Merge branch 'dev' into detection_range_model

ocean-tracking-network · Mar 5, 2024 · 05fff7f · 05fff7f
2 parents daa77fe + f016ab1
commit 05fff7f
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,11 +1,12 @@
 ^Meta$
 ^doc$
-ReadMe.md
-CONTRIBUTING.md
-glatos.pdf
+^ReadMe\.md$
+^CONTRIBUTING\.md$
+^glatos\.pdf$
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^README-.*\.png$
 ^\.github$
+^R/util-intern_pkg_man\.r$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          error-on: '"error"'
diff --git a/.github/workflows/document.yaml b/.github/workflows/document.yaml
@@ -13,7 +13,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
@@ -13,7 +13,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,38 +2,40 @@ Package: glatos
 Type: Package
 Title: A package for the Great Lakes Acoustic Telemetry Observation System
 Description: Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
-Version: 0.8.0.9000
-Date: 2024-01-04
+Version: 0.8.0.9004
+Date: 2024-02-16
 Depends: R (>= 3.5.0)
 Imports:
 		av,
 		data.table,
 		dplyr,
 		fasterize,
-		fasttime,
 		gdalUtilities,
 		geodist,
 		gdistance,
 		geosphere,
 		jsonlite,
-		knitr,
 		lubridate,
 		magrittr,
-		methods,
 		plotrix,
 		purrr,
 		raster,
 		readxl,
-		rmarkdown,
 		sf,
 		sp,
 		tibble,
-		tidyr
+		tidyr,
+		units,
+		zip
 Suggests: 
 		gganimate,
 		gifski,
+		knitr,
+		methods,
 		png,
-    testthat (>= 3.0.0),
+		rmarkdown,
+		terra,
+		testthat (>= 3.0.0),
 		tint
 URL: https://github.com/ocean-tracking-network/glatos
 BugReports: https://github.com/ocean-tracking-network/glatos/issues
@@ -49,7 +51,7 @@ Authors@R: c(
 License: GPL-2
 LazyLoad: yes
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

diff --git a/NEWS.md b/NEWS.md
@@ -1,15 +1,36 @@
+----
 
 # glatos 0.8.0 (dev)
 
 
-### Bug fixes
+### Bug fixes and minor changes
+
+- Add `@srs` slot to `greatLakesTrLayer` data object and rename file 
+  'data/greatLakesTrLayer.rda'.
+    - fixes [issue #213](https://github.com/ocean-tracking-network/glatos/issues/213)
+
+- Fix bug in `read_glatos_workbook()` where timestamps during daylight savings 
+  were shifted one hour on linux operating system (not an issue on windows or 
+  mac).
+    - fixes [issue #208](https://github.com/ocean-tracking-network/glatos/issues/208)
+
+- Omit data.table from class of object returned by `read_glatos_detections()`  
+  and `read_glatos_receivers()`. 
+    - fixes [issue #200](https://github.com/ocean-tracking-network/glatos/issues/200)
 
 - Fix typo in Description to Suggest 'gifski' (not 'gifsky'). 
     - fixes [issue #185](https://github.com/ocean-tracking-network/glatos/issues/185)
 
 
 ### New features
 
+#### 2024-01-19
+
+- In `make_frames()`, allow `terra::SpatVector` input for background map 
+  (`bg_map` arg).
+    - add test for `terra::SpatVector` input
+
+
 #### 2023-08-30
 
 - Add new functions to create, check, and validate `glatos_animals` objects:
@@ -62,6 +83,20 @@
   using VDAT.exe (e.g., using `vdat_convert()`).
 
 
+----
+
+# glatos 0.7.1 (2024-01-19)
+
+
+### Bug fixes and minor changes
+
+
+- Fix bug introduced in glatos 0.7.0 where x and y limits were switched 
+  when `bg_map` was supplied.
+    - Add test for various inputs of `background_xlim`, `background_ylim`, and 
+      `bg_map` to function `make_frames`.
+
+
 ----
 
 # glatos 0.7.0 (2024-01-04)

diff --git a/R/class-glatos_animals.r b/R/class-glatos_animals.r
@@ -71,24 +71,28 @@
 #' ga_tbl <- as_glatos_animals(x_tbl)
 #'
 #'
+#' # All below will error as invalid
+#'
 #' # data.frame input; missing column name
 #' library(dplyr) # for rename
 #' x2 <- rename(x,
 #'   fish_name = animal_id,
 #'   release_timestamp = utc_release_date_time
 #' )
 #'
-#' ga2 <- as_glatos_animals(x2)
-#'
+#' try(
+#'   ga2 <- as_glatos_animals(x2)
+#' )
 #'
-#' # data.grame input; wrong column class
+#' # data.frame input; wrong column class
 #' x3 <- mutate(x,
 #'   animal_id = as.integer(animal_id),
 #'   utc_release_date_time = as.character(utc_release_date_time)
 #' )
 #'
-#' ga3 <- as_glatos_animals(x3)
-#'
+#' try(
+#'   ga3 <- as_glatos_animals(x3)
+#' )
 #'
 #' # Validation and checking
 #'

diff --git a/R/class-glatos_detections.r b/R/class-glatos_detections.r
@@ -73,24 +73,28 @@
 #' gd_tbl <- as_glatos_detections(x_tbl)
 #'
 #'
+#' # All below will error as invalid
+#'
 #' # data.frame input; missing column name
 #' library(dplyr) # for rename
 #' x2 <- rename(x,
 #'   fish_id = animal_id,
 #'   det_date_time = detection_timestamp_utc
 #' )
 #'
-#' gd2 <- as_glatos_detections(x2)
-#'
+#' try(
+#'   gd2 <- as_glatos_detections(x2)
+#' )
 #'
 #' # data.frame input; wrong column class
 #' x3 <- mutate(x,
 #'   animal_id = as.integer(animal_id),
 #'   detection_timestamp_utc = as.character(detection_timestamp_utc)
 #' )
 #'
-#' gr3 <- as_glatos_detections(x3)
-#'
+#' try(
+#'   gr3 <- as_glatos_detections(x3)
+#' )
 #'
 #' # Validation and checking
 #'

diff --git a/R/class-glatos_receivers.r b/R/class-glatos_receivers.r
@@ -86,6 +86,7 @@
 #'
 #' gr_tbl <- as_glatos_receivers(x_tbl)
 #'
+#' # All below will error as invalid
 #'
 #' # data.frame input; missing column name
 #' library(dplyr) # for rename
@@ -94,17 +95,19 @@
 #'   deploy_timestamp = deploy_date_time
 #' )
 #'
-#' gr2 <- as_glatos_receivers(x2)
-#'
+#' try(
+#'   gr2 <- as_glatos_receivers(x2)
+#' )
 #'
 #' # data.frame input; wrong column class
 #' x3 <- mutate(x,
 #'   ins_serial_no = as.integer(ins_serial_no),
 #'   deploy_date_time = as.character(deploy_date_time)
 #' )
 #'
-#' gr3 <- as_glatos_receivers(x3)
-#'
+#' try(
+#'   gr3 <- as_glatos_receivers(x3)
+#' )
 #'
 #' # Validation and checking
 #'

diff --git a/R/load-read_glatos_detections.r b/R/load-read_glatos_detections.r
@@ -53,9 +53,9 @@ read_glatos_detections <- function(det_file, version = NULL) {
   # Identify detection file version
   id_det_version <- function(det_file) {
     det_col_names <- names(data.table::fread(det_file, nrows = 0))
-    if (all(glatos:::glatos_detection_schema$v1.4$name %in% det_col_names)) {
+    if (all(glatos_detection_schema$v1.4$name %in% det_col_names)) {
       return("1.4")
-    } else if (all(glatos:::glatos_detection_schema$v1.3$name %in% det_col_names)) {
+    } else if (all(glatos_detection_schema$v1.3$name %in% det_col_names)) {
       return("1.3")
     } else {
       stop("Detection file version could not be identified.")
@@ -65,15 +65,15 @@ read_glatos_detections <- function(det_file, version = NULL) {
   if (is.null(version)) {
     version <- id_det_version(det_file)
   } else if (!(paste0("v", version) %in%
-    names(glatos:::glatos_detection_schema))) {
+    names(glatos_detection_schema))) {
     stop(paste0("Detection file version ", version, " is not supported."))
   }
 
   #-Detections v1.3 or v1.4-----------------------------------------------------
   if (version %in% c("1.3", "1.4")) {
     vversion <- paste0("v", version)
 
-    col_classes <- glatos:::glatos_detection_schema[[vversion]]$type
+    col_classes <- glatos_detection_schema[[vversion]]$type
     timestamp_cols <- which(col_classes == "POSIXct")
     date_cols <- which(col_classes == "Date")
     col_classes[c(timestamp_cols, date_cols)] <- "character"
@@ -89,9 +89,9 @@ read_glatos_detections <- function(det_file, version = NULL) {
     options(lubridate.fasttime = TRUE)
     for (j in timestamp_cols) {
       data.table::set(dtc,
-        j = glatos:::glatos_detection_schema[[vversion]]$name[j],
+        j = glatos_detection_schema[[vversion]]$name[j],
         value = lubridate::parse_date_time(
-          dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]],
+          dtc[[glatos_detection_schema[[vversion]]$name[j]]],
           orders = "ymd HMS",
           tz = "UTC"
         )
@@ -100,15 +100,15 @@ read_glatos_detections <- function(det_file, version = NULL) {
     # coerce dates to date
     for (j in date_cols) {
       data.table::set(dtc,
-        j = glatos:::glatos_detection_schema[[vversion]]$name[j],
-        value = ifelse(dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]] == "",
+        j = glatos_detection_schema[[vversion]]$name[j],
+        value = ifelse(dtc[[glatos_detection_schema[[vversion]]$name[j]]] == "",
           NA,
-          dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]]
+          dtc[[glatos_detection_schema[[vversion]]$name[j]]]
         )
       )
       data.table::set(dtc,
-        j = glatos:::glatos_detection_schema[[vversion]]$name[j],
-        value = as.Date(dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]])
+        j = glatos_detection_schema[[vversion]]$name[j],
+        value = as.Date(dtc[[glatos_detection_schema[[vversion]]$name[j]]])
       )
     }
   }
@@ -128,7 +128,9 @@ read_glatos_detections <- function(det_file, version = NULL) {
     ))
   }
 
-  # assign class
+  # strip data.table and assign glatos_detections class
+  data.table::setDF(dtc)
+
   dtc <- as_glatos_detections(dtc)
 
   return(dtc)

diff --git a/R/load-read_glatos_receivers.r b/R/load-read_glatos_receivers.r
@@ -49,9 +49,9 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   # Identify file version
   id_file_version <- function(rec_file) {
     col_names <- names(data.table::fread(rec_file, nrows = 0))
-    if (all(glatos:::glatos_receivers_schema$v1.1$name %in% col_names)) {
+    if (all(glatos_receivers_schema$v1.1$name %in% col_names)) {
       return("1.1")
-    } else if (all(glatos:::glatos_receivers_schema$v1.0$name %in% col_names)) {
+    } else if (all(glatos_receivers_schema$v1.0$name %in% col_names)) {
       return("1.0")
     } else {
       stop("Receiver location file version could not be identified.")
@@ -61,7 +61,7 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   if (is.null(version)) {
     version <- id_file_version(rec_file)
   } else if (!(paste0("v", version) %in%
-    names(glatos:::glatos_receivers_schema))) {
+    names(glatos_receivers_schema))) {
     stop(paste0(
       "Receiver locations file version ", version,
       " is not supported."
@@ -72,7 +72,7 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   if (version %in% c("1.0", "1.1")) {
     ver_txt <- paste0("v", version)
 
-    col_classes <- glatos:::glatos_receivers_schema[[ver_txt]]$type
+    col_classes <- glatos_receivers_schema[[ver_txt]]$type
     timestamp_cols <- which(col_classes == "POSIXct")
     date_cols <- which(col_classes == "Date")
     col_classes[c(timestamp_cols, date_cols)] <- "character"
@@ -109,7 +109,9 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   }
   #-end v1.x----------------------------------------------------------------
 
-  # assign class
+  # strip data.table and assign glatos_receivers class
+  data.table::setDF(rec)
+
   rec <- as_glatos_receivers(rec)
 
   return(rec)