Merge branch 'dev' into dev-no-tibble

ocean-tracking-network · Aug 15, 2024 · 8c54fd4 · 8c54fd4
2 parents c7fc9f2 + d4d106f
commit 8c54fd4
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diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
@@ -46,7 +46,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache styler
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.styler-location.outputs.location }}
           key: ${{ runner.os }}-styler-${{ github.sha }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,7 +22,6 @@ Imports:
 		readxl,
 		sf,
 		sp,
-		units,
 		zip
 Suggests: 
 		gganimate,
@@ -48,7 +47,7 @@ Authors@R: c(
 License: GPL-2
 LazyLoad: yes
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

diff --git a/NAMESPACE b/NAMESPACE
@@ -100,7 +100,7 @@ importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(graphics,symbols)
 importFrom(graphics,text)
-importFrom(lubridate,parse_date_time)
+importFrom(lubridate,fast_strptime)
 importFrom(stats,approx)
 importFrom(stats,dnorm)
 importFrom(stats,ecdf)

diff --git a/R/extdata.r b/R/extdata.r
@@ -8,8 +8,8 @@
 #'
 #' @section Filename: walleye_detections.zip
 #'
-#' @usage
-#' system.file("extdata", "walleye_detections.zip", package="glatos")
+#' @examples
+#' system.file("extdata", "walleye_detections.zip", package = "glatos")
 #'
 #' @author Todd Hayden
 #'
@@ -37,8 +37,8 @@ NULL
 #'
 #' @section Filename: SMRSL_GLATOS_20140828.xlsm
 #'
-#' @usage
-#' system.file("extdata", "SMRSL_GLATOS_20140828.xlsm", package="glatos")
+#' @examples
+#' system.file("extdata", "SMRSL_GLATOS_20140828.xlsm", package = "glatos")
 #'
 #' @author Chris Holbrook
 #'
@@ -53,12 +53,12 @@ NULL
 #'
 #' @format Folder contains 30 sequentially labeled .png image files
 #'
-#' @name video images
+#' @name video-images
 #'
 #' @section Filename: frames
 #'
-#' @usage
-#' system.file("extdata", "frames", package="glatos")
+#' @examples
+#' system.file("extdata", "frames", package = "glatos")
 #'
 #' @author Todd Hayden
 #'
@@ -77,8 +77,8 @@ NULL
 #'
 #' @section Filename: shoreline.zip
 #'
-#' @usage
-#' system.file("extdata", "shoreline.zip", package="glatos")
+#' @examples
+#' system.file("extdata", "shoreline.zip", package = "glatos")
 #'
 #' @author Todd Hayden
 #'
@@ -95,7 +95,7 @@ NULL
 #'
 #' @section Filename: otn_aat_animals.csv
 #'
-#' @usage
+#' @examples
 #' system.file("extdata", "otn_aat_animals.csv", package = "glatos")
 #'
 #' @source Ryan Gosse, Ocean Tracking Network
@@ -111,7 +111,7 @@ NULL
 #'
 #' @section Filename: otn_aat_receivers.csv
 #'
-#' @usage
+#' @examples
 #' system.file("extdata", "otn_aat_receivers.csv", package = "glatos")
 #'
 #' @source Ryan Gosse, Ocean Tracking Network
@@ -127,7 +127,7 @@ NULL
 #'
 #' @section Filename: otn_aat_tag_releases.csv
 #'
-#' @usage
+#' @examples
 #' system.file("extdata", "otn_aat_tag_releases.csv", package = "glatos")
 #'
 #' @source Ryan Gosse, Ocean Tracking Network

diff --git a/R/load-prepare_deploy_sheet.R b/R/load-prepare_deploy_sheet.R
@@ -36,6 +36,13 @@
 #' @export
 
 prepare_deploy_sheet <- function(path, header_line = 5, sheet_name = 1, combine_arr_stn = TRUE) {
+  ##  Declare global variables for NSE & R CMD check
+  DEPLOY_LAT <- DEPLOY_LONG <- INS_MODEL_NO <-
+    `DEPLOY_DATE_TIME   (yyyy-mm-ddThh:mm:ss)` <-
+    `RECOVER_DATE_TIME (yyyy-mm-ddThh:mm:ss)` <- STATION_NO <-
+    OTN_ARRAY <- station <- ins_model_no <- deploy_lat <- deploy_long <-
+    deploy_date_time <- recover_date_time <- NULL
+
   deploy_sheet <- readxl::read_excel(path,
     sheet = sheet_name,
     skip = header_line - 1,

diff --git a/R/load-prepare_tag_sheet.R b/R/load-prepare_tag_sheet.R
@@ -31,6 +31,10 @@
 #' @export
 
 prepare_tag_sheet <- function(path, header_line = 5, sheet_name = 2) {
+  ##  Declare global variables for NSE & R CMD check
+  TAG_CODE_SPACE <- TAG_ID_CODE <- EST_TAG_LIFE <- UTC_RELEASE_DATE_TIME <-
+    SEX <- RELEASE_LATITUDE <- RELEASE_LONGITUDE <- SCIENTIFIC_NAME <- NULL
+
   tag_sheet <- readxl::read_excel(path, sheet = sheet_name, skip = header_line - 1)
   tag_sheet <- tag_sheet %>% dplyr::mutate(
     transmitter_id = paste(TAG_CODE_SPACE, TAG_ID_CODE, sep = "-"),

diff --git a/R/load-read_glatos_detections.r b/R/load-read_glatos_detections.r
@@ -16,8 +16,8 @@
 #'   never need to set this argument (`NULL` should work).
 #'
 #' @details Data are loaded using [fread][data.table::fread] and timestamps are
-#' coerced to POSIXct using [fastPOSIXct][fasttime::fastPOSIXct]. All times must
-#' be in UTC timezone per GLATOS standard.
+#' coerced to POSIXct using [fast_strptime][lubridate::fast_strptime]. All times
+#' must be in UTC timezone per GLATOS standard.
 #'
 #' @details Column `animal_id` is considered a required column by many other
 #'   functions in this package, so it will be created if any records are `NULL`.
@@ -40,7 +40,7 @@
 #'
 #' det <- read_glatos_detections(det_file)
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #'
 #' @export
 read_glatos_detections <- function(det_file, version = NULL) {
@@ -84,16 +84,13 @@ read_glatos_detections <- function(det_file, version = NULL) {
       na.strings = c("", "NA")
     )
 
-    # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-    #  timestamp must be in UTC; and tz argument sets the tzone attr only
-    options(lubridate.fasttime = TRUE)
+    # coerce timestamps to POSIXct
     for (j in timestamp_cols) {
       data.table::set(dtc,
         j = glatos_detection_schema[[vversion]]$name[j],
-        value = lubridate::parse_date_time(
+        value = lubridate::fast_strptime(
           dtc[[glatos_detection_schema[[vversion]]$name[j]]],
-          orders = "ymd HMS",
-          tz = "UTC"
+          format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
         )
       )
     }

diff --git a/R/load-read_glatos_receivers.r b/R/load-read_glatos_receivers.r
@@ -15,7 +15,7 @@
 #'   `"1.0"`. Any other values will trigger an error.
 #'
 #' @details Data are loaded using [fread][data.table::fread] and timestamps are
-#'   coerced to POSIXct using [fastPOSIXct][fasttime::fastPOSIXct]. All
+#'   coerced to POSIXct using [fast_strptime][lubridate::fast_strptime]. All
 #'   timestamps must be 'YYYY-MM-DD HH:MM' format and in UTC timezone per GLATOS
 #'   standard.
 #'
@@ -36,7 +36,7 @@
 #'
 #' rcv <- read_glatos_receivers(rec_file)
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #'
 #' @export
 read_glatos_receivers <- function(rec_file, version = NULL) {
@@ -80,16 +80,13 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
     # read data
     rec <- data.table::fread(rec_file, sep = ",", colClasses = col_classes)
 
-    # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-    #  timestamp must be in UTC; and tz argument sets the tzone attr only
-    options(lubridate.fasttime = TRUE)
+    # coerce timestamps to POSIXct
     for (j in timestamp_cols) {
       data.table::set(rec,
         j = glatos_receivers_schema[[ver_txt]]$name[j],
-        value = lubridate::parse_date_time(
+        value = lubridate::fast_strptime(
           rec[[glatos_receivers_schema[[ver_txt]]$name[j]]],
-          orders = "ymd HMS",
-          tz = "UTC"
+          format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
         )
       )
     }

diff --git a/R/load-read_otn_deployments.R b/R/load-read_otn_deployments.R
@@ -18,7 +18,7 @@
 #'
 #' @details
 #' Data are loaded using [data.table::fread()] package and timestamps
-#' are coerced to POSIXct using the [fasttime::fastPOSIXct()]. All
+#' are coerced to POSIXct using [lubridate::fast_strptime()]. All
 #' times must be in UTC timezone per GLATOS standard.
 #'
 #' @details
@@ -39,7 +39,7 @@
 #' dep <- read_otn_deployments(deployment_file)
 #' }
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #' @importFrom dplyr mutate
 #' @export
 read_otn_deployments <- function(deployment_file,
@@ -73,7 +73,10 @@ read_otn_deployments <- function(deployment_file,
   for (j in timestamp_cols) {
     data.table::set(dtc,
       j = otn_deployments_schema$name[j],
-      value = lubridate::parse_date_time(dtc[[otn_deployments_schema$name[j]]], orders = "ymd", tz = "UTC")
+      value = lubridate::fast_strptime(
+        dtc[[otn_deployments_schema$name[j]]],
+        format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
+      )
     )
   }
   # coerce dates to date

diff --git a/R/load-read_otn_detections.r b/R/load-read_otn_detections.r
@@ -9,7 +9,7 @@
 #'
 #' @details
 #' Data are loaded using [data.table::fread()] package and timestamps
-#' are coerced to POSIXct using the [fasttime::fastPOSIXct()]. All
+#' are coerced to POSIXct using [lubridate::fast_strptime()]. All
 #' times must be in UTC timezone per GLATOS standard.
 #'
 #' @details
@@ -28,7 +28,7 @@
 #' )
 #' det <- read_otn_detections(det_file)
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #'
 #' @export
 read_otn_detections <- function(det_file) {
@@ -53,13 +53,14 @@ read_otn_detections <- function(det_file) {
     dtc$tagname <- dtc$fieldnumber
     dtc$codespace <- purrr::map(dtc$fieldnumber, get_codemap)
   }
-  # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-  #  timestamp must be in UTC; and tz argument sets the tzone attr only
-  options(lubridate.fasttime = TRUE)
+  # coerce timestamps to POSIXct
   for (j in timestamp_cols) {
     data.table::set(dtc,
       j = otn_detection_schema$name[j],
-      value = lubridate::parse_date_time(dtc[[otn_detection_schema$name[j]]], orders = "ymd HMS", tz = "UTC")
+      value = lubridate::fast_strptime(
+        dtc[[otn_detection_schema$name[j]]],
+        format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
+      )
     )
   }
   # coerce dates to date

diff --git a/R/load-read_vdat_csv.r b/R/load-read_vdat_csv.r
@@ -1,7 +1,5 @@
 #' Read data from an Innovasea Fathom VDAT CSV file
 #'
-#' Read data from an Innovasea Fathom VDAT CSV file
-#'
 #' @param src A character string with path and name of an Innovasea VDAT CSV
 #'   detection file. If only file name is given, then the file must be located
 #'   in the working directory.
@@ -136,6 +134,9 @@ read_vdat_csv <- function(src,
     return()
   }
 
+  ##  Declare global variables for NSE & R CMD check
+  record_type <- NULL
+
   # Identify vdat csv format version and vdat.exe version that created input csv
   vdat_header <- data.table::fread(file = src, nrows = 1L, header = FALSE)
 
@@ -218,13 +219,13 @@ read_vdat_csv <- function(src,
     keep.by = FALSE
   )
 
-  data(vdat_csv_schema)
+  utils::data("vdat_csv_schema", envir = environment())
 
   vdat_csv_schema <- vdat_csv_schema[[paste0("v", src_version$fathom_csv)]]
 
 
   # Preallocate list; element = record type
-  vdat <- setNames(
+  vdat <- stats::setNames(
     object = vector("list", length(vdat_list)),
     nm = names(vdat_list)
   )

diff --git a/R/load-write_vdat_csv.r b/R/load-write_vdat_csv.r
@@ -74,6 +74,11 @@ write_vdat_csv <- function(vdat,
                            out_file = NULL,
                            output_format = "csv.fathom",
                            include_empty = FALSE) {
+  ##  Declare global variables for NSE & R CMD check
+  record_type <- dt2 <- `Device Time (UTC)` <- `Time Correction (s)` <-
+    `Ambient (deg C)` <- `Ambient Min (deg C)` <- `Ambient Max (deg C)` <-
+    `Ambient Mean (deg C)` <- `Internal (deg C)` <- ..txt_cols <- txt <- NULL
+
   # Check input class
   if (!inherits(vdat, "vdat_list")) {
     stop(
@@ -107,7 +112,7 @@ write_vdat_csv <- function(vdat,
   if (out_file_type == "dir") {
     out_file_name <- gsub("\\.vrl$|\\.vdat$",
       out_file_ext,
-      tail(vdat$DATA_SOURCE_FILE$`File Name`, 1),
+      utils::tail(vdat$DATA_SOURCE_FILE$`File Name`, 1),
       ignore.case = TRUE
     )
 
@@ -142,12 +147,12 @@ write_vdat_csv <- function(vdat,
 
   # Compress each list element into a character vector
 
-  vdat_lines_body <- setNames(
+  vdat_lines_body <- stats::setNames(
     object = vector("list", length(record_types)),
     record_types
   )
 
-  vdat_lines_header <- setNames(
+  vdat_lines_header <- stats::setNames(
     object = vector("list", length(record_types)),
     record_types
   )

diff --git a/R/package-glatos.r b/R/package-glatos.r
@@ -35,12 +35,12 @@
 #'
 #'   \item{[real_sensor_values]}{ Converts 'raw' transmitter sensor (e.g.,
 #'   depth, temperature) to 'real'-scale values (e.g., depth in meters) using
-#'   transmitter specification data (e.g., from read\_vemco\_tag\_specs).} }
+#'   transmitter specification data (e.g., from [read_vemco_tag_specs]).} }
 #'
 #' @section Filtering and summarizing: \describe{
 #'   \item{[min_lag]}{
 #'   Facilitates identification and removal of false positive detections by
-#'   calculating the minimum time interval (min\_lag) between successive
+#'   calculating the minimum time interval (min_lag) between successive
 #'   detections.}
 #'
 #'  \item{[false_detections]}{ Removes potential false positive detections
@@ -124,7 +124,10 @@
 #' @importFrom grDevices bmp colorRampPalette dev.new dev.off jpeg png rainbow
 #'   tiff
 #' @importFrom dplyr %>%
-globalVariables(".") # to avoid R CMD check note
+"_PACKAGE"
+
+# avoid R CMD check note
+globalVariables(".")
 
 # package startup message
 .onAttach <- function(libname, pkgname) {

diff --git a/R/proc-min_lag.r b/R/proc-min_lag.r
@@ -64,6 +64,10 @@
 #' @export
 
 min_lag <- function(det) {
+  ##  Declare global variables for NSE & R CMD check
+  ord <- transmitter_codespace <- transmitter_id <- receiver_sn <-
+    detection_timestamp_utc <- NULL
+
   # coerce to data.table
   dtc <- data.table::as.data.table(det)
 

diff --git a/R/proc-real_sensor_values.r b/R/proc-real_sensor_values.r
@@ -110,6 +110,10 @@
 #' @export
 
 real_sensor_values <- function(det, tag_specs) {
+  ##  Declare global variables for NSE & R CMD check
+  ord <- transmitter_codespace <- transmitter_id <- code_space <- id_code <-
+    sensor_value_real <- sensor_intercept <- sensor_value <- sensor_slope <- NULL
+
   # coerce to data.table
   dtc <- data.table::as.data.table(det)