merge main; resolve conflicts

ocean-tracking-network · Sep 20, 2024 · a7d580f · a7d580f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ 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: 0.8.0.9012
-Date: 2024-09-17
+Version: 0.8.0
+Date: 2024-09-18
 Depends: R (>= 3.6.0)
 Imports:
 		av,
@@ -24,7 +24,6 @@ Suggests:
     ggplot2,
 		gifski,
 		knitr,
-		mapview,
 		methods,
 		png,
 		purrr,

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,10 @@
 ----
 
-# glatos 0.8.0 (dev)
+# glatos 0.8.9011 (2024-09-18)
 
 
 ## Breaking changes
 
-
 - Changed `make_transition()` to use `jarasterize()` (see New Features) and 
   added input arg `buffer`.
   - Removed dependence on gdalUtilities.
@@ -25,44 +24,23 @@ from earlier versions.
 - Removed 'gganimate_handout' (pdf and html) from 'vignettes'.
 
 
-### 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
 
-#### 2024-08-28
-
-- New function `jarasterize()` to allow rasterization 
-  (esp. with `all_touched = TRUE`) using only `sf` and `raster`. 
-  Used by `make_transition()`.
+- Add new function `vue_convert()` to convert VRL file to CSV file (detection
+  records only; receiver event log records are not supported). 
+    - replaces `vrl2csv()` (deprecated).
+
+- Add new function `vdat_convert()` to convert VRL or VDAT files to 
+  Fathom/VDAT CSV. 
 
-- New function `scale_meters_to_degrees()` to inform selection of `res` argument 
-  to `make_transition()`.
-
-#### 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 for reading data exported from VRL with VUE software.
+    - `read_vue_detection_csv()` to read data from detection file exported 
+    from VUE or created using `vue_convert()` or `vrl2csv()`.
+    - `read_vue_event_csv()` to read data from receiver event log file exported 
+    from VUE.
+
+- Add new function `read_vdat_csv()` to read data exported from VRL or VDAT 
+  using VDAT.exe (e.g., using `vdat_convert()`).
 
 - Add new functions to create, check, and validate `glatos_animals` objects:
     - `glatos_animals()` to construct a `glatos_animals` object from
@@ -102,22 +80,42 @@ from earlier versions.
       names and classes.
     - fixes [issue #126](https://github.com/ocean-tracking-network/glatos/issues/126)
     - fixes [issue #78](https://github.com/ocean-tracking-network/glatos/issues/78)
-
-- Add new function `vue_convert()` to convert VRL file to CSV file (detection
-  records only; receiver event log records are not supported). 
-    - replaces `vrl2csv()` (deprecated).
-
-- Add new function `vdat_convert()` to convert VRL or VDAT files to 
-  Fathom/VDAT CSV. 
-
-- Add new functions for reading data exported from VRL with VUE software.
-    - `read_vue_detection_csv()` to read data from detection file exported 
-    from VUE or created using `vue_convert()` or `vrl2csv()`.
-    - `read_vue_event_csv()` to read data from receiver event log file exported 
-    from VUE.
+
+- New function `jarasterize()` to allow rasterization 
+  (esp. with `all_touched = TRUE`) using only `sf` and `raster`. 
+  Used by `make_transition()`.
 
-- Add new function `read_vdat_csv()` to read data exported from VRL or VDAT 
-  using VDAT.exe (e.g., using `vdat_convert()`).
+- Add new function `scale_meters_to_degrees()` to inform selection of `res` 
+  argument to `make_transition()`.
+
+- In `make_frames()`, allow `terra::SpatVector` input for background map 
+  (`bg_map` arg).
+    - add test for `terra::SpatVector` input
+
+
+### 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)
+
+- Various changes to resolve R CMD check errors, warning, and notes (generally
+  not user-facing).
+
+
+----
 
 
 # glatos 0.7.3 (2024-04-09)

diff --git a/R/package-glatos.r b/R/package-glatos.r
@@ -1,119 +1,8 @@
-#' An R package for the Great Lakes Acoustic Telemetry Observation System
-#'
-#' `glatos` is an R package with functions useful to members of the Great
-#' Lakes Acoustic Telemetry Observation System (<https://glatos.glos.us>).
-#' Functions may be generally useful for processing, analyzing, simulating, and
-#' visualizing acoustic telemetry data, but are not strictly limited to acoustic
-#' telemetry applications.
-#'
-#' @section Package status: *This package is in early development and its
-#'   content is evolving.* To access the package or contribute code, join the
-#'   project at (<https://github.com/ocean-tracking-network/glatos>). If you
-#'   encounter problems or have questions or suggestions, please post a new
-#'   issue or email <cholbrook@usgs.gov> (maintainer: Chris Holbrook).
-#'
-#' @section Installation: Installation instructions can be found at
-#'   <https://github.com/ocean-tracking-network/glatos/wiki/installation-instructions>.
-#'
-#'
-#'
-#' @section Data loading and processing: \describe{
-#'
-#'   \item{[read_glatos_detections] and [read_otn_detections]}{ Fast
-#'   data loading from standard GLATOS and OTN data files to a single structure
-#'   that is compatible with other glatos functions.}
-#'
-#'   \item{[read_glatos_receivers] and [read_otn_deployments]}{
-#'   Reads receiver location histories from standard GLATOS and OTN data files
-#'   to a single structure that is compatible with other glatos functions.}
-#'
-#'   \item{[read_glatos_workbook]}{ Reads project-specific receiver history
-#'   and fish taggging and release data from a standard glatos workbook file.}
-#'
-#'   \item{[read_vemco_tag_specs]}{ Reads transmitter (tag) specifications
-#'   and operating schedule.}
-#'
-#'   \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]).} }
-#'
-#' @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
-#'   detections.}
-#'
-#'  \item{[false_detections]}{ Removes potential false positive detections
-#'  using "short interval" criteria (see [min_lag]).}
-#'
-#'  \item{[detection_events]}{ Distills detection data down to a much
-#'  smaller number of discrete detection events, defined as a change in location
-#'  or time gap that exceeds a threshold.}
-#'
-#'  \item{[summarize_detections]}{ Calculates number of fish detected,
-#'  number of detections, first and last detection timestamps, and/or mean
-#'  location of receivers or groups, depending on specific type of summary
-#'  requested.}
-#'
-#'  \item{[residence_index]}{ calculates the relative proportion of time
-#'  spent at each location.}
-#'
-#'  \item{[REI]}{ calculates the relative activity at each receiver based
-#'  on number of unique species and individual animals.}
-#' }
-#'
-#' @section Visualization and data exploration: \describe{
-#' \item{[abacus_plot]}{ Useful for exploring movement patterns of
-#' individual tagged animals through time.}
-#'
-#' \item{[detection_bubble_plot]}{ Useful for exploring distribution of
-#' tagged individuals among receivers.}
-#'
-#' \item{[interpolate_path], [make_frames], and [make_video]}{
-#' Interpolate spatio-temporal movements, between detections, create video
-#' frames, and stitch frames together to create animated video file using FFmpeg
-#' software.}
-#'
-#' \item{[adjust_playback_time]}{ Modify playback speed of videos and
-#' optionally convert between video file formats. Requires FFmpeg.}
-#' }
-#'
-#' @section Simulation functions for system design and evaluation: \describe{
-#' \item{[calc_collision_prob]}{ Estimates the probability of collisions
-#' for pulse-position-modulation type co-located telemetry transmitters. This is
-#' useful for determining the number of fish to release or tag specifications
-#' (e.g., delay).}
-#'
-#' \item{[receiver_line_det_sim]}{ Simulates detection of acoustic-tagged
-#' fish crossing a receiver line (or single receiver). This is useful for
-#' determining optimal spacing of receviers in a line and tag specifications
-#' (e.g., delay).}
-#'
-#' \item{[crw_in_polygon], [transmit_along_path], and
-#' [detect_transmissions]}{ Individually simulate random fish movement paths
-#' within a water body ([crw_in_polygon]: a random walk in a polygon), tag
-#' signal transmissions along those paths ([transmit_along_path]: time series
-#' and locations of transmissions based on tag specs), and detection of those
-#' transmittions by receivers in a user-defined receiver network
-#' ([detect_transmissions]: time series and locations of detections based on
-#' detection range curve). Collectively, these functions can be used to explore,
-#' compare, and contrast theoretical performance of a wide range of transmitter
-#' and receiver network designs.}
-#' }
-#'
-#' @section Convert glatos data objects to other package classes: \describe{
-#' \item{[convert_glatos_to_att]}{ Converts glatos_detections and
-#' glatos_receiver objects to ATT for compatibility with the Animal Tracking
-#' Toolbox(https://github.com/vinayudyawer/ATT) and the VTrack package.}
-#'
-#' \item{[convert_otn_erddap_to_att]}{ Converts glatos_detections and
-#' transmitter, receiver, and animal metadata from the OTN ERDDAP to ATT format
-#' for compatibility with the Animal Tracking
-#' Toolbox(https://github.com/vinayudyawer/ATT) and the VTrack package.}
-#' }
-
+#' ```{r child = "ReadMe.md"}
+#' ```
 #' @docType package
 #' @name glatos
+#'
 #' @import data.table sp
 #' @importFrom graphics abline axis box legend lines mtext par points symbols
 #'   text
@@ -129,10 +18,13 @@
 # avoid R CMD check note
 globalVariables(".")
 
+# current nickname
+nickname <- function() "very-refreshing-lemonade"
+
 # package startup message
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage(paste0(
     "version ", utils::packageVersion("glatos"),
-    " ('very-refreshing-lemonade')"
+    " ('", nickname(), "')"
   ))
 }
diff --git a/R/util-vdat.r b/R/util-vdat.r
@@ -637,11 +637,12 @@ get_local_vdat_template <- function(vdat_exe_path = NULL) {
 
   vdat_schema <- system2(vdat_cmd, vdat_call, stdout = TRUE)
 
-  # remove ï»¿" BOM from start of first row if present
+  # remove BOM from start of first row if present
   check_bom <- vdat_schema[1]
   Encoding(check_bom) <- "latin1"
 
-  if (grepl("^ï»¿", check_bom)) {
+
+  if (length(suppressMessages(tools::showNonASCII(check_bom))) > 0) {
     Encoding(vdat_schema[1]) <- "latin1"
     vdat_schema[1] <- iconv(vdat_schema[1], "latin1", "ascii", sub = "")
   }