ActiGraph activity counts from raw acceleration data
 #'     by passing in a data frame with a time stamp, X, Y, and Z axis. This function

R/compareCountsModule.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title compareCountsModuleUI
 #' @description UI for compareCountsModule
 #' @noRd

R/countsModule.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title countsModuleUI
 #' @description UI for countsModuleUI
 #' @noRd

R/get_counts.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title get_counts
 #' @description Main function to extract counts from the Actigraph GT3X Files.
 #' @param path Full path name to the GT3X File
@@ -7,7 +11,7 @@
 #' @param return.data Return the data frame to the R Global Environment, Default: TRUE
 #' @param verbose Print the progress of the Actigraph raw data conversion to counts, Default: FALSE.
 #' @param tz the desired timezone, Default: \code{UTC}
-#' @param parser The parser to use when reading in the data. Parser values include pygt3x, ggir, and gt3x (uncalibrated reader).
+#' @param parser The parser to use when reading in the data. Parser values include pygt3x, GGIR, and read.gt3x options.
 #' @param ... arguments passed to \code{\link[data.table]{fwrite}}
 #' @return Returns a CSV file if write.file is TRUE or a data frame if return.data is TRUE
 #' @details Main function to extract counts from the Actigraph GT3X Files.
@@ -26,7 +30,7 @@
 get_counts <- function(
   path, epoch, lfe_select = FALSE, write.file = FALSE,
   return.data = TRUE, verbose = FALSE, tz = "UTC",
-  parser = c("pygt3x", "ggir", "uncalibrated"), ...
+  parser = c("pygt3x", "GGIR", "read.gt3x"), ...
 ){
 
   if(verbose){

R/get_sleep.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @export
 #' @keywords internal
 .get_sleep <- function(raw, ...) {

R/get_timestamps.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 .get_timestamps <- function(raw, epoch, frequency, tz) {
 
   if("start_time" %in% names(attributes(raw))){
@@ -25,7 +29,7 @@
 
   samples_per_epoch <- frequency * epoch
 
-  utils::tail(raw$time, samples_per_epoch * 3) %>%
+  utils::tail(raw$time, samples_per_epoch * 10) %>%
   lubridate::floor_date(paste(epoch, "sec")) %>%
   as.character(.) %>%
   rle(.) %>%

R/global_vars.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 if(getRversion() >= "2.15.1")  utils::globalVariables(c(
   ".", "Axis1", "Axis2", "Axis3", "Vector.Magnitude", "time"
 ))

R/helpers.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title .check_idle_sleep
 #' @description Check for missing raw data in the Actigraph file
 #' @param raw A data frame of the raw Actigraph data that will be checked for missing data.

R/rawDataModule.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 #' @title rawDataModuleUI
 #' @description UI for rawDataModuleUI
 #' @noRd
@@ -8,7 +12,7 @@ rawDataModuleUI <- function(id) {
   shiny::sidebarLayout(
     shiny::sidebarPanel(
       shiny::fileInput(ns("gt3xFile"), "Choose GT3X File", multiple = FALSE, accept = c(".gt3x")),
-      shiny::radioButtons(ns("parser"), "Select your parser", choices = c("pygt3x", "ggir", "uncalibrated", "agcalibrate"), inline = TRUE, selected = 0),
+      shiny::radioButtons(ns("parser"), "Select your parser", choices = c("pygt3x", "GGIR", "read.gt3x", "agcalibrate"), inline = TRUE, selected = 0),
       shiny::uiOutput(ns("dateAccessed")),
       shiny::uiOutput(ns("timeSlot")),
       shiny::selectInput(ns("axisRaw"), "Raw Axis", choices = c("X", "Y", "Z", "Vector.Magnitude"), selected = "Y"),
@@ -119,16 +123,16 @@ rawDataModuleServer <- function(id) {
 
     # Data Processing ----
 
-    # Read in the uncalibrated data with the read.gt3x function
-    uncalibratedData <- shiny::reactive({
+    # Read in the data with the read.gt3x function
+    rawData <- shiny::reactive({
       shiny::req(input$gt3xFile)
       read.gt3x::read.gt3x(input$gt3xFile$datapath, asDataFrame = TRUE)
     })
 
     # Read in the calibrated data with the read.gt3x function
     calibratedData <- shiny::reactive({
       shiny::req(input$gt3xFile, input$parser)
-      if(input$parser == "agcalibrate") data <- agcalibrate(uncalibratedData())
+      if(input$parser == "agcalibrate") data <- agcalibrate(rawData())
       if(input$parser != "agcalibrate") data <- agread(path = input$gt3xFile$datapath, parser = input$parser)
       data$Vector.Magnitude <- sqrt(data$X^2 + data$Y^2 + data$Z^2)
       return(data)
@@ -232,18 +236,19 @@ rawDataModuleServer <- function(id) {
 
     output$sampleFrequency <- shiny::renderText({
       shiny::req(input$gt3xFile)
-      sf <- .get_frequency(uncalibratedData())
+      sf <- .get_frequency(rawData())
       paste("The sample frequency is", sf, "Hertz.")
     })
 
+
     output$calibrationMethod <- shiny::renderUI({
       shiny::req(input$gt3xFile, input$parser)
       msgParser <-
         switch(input$parser,
                "pygt3x" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is calibrated using the ActiGraph's pygt3x python module."),
-               "ggir" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is calibrated using the GGIR g.calibrate function."),
-               "uncalibrated" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is uncalibrated and read with the R read.gt3x package."),
-               "agcalibrate" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is calibrated using a C++ version of the GGIR g.calibrate function."))
+               "GGIR" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is read with the read.gt3x R package and calibrated with GGIR autocalibration."),
+               "read.gt3x" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is read with the read.gt3x R package."),
+               "agcalibrate" = paste("<b><br>You chose the", input$parser, "parser.</b>", "<br>Description: Data is read with the read.gt3x R package and calibrated using a C++ version of the GGIR autocalibration."))
       shiny::HTML(msgParser)
     })
 

R/zzz.R

@@ -1,3 +1,7 @@
+# Copyright © 2022 University of Kansas. All rights reserved.
+#
+# Creative Commons Attribution NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
+
 pygt3x <- NULL
 
 .onLoad <- function(libname, pkgname) {