Merge pull request #48 from pydemull/dev

Dev

Author: pydemull

.github/workflows/R-CMD-check.yaml

@@ -28,7 +28,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pkgdown.yaml

@@ -16,7 +16,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -26,7 +26,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Restore R package cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

.github/workflows/test-coverage.yaml

@@ -1,32 +1,44 @@
-# File from: https://github.com/r-lib/actions/blob/v2/examples/test-coverage.yaml
-
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Workflow derived from https://github.com/rstudio/shinytest2/tree/main/actions/test-app/example-test-app-description.yaml
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: Test app w/ {renv}
 
 jobs:
-  test-coverage:
-    runs-on: ubuntu-latest
+  test-app:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: release}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: ${{ matrix.config.r }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-renv@v2
+
+      - uses: rstudio/shinytest2/actions/test-app@actions/v1
         with:
-          extra-packages: any::covr
-          needs: coverage
+          app-dir: "."
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE, clean = FALSE)

DESCRIPTION

@@ -60,7 +60,9 @@ Suggests:
     tibble,
     rlang,
     tinytex,
-    shinytest2
+    shinytest2,
+    pkgdown,
+    callr
 Language: en-US
 Depends: R (>= 3.4.0)
 Config/testthat/edition: 3

NEWS.md

@@ -1,4 +1,5 @@
 # activAnalyzer (development version)
+* When collapsing data from a shorter epoch to a longer epoch, NAs are introduced in the 'wearing' column provided by the PhysicalActivity package during nonwear time analysis. This generated a bug when computing the accumulation metrics because the detection of the bouts partly depends on the labels provided in this column. This has been corrected by replacing NAs by "Nonwear".
 
 # activAnalyzer 2.1.0
 * Moved 'assertthat' from Suggests to Imports field in DESCRIPTION.

R/compute_accumulation_metrics.R

@@ -104,19 +104,35 @@ if (is.null(dates)) {
   selected_dates <- attributes(as.factor(data$date))$levels
 } else {
     selected_dates <- attributes(as.factor(dates))$levels
-    }
-data <- 
-  data %>% 
-  dplyr::filter(date %in% as.Date(selected_dates) &
-                  .data[[col_time]] >= hms::as_hms(valid_wear_time_start) &
-                  .data[[col_time]] <= hms::as_hms(valid_wear_time_end)
-                ) %>%
-  dplyr::mutate(new_intensity_category = 
-                  dplyr::if_else(.data[[col_cat_int]] == "LPA" | .data[[col_cat_int]] == "MVPA", "PA",
-                      dplyr::if_else(.data[[col_cat_int]] == "SED", "SED",
-                          dplyr::if_else(.data[[col_cat_int]] == "Nonwear", "Nonwear", NA
-                  )))
-  )
+}
+  
+  # Fix bug: Convert Nas to "Nonwear"
+  data[[col_cat_int]] <- dplyr::if_else(is.na(data[[col_cat_int]]), "Nonwear", data[[col_cat_int]])
+  
+  data <-
+    data %>%
+    dplyr::filter(
+      date %in% as.Date(selected_dates) &
+        .data[[col_time]] >= hms::as_hms(valid_wear_time_start) &
+        .data[[col_time]] <= hms::as_hms(valid_wear_time_end)
+    ) %>%
+    dplyr::mutate(
+      new_intensity_category =
+        dplyr::if_else(
+          .data[[col_cat_int]] == "LPA" |
+            .data[[col_cat_int]] == "MVPA",
+          "PA",
+          dplyr::if_else(
+            .data[[col_cat_int]] == "SED",
+            "SED",
+            dplyr::if_else(
+              .data[[col_cat_int]] == "Nonwear",
+              "Nonwear",
+              dplyr::if_else(is.na(.data[[col_cat_int]]), "Nonwear", "Nonwear")
+            )
+          )
+        )
+    )
 
 # Updating bouts IDs
 data$new_intensity_category <- as.factor(data$new_intensity_category)

R/do_all_analyses.R

@@ -8,7 +8,7 @@
 #' @return
 #' A dataset (1 row) with all computed metrics.
 
-do_all_analyses <- function(){
+do_all_analyses <- function(to_epoch = 60){
 
   # Load file
   file <- system.file("extdata", "acc.agd", package = "activAnalyzer")
@@ -17,7 +17,7 @@ do_all_analyses <- function(){
   mydata <- prepare_dataset(data = file)
 
   # Detect nonwear time
-  mydata_with_wear_marks <- mydata %>% mark_wear_time()
+  mydata_with_wear_marks <- mydata %>% mark_wear_time(to_epoch = to_epoch)
 
   # Add intensity marks
   mydata_with_intensity_marks <- mark_intensity(data = mydata_with_wear_marks)

renv.lock

@@ -332,13 +332,13 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.2.0",
+      "Version": "5.2.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9"
+      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
     },
     "data.table": {
       "Package": "data.table",