Pygt3x 0.7.1

.Rbuildignore

@@ -7,4 +7,6 @@
 ^README\.Rmd$
 ^tests/testthat/test_gcalibrateC\.R$
 ^man/figures
-.vscode/
+.vscode/
+^\.positai$
+^\.claude$

.gitignore

@@ -3,4 +3,5 @@
 .RData
 .Ruserdata
 .DS_Store
-.vscode/
+.vscode/
+.positai

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: agcounts
 Type: Package
 Title: Calculate 'ActiGraph' Counts from Accelerometer Data
-Version: 0.6.9
+Version: 0.7.0
 Authors@R: c(
     person(c("Brian", "C."), "Helsel", email = "[email protected]", role = c("aut", "cre")),
     person(c("Paul", "R."), "Hibbing", role = "ctb"),
     person(c("Robert N."), "Montgomery", role = "ctb"),
     person(c("Eric D."), "Vidoni", role = "ctb"),
     person("Jonathan", "Clutton", role = "ctb"),
+    person("John", "Muschelli", role = "ctb"),
     person("University of Kansas", role = "cph")
     )
 Description: Calculate 'ActiGraph' counts from the X, Y, and Z axes of a triaxial 
@@ -20,7 +21,6 @@ Depends:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
 Imports: 
     data.table,
     gsignal,
@@ -54,3 +54,6 @@ LinkingTo:
     RcppArmadillo
 URL: https://github.com/bhelsel/agcounts
 BugReports: https://github.com/bhelsel/agcounts/issues
+SystemRequirements: C++14
+Config/roxygen2/version: 8.0.0
+

R/agread.R

@@ -30,13 +30,24 @@ agread <- function(path, parser = c("pygt3x", "GGIR", "read.gt3x"), tz = "UTC",
     parser <- "GGIR"
   }
   switch(parser,
-         "pygt3x" = .pygt3xReader(path = path, verbose = verbose, ...),
-         "GGIR" = .ggirReader(path = path, verbose = verbose, ...),
-         "read.gt3x" = .gt3xReader(path = path, verbose = verbose, ...),
+         "pygt3x" = .pygt3xReader(path = path, verbose = verbose, tz = tz, ...),
+         "GGIR" = .ggirReader(path = path, verbose = verbose, tz = tz, ...),
+         "read.gt3x" = .gt3xReader(path = path, verbose = verbose, tz = tz, ...),
          stop("No method exists yet for ", sQuote(parser), call. = FALSE)
   )
 }
 
+pygt3x_module_version = function() {
+  if (!reticulate::py_available(initialize = TRUE)) {
+    return(NA)
+  }
+  if (!reticulate::py_module_available("pygt3x")) {
+    return(NA)
+  }
+  pkgs = reticulate::py_list_packages()
+  package_version(pkgs[pkgs$package == "pygt3x", "version"])
+}
+
 .pygt3xReader <- function(path, tz = "UTC", verbose = FALSE, ...){
   reader <- NULL
   if(!reticulate::py_module_available("pygt3x")) stop('Python module "pygt3x" not found.')
@@ -49,14 +60,19 @@ agread <- function(path, parser = c("pygt3x", "GGIR", "read.gt3x"), tz = "UTC",
   # Import Classes
   FileReader <- Reader$FileReader
   to_pandas <- FileReader$to_pandas
+  py_module_version = pygt3x_module_version()
+  cn = c("time", "X", "Y", "Z")
+  if (py_module_version >= package_version("0.7.1")) {
+    cn = c(cn, "IdleSleepMode")
+  }
   # Read and calibrate data
   with(FileReader(path) %as% reader, {
     raw = to_pandas(reader)
     raw = reset_index(raw)})
   # Return Data
-  colnames(raw) <- c("time", "X", "Y", "Z")
+  colnames(raw) <- cn
   raw$time <- as.POSIXct(raw$time, origin = "1970-01-01 00:00:00", tz=tz)
-  meta <- read.gt3x::parse_gt3x_info(path)
+  meta <- read.gt3x::parse_gt3x_info(path, tz = tz)
   attr(raw, "start_time") <- meta$`Start Date` %>% lubridate::force_tz(tz)
   attr(raw, "stop_time") <- meta$`Stop Date` %>% lubridate::force_tz(tz)
   raw
@@ -66,7 +82,7 @@ agread <- function(path, parser = c("pygt3x", "GGIR", "read.gt3x"), tz = "UTC",
   if(verbose) print("Reading data with read.gt3x and calibrating with GGIR.")
   I <- GGIR::g.inspectfile(datafile = path)
   C <- GGIR::g.calibrate(datafile = path, use.temp = FALSE, printsummary = FALSE, inspectfileobject = I)
-  raw <- read.gt3x::read.gt3x(path, asDataFrame = TRUE, imputeZeroes = TRUE)
+  raw <- .gt3xReader(path, tz = tz, verbose = verbose, ...)
   raw[, 2:4] <- scale(raw[, 2:4], center = -C$offset, scale = 1/C$scale)
   if(C$nhoursused==0) message("\n There is not enough data to perform the GGIR autocalibration method. Returning data as read by read.gt3x.")
   raw

src/Makevars

@@ -0,0 +1 @@
+CXX_STD = CXX14

src/Makevars.win

@@ -0,0 +1 @@
+CXX_STD = CXX14

src/gcalibrate.cpp

@@ -1,4 +1,4 @@
-// [[Rcpp::plugins(cpp11)]]
+// [[Rcpp::plugins(cpp14)]]
 #include <RcppArmadillo.h>
 #include <iostream>
 #include <vector>

src/resample_helpers.cpp

@@ -1,4 +1,4 @@
-// [[Rcpp::plugins(cpp11)]]
+// [[Rcpp::plugins(cpp14)]]
 #include <Rcpp.h>
 using namespace Rcpp;
 
@@ -25,4 +25,3 @@ NumericMatrix upsampleC(NumericMatrix X, double b_fp) {
   }
   return out;
 }
-

tests/testthat/_snaps/shinyUI.md

@@ -59,7 +59,7 @@
             <h5><b>Plot Settings for Raw Data</b></h5>
             <div class="form-group shiny-input-container">
               <label class="control-label" id="rawDataModule-gt3xPlotColor-label" for="rawDataModule-gt3xPlotColor">Plot Color (accepts color name or hex code)</label>
-              <input id="rawDataModule-gt3xPlotColor" type="text" class="shiny-input-text form-control" value="#000000"/>
+              <input id="rawDataModule-gt3xPlotColor" type="text" class="shiny-input-text form-control" value="#000000" data-update-on="change"/>
             </div>
             <div id="rawDataModule-rangeXraw" class="shiny-html-output"></div>
             <div id="rawDataModule-rangeYraw" class="shiny-html-output"></div>
@@ -136,7 +136,7 @@
             </div>
             <div class="form-group shiny-input-container">
               <label class="control-label" id="countsModule-countsPlotColor-label" for="countsModule-countsPlotColor">Plot Color (accepts color name or hex code)</label>
-              <input id="countsModule-countsPlotColor" type="text" class="shiny-input-text form-control" value="#000000"/>
+              <input id="countsModule-countsPlotColor" type="text" class="shiny-input-text form-control" value="#000000" data-update-on="change"/>
             </div>
             <div id="countsModule-rangeCounts" class="shiny-html-output"></div>
           </form>
@@ -208,7 +208,7 @@
             <div id="compareCountsModule-rangeYBlandAltman" class="shiny-html-output"></div>
             <div class="form-group shiny-input-container">
               <label class="control-label" id="compareCountsModule-agdPlotColor-label" for="compareCountsModule-agdPlotColor">Plot Color (accepts color name or hex code)</label>
-              <input id="compareCountsModule-agdPlotColor" type="text" class="shiny-input-text form-control" value="#000000"/>
+              <input id="compareCountsModule-agdPlotColor" type="text" class="shiny-input-text form-control" value="#000000" data-update-on="change"/>
             </div>
           </form>
         </div>

tests/testthat/test_agread.R

@@ -5,7 +5,12 @@ testthat::test_that("Check that data can be read into agcounts using pygt3x", {
   file <- system.file("extdata/example.gt3x", package = "agcounts")
   pygt3x <- agread(path = file, parser = "pygt3x", verbose = FALSE)
   expect_equal(nrow(pygt3x), 18000)
-  expect_equal(ncol(pygt3x), 4)
+  py_module_version = agcounts:::pygt3x_module_version()
+  if (py_module_version >= package_version("0.7.1")) {
+    expect_equal(ncol(pygt3x), 5L)
+  } else {
+    expect_equal(ncol(pygt3x), 4L)
+  }
 })
 
 
@@ -21,6 +26,9 @@ testthat::test_that("Check that data can be read into agcounts using each agread
   expect_equal(nrow(rawData), 18000)
   expect_equal(ncol(rawData), 4)
 
+  invisible(capture.output(rawData <- agread(path = file, parser = "read.gt3x", verbose = FALSE, tz = "EST")))
+  expect_true(lubridate::tz(rawData$time) == "EST")
+
   raw <- read.gt3x(path = file, asDataFrame = TRUE)
   sf <- agcounts:::.get_frequency(raw)
   invisible(capture.output(agcalibrated <- agcalibrate(raw)))

tests/testthat/test_shinyServer.R

@@ -18,7 +18,12 @@ testthat::test_that("Shiny app rawDataModuleServer loads raw acceleration data",
     testthat::compare(input$parser, "pygt3x")
 
     # Test the Calibrated Data
-    testthat::expect_equal(ncol(calibratedData()), 5)
+    py_module_version = agcounts:::pygt3x_module_version()
+    if (py_module_version >= package_version("0.7.1")) {
+      testthat::expect_equal(ncol(calibratedData()), 6L)
+    } else {
+      testthat::expect_equal(ncol(calibratedData()), 5L)
+    }
     testthat::expect_equal(nrow(calibratedData()), 18000)
     testthat::compare(mean(calibratedData()$X), 0.9727254, tolerance = 1e-7)
     testthat::compare(mean(calibratedData()$Y), 0.6042353, tolerance = 1e-7)