build for v.1.1.0

ABbiodiversity · Oct 12, 2023 · f2366ba · f2366ba
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diff --git a/.DS_Store b/.DS_Store
diff --git a/NEWS.md b/NEWS.md
@@ -2,14 +2,16 @@
 
 ## Major changes
 
-* `wildRtrax` now honours WildTrax report structures. See more here. 
+* `wildRtrax` now honours new WildTrax report structures. Future changes will incorporate standardized naming in syncing functions.
 * Replaced geospatial functionalities from `rgdal`, `rgeos` and `maptools` with `sf`, `sp` and `terra` packages. Added functionality with the `suntools` package. Users should re-download the package by October 2023 in-line with the former package retirement: https://geocompx.org/post/2023/rgdal-retirement/.
 
 ## Minor changes
 
-* Tweaks to [Acoustic data wrangling](https://abbiodiversity.github.io/wildRtrax/articles/acoustic-data-wrangling.html).
+* Tweaks to [Acoustic data wrangling](https://abbiodiversity.github.io/wildRtrax/articles/acoustic-data-wrangling.html) for (#16)
 * Addition of geospatial assets. Users should be warned package size is now ~40 MB.
-* Moved TMTT predictions from csv to .RDS.
+* Moved TMTT predictions from csv to .RDS file.
+* Work flow repairs to `wt_get_species()` and `wt_tidy_species()` (#21)
+* Replaced `utils::read.csv()` to `readr::read_csv()` in `wt_download_report()` (#20)
 
 # wildRtrax 1.0.1
 

diff --git a/R/acoustic-pre-processing.R b/R/acoustic-pre-processing.R
@@ -351,10 +351,11 @@ wt_run_ap <- function(x = NULL, fp_col = file_path, audio_dir = NULL, output_dir
   # Track progress of run
   # progressr::with_progress({
   #   p <- progressr::progressor(steps = nrow(files))
-    files <- files %>%
+    files <- files %>>%
+      "Starting AP run - this may take a while depending on your machine..." %>>%
       tibble::as_tibble() %>%
       dplyr::rename("file_path" = 1) %>%
-      furrr::future_map(.x = .$file_path, .f = ~ system2(path_to_ap, sprintf('audio2csv "%s" "Towsey.Acoustic.yml" "%s" "-p"', .x, output_dir)), furrr_options(seed = T))
+      furrr::future_map(.x = .$file_path, .f = ~ suppressMessages(system2(path_to_ap, sprintf('audio2csv "%s" "Towsey.Acoustic.yml" "%s" "-p"', .x, output_dir)), furrr_options(seed = T)))
   # })
   return(message('Done!'))
 
@@ -401,7 +402,7 @@ wt_glean_ap <- function(x = NULL, input_dir, purpose = c("quality","abiotic","bi
   if (dir.exists(input_dir)) {
     ind <-
       fs::dir_ls(input_dir, regexp = "*.Indices.csv", recurse = T) %>%
-      map_dfr( ~ read_csv(., progress = F)) %>%
+      map_dfr( ~ read_csv(., show_col_types = F)) %>%
       relocate(c(FileName, ResultMinute)) %>%
       select(-c(ResultStartSeconds, SegmentDurationSeconds,RankOrder,ZeroSignal)) %>%
       pivot_longer(!c(FileName, ResultMinute),
@@ -757,9 +758,8 @@ wt_make_aru_tasks <- function(input, output=NULL, task_method = c("1SPM","1SPT",
   }
 }
 
-#' Upload hits from a Wildlife Acoustics classifier
+#' Convert Kaleidoscope output to tags
 #'
-#' @section `wt_kaleidoscope_tags`
 #'
 #' @description `wt_kaleidoscope_tags` Takes the classifier output from Wildlife Acoustics Kaleidoscope and converts them into a WildTrax tag template for upload
 #'
@@ -845,7 +845,7 @@ wt_kaleidoscope_tags <- function (input, output, tz, freq_bump = T) {
 
 }
 
-#' Takes the classifier output from Wildlife Acoustics Songscope and converts them into a WildTrax tag template for upload
+#' Convert Songscope output to tags
 #'
 #' @param input Character; The path to the input csv
 #' @param output Character; Path where the output file will be stored
@@ -859,13 +859,6 @@ wt_kaleidoscope_tags <- function (input, output, tz, freq_bump = T) {
 #' @import dplyr tidyr readr pipeR stringr lubridate tibble
 #' @export
 #'
-#' @examples
-#' \dontrun{
-#' wt_songscope_tags(input = input.csv, output = tags.csv,
-#' species_code, = "CONI", method = "1SPT",
-#' vocalization_type = "Call", task_length = 180)
-#' }
-#'
 #' @return A csv formatted as a WildTrax tag template
 
 wt_songscope_tags <- function (input, output = c("env","csv"),

diff --git a/R/wildRtrax.R b/R/wildRtrax.R
@@ -40,4 +40,4 @@ utils::globalVariables(c("%>>%", ".", "name", "size_Mb", "file_path", "file_ext"
                          "tag_spectrogram_url",
                          "task_method",
                          "wt_spp_table","<<-","clip_type","output_filename","image_date_time",
-                         "unlist", "PC", "sens"))
+                         "unlist", "PC", "sens","organizationId","organizationName"))
diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@
 
 ## Installation
 
-You can install version 1.0 of `wildRtrax` directly from this repository with:
+You can install version 1.1.0 of `wildRtrax` directly from this repository with:
 
 ``` r
 # install.packages("remotes")
@@ -35,12 +35,12 @@ The development version of the package will be periodically merged and will be r
 All functions begin with a `wt_*` prefix. Column names and metadata align with the WildTrax infrastructure. The goal is to follow the work flow of pre-processing, linking with WildTrax, download and analysis. Some functions are built specifically for ARUs :sound:, cameras :camera: or point counts :bird:, while others are used for all sensors. :bat: denotes ultrasonic functionalities.
 
 - Pre-process acoustic data
-  - `wt_audio_scanner()` :sound:
+  - `wt_audio_scanner()` :sound: :bat:
   - `wt_run_ap()` :sound:
   - `wt_glean_ap()` :sound:
   - `wt_signal_level()` :sound:
-  - `wt_chop()` :sound:
-  - `wt_make_aru_tasks()` :sound:
+  - `wt_chop()` :sound: :bat:
+  - `wt_make_aru_tasks()` :sound: :bat:
   - `wt_songscope_tags()` :sound:
   - `wt_kaleidoscope_tags()` :sound: :bat:
 - Download data from WildTrax
@@ -49,15 +49,15 @@ All functions begin with a `wt_*` prefix. Column names and metadata align with t
   - `wt_download_report()` :camera: :sound: :bird: :bat:
     - Available reports: `main, project, location, recording, image_set, image, tag, point_count, megadetector, megaclassifer, birdnet`
   - `wt_get_species()` :camera: :sound: :bird: :bat:
-  - `wt_download_tags()` :sound:
+  - `wt_download_tags()` :sound: :bat:
 - Analyze data
   - `wt_summarise_cam()` :camera:
   - `wt_ind_detect()` :camera:
 - Convenience functions
   - `wt_location_distances()` :sound: :camera: :bird: :bat:
   - `wt_tidy_species()` :sound: :camera: :bird: :bat:
   - `wt_replace_tmtt()` :sound:
-  - `wt_make_wide()` :sound: :camera: :bird: :bat:
+  - `wt_make_wide()` :sound: :bird: :bat:
   - `wt_format_occupancy()` :sound: :bird:
   - `wt_qpad_offsets()` :sound: :bird:
 
@@ -68,12 +68,11 @@ To report bugs, request additional features, or get help using the package, plea
 
 ## Contributors
 
-* `wildRtrax` is authored and created by [Alexander G. MacPhail](https://github.com/agmacpha), created and maintained by [Marcus Becker](https://github.com/mabecker89) and created by [Dr. Elly Knight](https://github.com/ecknight). The [Alberta Biodiversity Monitoring Institute](http://https://abmi.ca/home.html) provides ongoing support, development and funding for the package.
-* Many thanks to [Dr. Richard Hedley](https://richardwhedley.wordpress.com/) for providing the basis for the `wt_wac_info()` internal function for *wac* file support
+* `wildRtrax` is authored, created and maintained by [Alexander G. MacPhail](https://github.com/agmacpha) and [Marcus Becker](https://github.com/mabecker89), with significant contributions from [Dr. Elly Knight](https://github.com/ecknight) and [Dr. Richard Hedley](https://richardwhedley.wordpress.com/). We encourage ongoing contributions and collaborations to improve the package into the future. The [Alberta Biodiversity Monitoring Institute](https://abmi.ca) provides ongoing support, development and funding.
 
 ## License
 
-This R package is licensed under [MIT license](https://github.com/ABbiodiversity/wildRtrax/blob/master/LICENSE)© 2023 Marcus Becker, Alex MacPhail, Elly Knight and the [Alberta Biodiversity Monitoring Institute](http://https://abmi.ca/home.html).
+This R package is licensed under [MIT license](https://github.com/ABbiodiversity/wildRtrax/blob/master/LICENSE)© 2023 Marcus Becker, Alex MacPhail, Elly Knight and the [Alberta Biodiversity Monitoring Institute](https://abmi.ca).
 
 ## Code of Conduct
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -41,6 +41,7 @@ reference:
   - wildRtrax
 news:
   releases:
+  - text: wildRtrax 1.1.0
   - text: wildRtrax 1.0.1
   - text: wildRtrax 1.0.0
   - text: wildRtrax 0.1.0

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html