Merge pull request #17 from bhelsel/development

Merge development to master for agcounts 0.6.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: agcounts
 Type: Package
 Title: R Package for Extracting Actigraphy Counts from Accelerometer Data
-Version: 0.6.1
+Version: 0.6.2
 Authors@R: c(
     person(c("Brian", "C."), "Helsel", email = "bhelsel80@gmail.com",
         role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,8 @@
+# agcounts 0.6.2
+* Update the Shiny rawDataModule UI and Server to filter by AM or PM to make plotting faster
+* Improved test coverage from 19 to 56% by adding tests for the Shiny UI, `gcalibrateC`, `get_counts`, `agread`.
+* Updated the test_actilife_counts.R file using a new data set that was uploaded for `gcalibrateC` testing.
+
 # agcounts 0.6.1
 
 * Added `start_time` and `stop_time` attributes to data read by the `pygt3x` calibrated reader.

R/rawDataModule.R

@@ -10,6 +10,7 @@ rawDataModuleUI <- function(id) {
       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::uiOutput(ns("dateAccessed")),
+      shiny::uiOutput(ns("timeSlot")),
       shiny::selectInput(ns("axisRaw"), "Raw Axis", choices = c("X", "Y", "Z", "Vector.Magnitude"), selected = "Vector.Magnitude"),
       shiny::uiOutput(ns("applyRaw")),
       shiny::uiOutput(ns("applyEpoch")),
@@ -58,6 +59,11 @@ rawDataModuleServer <- function(id) {
       shiny::selectInput(session$ns("dateAccessed"), "Choose a date", choices = dates, selected = dates[1])
     })
 
+    output$timeSlot <- shiny::renderUI({
+      shiny::req(input$gt3xFile, input$parser)
+      shiny::radioButtons(session$ns("timeSlot"), "Choose AM or PM", choices = c("AM", "PM"), selected = "AM")
+    })
+
     output$applyRaw <- shiny::renderUI({
       shiny::req(input$axisRaw == "Vector.Magnitude")
       shiny::radioButtons(session$ns("applyRaw"),
@@ -129,9 +135,14 @@ rawDataModuleServer <- function(id) {
 
     # Filter data by dateAccessed to make processing faster
     filteredData <- shiny::reactive({
-      shiny::req(calibratedData(), input$dateAccessed)
+      shiny::req(calibratedData(), input$dateAccessed, input$timeSlot)
       date2filter <- as.Date(input$dateAccessed, "%B %d, %Y")
-      data <- calibratedData()[as.Date(calibratedData()$time) == date2filter, ]
+
+      if(input$timeSlot == "AM"){
+        data <- calibratedData()[as.Date(calibratedData()$time) == date2filter & as.numeric(format(calibratedData()$time, "%H") < 12), ]
+      } else{
+        data <- calibratedData()[as.Date(calibratedData()$time) == date2filter & as.numeric(format(calibratedData()$time, "%H") >= 12), ]
+      }
     })
 
     processedData <- shiny::reactive({

tests/testthat/_snaps/compareCountsModule.md

@@ -0,0 +1,71 @@
+# shiny compareCountsModuleUI creates expected HTML
+
+    Code
+      .testHTML_compareCountsModuleUI("compareCountsModule")
+    Output
+      <div class="row">
+        <div class="col-sm-4">
+          <form class="well" role="complementary">
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="compareCountsModule-agdFile-label" for="compareCountsModule-agdFile">Choose the Matching AGD File</label>
+              <div class="input-group">
+                <label class="input-group-btn input-group-prepend">
+                  <span class="btn btn-default btn-file">
+                    Browse...
+                    <input id="compareCountsModule-agdFile" name="compareCountsModule-agdFile" type="file" style="position: absolute !important; top: -99999px !important; left: -99999px !important;" accept=".agd"/>
+                  </span>
+                </label>
+                <input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
+              </div>
+              <div id="compareCountsModule-agdFile_progress" class="progress active shiny-file-input-progress">
+                <div class="progress-bar"></div>
+              </div>
+            </div>
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="compareCountsModule-axisCounts2-label" for="compareCountsModule-axisCounts2">Count Axis</label>
+              <div>
+                <select id="compareCountsModule-axisCounts2"><option value="Axis1">Axis1</option>
+      <option value="Axis2">Axis2</option>
+      <option value="Axis3">Axis3</option>
+      <option value="Vector.Magnitude" selected>Vector.Magnitude</option></select>
+                <script type="application/json" data-for="compareCountsModule-axisCounts2" data-nonempty="">{"plugins":["selectize-plugin-a11y"]}</script>
+              </div>
+            </div>
+            <div class="form-group shiny-input-container">
+              <div class="checkbox">
+                <label>
+                  <input id="compareCountsModule-agdBlandAltmanPlot" type="checkbox"/>
+                  <span>Bland Altman Plot?</span>
+                </label>
+              </div>
+            </div>
+            <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="form-control" value="#000000"/>
+            </div>
+          </form>
+        </div>
+        <div class="col-sm-8" role="main">
+          <div class="tabbable">
+            <ul class="nav nav-tabs shiny-tab-input" id="comparisonTabset" data-tabsetid="4785">
+              <li class="active">
+                <a href="#tab-4785-1" data-toggle="tab" data-bs-toggle="tab" data-value="Visualization">Visualization</a>
+              </li>
+              <li>
+                <a href="#tab-4785-2" data-toggle="tab" data-bs-toggle="tab" data-value="Data">Data</a>
+              </li>
+            </ul>
+            <div class="tab-content" data-tabsetid="4785">
+              <div class="tab-pane active" data-value="Visualization" id="tab-4785-1">
+                <div class="shiny-plot-output html-fill-item" id="compareCountsModule-comparisonPlot" style="width:100%;height:400px;"></div>
+              </div>
+              <div class="tab-pane" data-value="Data" id="tab-4785-2">
+                <h5>Differences between ActiGraph counts and agcounts</h5>
+                <div class="reactable html-widget html-widget-output shiny-report-size html-fill-item-overflow-hidden html-fill-item" data-reactable-output="compareCountsModule-comparisonReactableTable" id="compareCountsModule-comparisonReactableTable" style="width:auto;height:auto;"></div>
+              </div>
+            </div>
+          </div>
+        </div>
+      </div>
+

tests/testthat/_snaps/countsModule.md

@@ -0,0 +1,76 @@
+# shiny countsModuleUI creates expected HTML
+
+    Code
+      .testHTML_countsModuleUI("countsModule")
+    Output
+      <div class="row">
+        <div class="col-sm-4">
+          <form class="well" role="complementary">
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="countsModule-epoch-label" for="countsModule-epoch">What epoch level?</label>
+              <input class="js-range-slider" id="countsModule-epoch" data-skin="shiny" data-min="1" data-max="60" data-from="30" data-step="1" data-grid="false" data-grid-snap="false" data-prettify-separator="," data-prettify-enabled="true" data-postfix=" seconds" data-keyboard="true" data-data-type="number"/>
+            </div>
+            <div class="form-group shiny-input-container">
+              <div class="checkbox">
+                <label>
+                  <input id="countsModule-lfe" type="checkbox"/>
+                  <span>Add a low frequency extension filter?</span>
+                </label>
+              </div>
+            </div>
+            <h5><b>Plot Settings for Calculate Counts</b></h5>
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="countsModule-axisCounts-label" for="countsModule-axisCounts">Counts Axis</label>
+              <div>
+                <select id="countsModule-axisCounts"><option value="Axis1">Axis1</option>
+      <option value="Axis2">Axis2</option>
+      <option value="Axis3">Axis3</option>
+      <option value="Vector.Magnitude" selected>Vector.Magnitude</option></select>
+                <script type="application/json" data-for="countsModule-axisCounts" data-nonempty="">{"plugins":["selectize-plugin-a11y"]}</script>
+              </div>
+            </div>
+            <div class="form-group shiny-input-container">
+              <div class="checkbox">
+                <label>
+                  <input id="countsModule-excludeZeros" type="checkbox"/>
+                  <span>Exclude zeros from the plot?</span>
+                </label>
+              </div>
+            </div>
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="countsModule-binwidthCounts-label" for="countsModule-binwidthCounts">Select a frequency polygon binwidth</label>
+              <input id="countsModule-binwidthCounts" type="number" class="form-control" value="30" step="10"/>
+            </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="form-control" value="#000000"/>
+            </div>
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="countsModule-rangeCounts-label" for="countsModule-rangeCounts">Select a range for the X axis</label>
+              <input class="js-range-slider" id="countsModule-rangeCounts" data-skin="shiny" data-type="double" data-min="0" data-max="10000" data-from="0" data-to="2000" data-step="1" data-grid="true" data-grid-num="10" data-grid-snap="false" data-prettify-separator="," data-prettify-enabled="true" data-postfix=" counts" data-keyboard="true" data-drag-interval="true" data-data-type="number"/>
+            </div>
+          </form>
+        </div>
+        <div class="col-sm-8" role="main">
+          <div class="tabbable">
+            <ul class="nav nav-tabs shiny-tab-input" id="countsTabset" data-tabsetid="4785">
+              <li class="active">
+                <a href="#tab-4785-1" data-toggle="tab" data-bs-toggle="tab" data-value="Visualization">Visualization</a>
+              </li>
+              <li>
+                <a href="#tab-4785-2" data-toggle="tab" data-bs-toggle="tab" data-value="Data">Data</a>
+              </li>
+            </ul>
+            <div class="tab-content" data-tabsetid="4785">
+              <div class="tab-pane active" data-value="Visualization" id="tab-4785-1">
+                <div class="shiny-plot-output html-fill-item" id="countsModule-countsPlot" style="width:100%;height:400px;"></div>
+              </div>
+              <div class="tab-pane" data-value="Data" id="tab-4785-2">
+                <h5>Total and average accelerometer counts from agcounts</h5>
+                <div class="reactable html-widget html-widget-output shiny-report-size html-fill-item-overflow-hidden html-fill-item" data-reactable-output="countsModule-countsReactableTable" id="countsModule-countsReactableTable" style="width:auto;height:auto;"></div>
+              </div>
+            </div>
+          </div>
+        </div>
+      </div>
+

tests/testthat/_snaps/rawDataModule.md

@@ -0,0 +1,97 @@
+# shiny rawDataModuleUI creates expected HTML
+
+    Code
+      .testHTML_rawDataModuleUI("rawDataModule")
+    Output
+      <div class="row">
+        <div class="col-sm-4">
+          <form class="well" role="complementary">
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="rawDataModule-gt3xFile-label" for="rawDataModule-gt3xFile">Choose GT3X File</label>
+              <div class="input-group">
+                <label class="input-group-btn input-group-prepend">
+                  <span class="btn btn-default btn-file">
+                    Browse...
+                    <input id="rawDataModule-gt3xFile" name="rawDataModule-gt3xFile" type="file" style="position: absolute !important; top: -99999px !important; left: -99999px !important;" accept=".gt3x"/>
+                  </span>
+                </label>
+                <input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
+              </div>
+              <div id="rawDataModule-gt3xFile_progress" class="progress active shiny-file-input-progress">
+                <div class="progress-bar"></div>
+              </div>
+            </div>
+            <div id="rawDataModule-parser" class="form-group shiny-input-radiogroup shiny-input-container shiny-input-container-inline" role="radiogroup" aria-labelledby="rawDataModule-parser-label">
+              <label class="control-label" id="rawDataModule-parser-label" for="rawDataModule-parser">Select your parser</label>
+              <div class="shiny-options-group">
+                <label class="radio-inline">
+                  <input type="radio" name="rawDataModule-parser" value="pygt3x"/>
+                  <span>pygt3x</span>
+                </label>
+                <label class="radio-inline">
+                  <input type="radio" name="rawDataModule-parser" value="ggir"/>
+                  <span>ggir</span>
+                </label>
+                <label class="radio-inline">
+                  <input type="radio" name="rawDataModule-parser" value="uncalibrated"/>
+                  <span>uncalibrated</span>
+                </label>
+                <label class="radio-inline">
+                  <input type="radio" name="rawDataModule-parser" value="agcalibrate"/>
+                  <span>agcalibrate</span>
+                </label>
+              </div>
+            </div>
+            <div id="rawDataModule-dateAccessed" class="shiny-html-output"></div>
+            <div id="rawDataModule-timeSlot" class="shiny-html-output"></div>
+            <div class="form-group shiny-input-container">
+              <label class="control-label" id="rawDataModule-axisRaw-label" for="rawDataModule-axisRaw">Raw Axis</label>
+              <div>
+                <select id="rawDataModule-axisRaw"><option value="X">X</option>
+      <option value="Y">Y</option>
+      <option value="Z">Z</option>
+      <option value="Vector.Magnitude" selected>Vector.Magnitude</option></select>
+                <script type="application/json" data-for="rawDataModule-axisRaw" data-nonempty="">{"plugins":["selectize-plugin-a11y"]}</script>
+              </div>
+            </div>
+            <div id="rawDataModule-applyRaw" class="shiny-html-output"></div>
+            <div id="rawDataModule-applyEpoch" class="shiny-html-output"></div>
+            <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="form-control" value="#000000"/>
+            </div>
+            <div id="rawDataModule-rangeXraw" class="shiny-html-output"></div>
+            <div id="rawDataModule-rangeYraw" class="shiny-html-output"></div>
+          </form>
+        </div>
+        <div class="col-sm-8" role="main">
+          <div class="tabbable">
+            <ul class="nav nav-tabs shiny-tab-input" id="rawTabset" data-tabsetid="4785">
+              <li class="active">
+                <a href="#tab-4785-1" data-toggle="tab" data-bs-toggle="tab" data-value="Visualization">Visualization</a>
+              </li>
+              <li>
+                <a href="#tab-4785-2" data-toggle="tab" data-bs-toggle="tab" data-value="Data">Data</a>
+              </li>
+              <li>
+                <a href="#tab-4785-3" data-toggle="tab" data-bs-toggle="tab" data-value="Notes">Notes</a>
+              </li>
+            </ul>
+            <div class="tab-content" data-tabsetid="4785">
+              <div class="tab-pane active" data-value="Visualization" id="tab-4785-1">
+                <div class="shiny-plot-output html-fill-item" id="rawDataModule-gt3xPlot" style="width:100%;height:400px;"></div>
+              </div>
+              <div class="tab-pane" data-value="Data" id="tab-4785-2">
+                <h5> Average Raw Acceleration Data by Hour </h5>
+                <div class="reactable html-widget html-widget-output shiny-report-size html-fill-item-overflow-hidden html-fill-item" data-reactable-output="rawDataModule-rawReactableTable" id="rawDataModule-rawReactableTable" style="width:auto;height:auto;"></div>
+              </div>
+              <div class="tab-pane" data-value="Notes" id="tab-4785-3">
+                <div id="rawDataModule-sampleFrequency" class="shiny-text-output"></div>
+                <div id="rawDataModule-calibrationMethod" class="shiny-html-output"></div>
+              </div>
+            </div>
+          </div>
+        </div>
+      </div>
+

tests/testthat/test_actilife_counts.R

@@ -1,17 +1,34 @@
 
 testthat::test_that("agcounts and Actilife counts are the same",{
-
-  gt3x.file <- system.file("extdata/testGT3X.RData", package = "agcounts")
-  load(gt3x.file)
-  testGT3X %<>% calculate_counts(raw = ., epoch = 1)
-
-  agd.file <- system.file("extdata/testAGD.RData", package = "agcounts")
-  load(agd.file)
-
-  expect_equal(nrow(testAGD), nrow(testGT3X))
-  compare(testAGD$` Axis1`, testGT3X$Axis1, tolerance = 0.05)
-  compare(testAGD$Axis2, testGT3X$Axis2, tolerance = 0.05)
-  compare(testAGD$Axis3, testGT3X$Axis3, tolerance = 0.05)
-  compare(round(testAGD$`Vector Magnitude`), testGT3X$Vector.Magnitude, tolerance = 0.05)
-
+
+  # Load Data
+  load(system.file("extdata/calibrationXaxis.RData", package = "agcounts"))
+  load(system.file("extdata/calibrationYaxis.RData", package = "agcounts"))
+  load(system.file("extdata/calibrationZaxis.RData", package = "agcounts"))
+  agdPath <- system.file("extdata/calibration1sec.agd", package = "agcounts")
+
+  # Recreate time stamps
+  sf = 30
+  start <- as.POSIXct("2023-04-24 15:02:00", tz = "UTC")
+  end <- as.POSIXct("2023-04-25 11:46:13", tz = "UTC") + 1
+  time <- seq(from = start, to = end - 0.001, by = 1/sf)
+
+  # Merge X, Y, and Z data together in a matrix
+  rawData <- data.frame(time, X, Y, Z)
+
+  # Calculate Counts
+  gt3xData <- calculate_counts(raw = rawData, epoch = 1)
+
+  # Read in agd data
+  agdData <- .read_agd(agdPath)$data
+
+  # Remove rows that are not in the gt3xData file
+  agdData <- agdData[-which(!agdData$time %in% gt3xData$time), ]
+
+  # Tests
+  expect_equal(nrow(agdData), nrow(gt3xData))
+  expect_equal(agdData$Axis1, gt3xData$Axis1)
+  expect_equal(agdData$Axis2, gt3xData$Axis2)
+  expect_equal(agdData$Axis3, gt3xData$Axis3)
+  expect_equal(agdData$Vector.Magnitude, gt3xData$Vector.Magnitude)
 })

tests/testthat/test_agread.R

@@ -0,0 +1,25 @@
+
+
+testthat::test_that("Check that data can be read into agcounts using each agread method", {
+
+  file <- system.file("extdata/example.gt3x", package = "agcounts")
+
+  pygt3x <- agread(path = file, parser = "pygt3x")
+  expect_equal(nrow(pygt3x), 16200)
+  expect_equal(ncol(pygt3x), 4)
+
+  ggir <- agread(path = file, parser = "ggir")
+  expect_equal(nrow(ggir), 16200)
+  expect_equal(ncol(ggir), 4)
+
+  uncalibrated <- agread(path = file, parser = "uncalibrated")
+  expect_equal(nrow(uncalibrated), 16200)
+  expect_equal(ncol(uncalibrated), 4)
+
+  raw <- read.gt3x(path = file, asDataFrame = TRUE)
+  sf <- .get_frequency(raw)
+  agcalibrated <- agcalibrate(raw)
+  expect_equal(nrow(agcalibrated), 16201) # Looks like agcalibrate produces 1 additional row of data
+  expect_equal(ncol(agcalibrated), 4)
+
+})