IslasGECI · devarops · Oct 16, 2025 · Oct 10, 2025 · Oct 10, 2025 · Oct 10, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,12 +9,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 ### Fixed
-- `classify_breed_stage()` takes into account "breeding fail" option.
 
 ### Changed
 
 ### Removed
 
+## [1.2.0] - 2025-10-10
+### Added
+- Deprecation warning for `write_bl_table()` function.
+
+### Fixed
+- `classify_breed_stage()` takes into account "breeding fail" option.
+- `construct_bl_table()` round coordinates to 6 decimal places to avoid floating point issues.
+
 ## [1.1.0] - 2025-09-09
 ### Added
 - `classify_breed_stage()` use the hatching and brood end dates to classify
@@ -30,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 - `clean_gps_from_txt()` deprecated. Use `clean_gps()` with `.txt` file instead.
 
-[unreleased]: https://github.com/IslasGECI/templater/compare/v1.1.0...HEAD
+[unreleased]: https://github.com/IslasGECI/templater/compare/v1.2.0...HEAD
+[1.2.0]: https://github.com/IslasGECI/templater/compare/v1.1.0...v1.2.0
 [1.1.0]: https://github.com/IslasGECI/templater/compare/v1.0.0...v1.1.0
 [1.0.0]: https://github.com/IslasGECI/templater/releases/tag/v1.0.0
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,24 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the following metadata."
+title: "seabird_tracking"
+type: software
+authors:
+  - family-names: "Olvera-Guerrero"
+    given-names: "Guillermo"
+    github: "MemoOlv"
+    orcid: "https://orcid.org/0000-0002-6900-5315"
+  - family-names: "Rojas-Mayoral"
+    given-names: Evaristo
+    orcid: "https://orcid.org/0000-0001-6812-9562"
+    github: devarops
+  - family-names: "Villasante-Barahona"
+    given-names: "Mario"
+    orcid: "https://orcid.org/0009-0001-7867-8570"
+    github: "mvillasante"
+repository-code: "https://github.com/IslasGECI/seabird_tracking"
+keywords:
+  - ecology
+  - R
+  - seabird
+  - tracking
+license: "agpl-3.0-only"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,12 +13,13 @@ Imports:
     bycatch,
     dplyr,
     geci.optparse,
+    lifecycle,
     lubridate,
     R6,
     readr,
     rjson,
     stringr,
-    tidyverse,
+    tidyverse
 LazyData: true
 License: AGPL-3.0-or-later
 Roxygen: list(markdown = TRUE)
@@ -33,4 +34,4 @@ Suggests:
     testthat,
     testtools,
 Type: Package
-Version: 1.1.0
+Version: 1.2.0
diff --git a/Makefile b/Makefile
@@ -65,6 +65,6 @@ green: format
 
 refactor: format
 	Rscript -e "devtools::test(stop_on_failure = TRUE)" \
-	&& (git add R/*.R tests/testthat/*.R && git commit -m "♻️  Refactor") \
+	&& (git add R/*.R tests/testthat/*.R && git commit -m "♻️ Refactor: ${message}") \
 	|| git  restore R/*.R tests/testthat/*.R
 	chmod g+w -R .
diff --git a/R/BL_data_format.R → R/birdlife_data_format.R b/R/BL_data_format.R → R/birdlife_data_format.R
@@ -4,6 +4,10 @@
 construct_bl_table <- function(breeding_status, tracking_data, config_content) {
   data_table <- join_seabird_breeding_status_with_tracking_data(breeding_status, tracking_data) |>
     mutate(track_id = bird_id, age = "adult", equinox = NA, argos_quality = NA)
+  data_table_with_trips <- data_table |>
+    classify_breed_stage() |>
+    bycatch::get_trips(config_content)
+
   ordered_columns <- c(
     "bird_id",
     "sex",
@@ -17,14 +21,15 @@ construct_bl_table <- function(breeding_status, tracking_data, config_content) {
     "equinox",
     "argos_quality"
   )
-  data_table_with_trips <- data_table |>
-    classify_breed_stage() |>
-    bycatch::get_trips(config_content)
-
   data_table_with_trips@data |>
     rename(time_gmt = time, latitude = Latitude, longitude = Longitude, track_id = tripID) |>
+    round_coordinates(6) |>
     select(all_of(ordered_columns))
 }
+round_coordinates <- function(data, digits = 6) {
+  data |>
+    mutate(latitude = round(latitude, digits), longitude = round(longitude, digits))
+}
 
 join_seabird_breeding_status_with_tracking_data <- function(breeding_status, tracking_data) {
   tracking_data_with_season <- tracking_data |>

diff --git a/R/cli.R b/R/cli.R
@@ -1,5 +1,30 @@
+#' Write a CSV with the tracking data as Seabird tracking Database requires.
+#'
+#' Reads breeding status data, tracking data, and configuration data, constructs a BirdLife (BL) table,
+#' and writes the resulting table to a CSV file. All input and output paths are provided via the `options` list.
+#'
+#' @param options A named list of file paths. Must contain:
+#'   \itemize{
+#'     \item \code{breeding-status-path}: Path to the breeding status CSV file.
+#'     \item \code{tracking-data-path}: Path to the tracking data CSV file.
+#'     \item \code{config-path}: Path to the configuration JSON file.
+#'     \item \code{output-path}: Path where the output CSV will be written.
+#'   }
+#'
+#' @return Invisibly returns \code{NULL}. Called for its side effect of writing a CSV file.
 #' @export
-write_bl_table <- function(options) {
+#'
+#' @examples
+#' \dontrun{
+#' options <- list(
+#'   "breeding-status-path" = "breeding_status.csv",
+#'   "tracking-data-path" = "gps-albatros-guadalupe.csv",
+#'   "config-path" = "config_file.json",
+#'   "output-path" = "result.csv"
+#' )
+#' write_birdlife_table(options)
+#' }
+write_birdlife_table <- function(options) {
   breeding_status <- read_csv(options[["breeding-status-path"]], show_col_types = FALSE)
   tracking_data <- read_csv(options[["tracking-data-path"]], show_col_types = FALSE)
   config_content <- read_config(options[["config-path"]])
@@ -8,6 +33,33 @@ write_bl_table <- function(options) {
 }
 
 #' @export
+write_bl_table <- function(options) {
+  lifecycle::deprecate_warn(
+    when = "1.2.0",
+    what = "write_bl_table()",
+    with = "write_birdlife_table()"
+  )
+  write_birdlife_table(options)
+}
+
+#' Get command-line options for domain-specific input files and output
+#'
+#' Constructs a set of command-line options for specifying file paths relevant to the seabird tracking domain,
+#' including breeding status data, tracking data, configuration, and output location.
+#'
+#' @return A named list of options with file paths for:
+#'   \itemize{
+#'     \item \code{breeding-status-path}: Breeding status CSV file
+#'     \item \code{tracking-data-path}: Tracking data CSV file
+#'     \item \code{config-path}: Configuration JSON file
+#'     \item \code{output-path}: Output CSV file
+#'   }
+#' The returned options are typically used to configure file locations for downstream data processing functions.
+#' @export
+#'
+#' @examples
+#' opts <- get_domain_specific_options()
+#' opts[["breeding-status-path"]]
 get_domain_specific_options <- function() {
   breeding_status_path <- geci.optparse::character_option(c("-b", "--breeding-status-path"), default = "/workdir/breeding_status.csv", help = "File path of the breeding_status_database")
   tracking_path <- geci.optparse::character_option(c("-t", "--tracking-data-path"), default = "/workdir/gps-albatros-guadalupe.csv", help = "File path of the tracking database")

diff --git a/R/seabird.tracking-package.R b/R/seabird.tracking-package.R
@@ -0,0 +1,7 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom lifecycle deprecated
+## usethis namespace: end
+NULL
diff --git a/README.md b/README.md
@@ -1,6 +1,5 @@
 <a href="https://www.islas.org.mx"><img src="https://www.islas.org.mx/img/logo.svg" align="right" width="256" /></a>
 
-# Template for R projects
-
-## Step to use
+# Seabird Tracking Data Processing
 
+**seabird_tracking** is a set of utilities to process raw seabird tracking data and construct standardized datasets for the Seabird Tracking Database.
diff --git a/tests/data/gps-albatros-guadalupe.csv b/tests/data/gps-albatros-guadalupe.csv
@@ -16,8 +16,8 @@ date,latitude,longitude,name,time
 2014-02-16,28.884113,-118.292143,LAAL05,13:00:00
 2014-02-17,28.884217,-118.291543,LAAL05,14:00:00
 2017-02-15,29.390127,-118.315544,1,11:00:00
-2017-02-17,32.203983,-118.396667,1,12:00:00
-2017-02-17,32.380726,-118.869003,1,13:00:00
+2017-02-17,32.203983000001,-118.396667,1,12:00:00
+2017-02-17,32.380726000001,-118.869003,1,13:00:00
 2017-02-21,28.884108,-118.291504,2,14:00:00
 2017-02-21,28.884073,-118.291519,2,15:00:00
 2017-02-22,28.884121,-118.291504,2,16:00:00
@@ -28,11 +28,11 @@ date,latitude,longitude,name,time
 2018-01-29,42.574684,-139.830383,4E8,12:00:00
 2018-01-29,42.460968,-139.748444,4E8,13:00:00
 2018-01-29,42.431324,-139.639725,4E8,14:00:00
-2016-01-29,42.168236,-140.09169,4E8,10:00:00
+2016-01-29,42.168236,-140.091690000001,4E8,10:00:00
 2016-01-29,42.574684,-139.830383,4E8,11:00:00
-2016-01-29,42.460968,-139.748444,4E8,12:00:00
+2016-01-29,42.460968,-139.74844400000001,4E8,12:00:00
 2016-01-29,42.431324,-139.639725,4E8,13:00:00
 2017-12-31,42.168236,-140.09169,4E8,22:00:00
 2017-12-31,42.574684,-139.830383,4E8,23:00:00
 2018-01-01,42.460968,-139.748444,4E8,00:01:00
-2018-01-01,42.431324,-139.639725,4E8,01:00:00
+2018-01-01,42.431324,-139.63972500000001,4E8,01:00:00
diff --git a/tests/testthat/test-BL_data_format.R → tests/testthat/test-birdlife_data_format.R b/tests/testthat/test-BL_data_format.R → tests/testthat/test-birdlife_data_format.R
@@ -28,6 +28,13 @@ describe("Construct BL table", {
     obtained_columns <- colnames(obtained_bl_table)
     expect_true(all(expected_columns %in% obtained_columns))
   })
+  are_all_rounded <- function(x, digits = 6) {
+    all(round(x, digits) == x, na.rm = TRUE)
+  }
+  it("Round coordinates", {
+    expect_true(are_all_rounded(obtained_bl_table$latitude, 6))
+    expect_true(are_all_rounded(obtained_bl_table$longitude, 6))
+  })
   it("Classify breed stage from joined data", {
     expected_breed_stage <- "chick-rearing"
     obtained_breed_stage <- obtained_bl_table[[1, "breed_stage"]]

diff --git a/tests/testthat/test-cli.R b/tests/testthat/test-cli.R
@@ -1,6 +1,6 @@
 describe("write_bl_table", {
   it("construct_bl_table ", {
-    output_path <- "/workdir/tests/data/bl_albatross_guadalupe.csv"
+    output_path <- "/workdir/tests/data/birdlife_albatross_guadalupe.csv"
     config_path <- "/workdir/tests/data/trips_config.json"
     testtools::if_exist_remove(output_path)
     options_list <- list(
@@ -9,7 +9,7 @@ describe("write_bl_table", {
       "tracking-data-path" = "/workdir/tests/data/gps-albatros-guadalupe.csv",
       "output-path" = output_path
     )
-    write_bl_table(options_list)
+    write_birdlife_table(options_list)
     expect_true(testtools::exist_output_file(output_path))
   })
 })

diff --git a/tests/testthat/test_version.R b/tests/testthat/test_version.R
@@ -1,6 +1,6 @@
 describe("Get version of the module", {
-  it("The version is 1.1.0", {
-    expected_version <- c("1.1.0")
+  it("The version is 1.2.0", {
+    expected_version <- c("1.2.0")
     obtained_version <- packageVersion("seabird.tracking")
     version_are_equal <- expected_version == obtained_version
     expect_true(version_are_equal)