From 321cb7e18229dd2158fce3688f59f7e3cb47abc8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciencia=20de=20Datos=20=E2=80=A2=20GECI?= Date: Thu, 2 Oct 2025 14:00:09 -0700 Subject: [PATCH 1/6] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20=20Refactor?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- CHANGELOG.md | 14 +++++++------- R/track_example.R | 7 ++++--- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 068fff3..12446a3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] +### Added +- `formatDT = "ymd_HMS"` in order to remove parse date time warning. +### Fixed + +### Changed + +### Removed ## [0.3.0] - 2025-06-25 @@ -19,13 +26,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [0.1.0] - 2024-10-03 -### Added - -### Fixed - -### Changed - -### Removed [unreleased]: https://github.com/IslasGECI/bycatch/compare/v0.1.0...HEAD [0.1.0]: https://github.com/IslasGECI/bycatch/releases/tag/v0.1.0 diff --git a/R/track_example.R b/R/track_example.R index 1a9855a..a33cf7e 100644 --- a/R/track_example.R +++ b/R/track_example.R @@ -8,11 +8,12 @@ get_summary_of_trips <- function(gps_data, config_content) { get_trips <- function(data, config_content) { dataGroup <- track2KBA::formatFields( dataGroup = data, - fieldID = "track_id", + fieldID = "track_id", fieldDate = "date_gmt", fieldTime = "time", - fieldLon = "longitude", - fieldLat = "latitude" + fieldLon = "longitude", + fieldLat = "latitude", + formatDT = "ymd_HMS" ) colony <- config_content$colony trips <- track2KBA::tripSplit( From cfe9e153d8ad9f0e13f2b44eb62652d147c60ad0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciencia=20de=20Datos=20=E2=80=A2=20GECI?= Date: Thu, 2 Oct 2025 14:07:45 -0700 Subject: [PATCH 2/6] =?UTF-8?q?=F0=9F=9B=91=F0=9F=A7=AA=20Fail=20tests?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv b/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv index f1ed99f..4cd1307 100644 --- a/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv +++ b/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device 8A6,male,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-04-01,14:50:03,-118.532453,29.145682,8A6,8A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3A6,female,I,TRUE,28.884478,-118.291855,2014,2014-01-28,03:00:06,-134.958717,37.7068,3A6,3A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3C4,female,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-03-30,06:50:04,-118.292263,28.884442,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS From 8db9fa81c6d367b412309ca162f5aaa23315f4a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciencia=20de=20Datos=20=E2=80=A2=20GECI?= Date: Thu, 2 Oct 2025 14:18:28 -0700 Subject: [PATCH 3/6] =?UTF-8?q?=E2=9C=85=20Pass=20tests?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- R/track_example.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/track_example.R b/R/track_example.R index a33cf7e..9bad628 100644 --- a/R/track_example.R +++ b/R/track_example.R @@ -10,7 +10,7 @@ get_trips <- function(data, config_content) { dataGroup = data, fieldID = "track_id", fieldDate = "date_gmt", - fieldTime = "time", + fieldTime = "time_gmt", fieldLon = "longitude", fieldLat = "latitude", formatDT = "ymd_HMS" From 0a9303861c87f0ab0284afc4a440f32d383c600c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciencia=20de=20Datos=20=E2=80=A2=20GECI?= Date: Thu, 2 Oct 2025 14:19:36 -0700 Subject: [PATCH 4/6] =?UTF-8?q?=F0=9F=97=82=EF=B8=8F=E2=9A=97=EF=B8=8F=20u?= =?UTF-8?q?pdate=20test=20data=20for=20corrected=20bird=5Flife=5Fformat?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv | 2 +- tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv | 2 +- tests/data/bl_sample_10_percent_5_ids.csv | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv b/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv index 1fba271..b5da930 100644 --- a/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv +++ b/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt_bad,argos_quality,common_name,site_name,colony_name,device 3C4,female,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-02-27,03:20:04,-118.292138,28.884665,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 8A6,male,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-03-03,16:40:03,-121.790533,34.555902,8A6,8A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3A6,female,I,TRUE,28.884478,-118.291855,2014,2014-02-01,12:10:06,-133.201215,41.094273,3A6,3A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS diff --git a/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv b/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv index 4cd1307..a8f91b0 100644 --- a/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv +++ b/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt_bad,argos_quality,common_name,site_name,colony_name,device 8A6,male,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-04-01,14:50:03,-118.532453,29.145682,8A6,8A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3A6,female,I,TRUE,28.884478,-118.291855,2014,2014-01-28,03:00:06,-134.958717,37.7068,3A6,3A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3C4,female,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-03-30,06:50:04,-118.292263,28.884442,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS diff --git a/tests/data/bl_sample_10_percent_5_ids.csv b/tests/data/bl_sample_10_percent_5_ids.csv index 7852c53..17e831f 100644 --- a/tests/data/bl_sample_10_percent_5_ids.csv +++ b/tests/data/bl_sample_10_percent_5_ids.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt_bad,argos_quality,common_name,site_name,colony_name,device 0A7,female,"E,C",TRUE,28.884888348810662,-118.291460434131,2014,2014-03-08,10:20:04,-116.468395,29.959652,0A7,0A7,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 0A7,female,"E,C",TRUE,28.884888348810662,-118.291460434131,2014,2014-03-03,08:11:06,-130.037593,40.550637,0A7,0A7,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3C4,female,"I,E,C",TRUE,28.88462085881453,-118.29206212098563,2014,2014-02-11,14:10:10,-118.318125,29.587763,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS From 257f8b75ef587b8f7087a21a60f1944ef5360373 Mon Sep 17 00:00:00 2001 From: Mario Villasante Date: Fri, 3 Oct 2025 13:14:23 -0700 Subject: [PATCH 5/6] =?UTF-8?q?Revert=20"=E2=99=BB=EF=B8=8F=20=20Refactor"?= =?UTF-8?q?=20Only=20remove=20the=20warnings=20This=20reverts=20commit=203?= =?UTF-8?q?21cb7e18229dd2158fce3688f59f7e3cb47abc8.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- R/track_example.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/track_example.R b/R/track_example.R index 9bad628..a33cf7e 100644 --- a/R/track_example.R +++ b/R/track_example.R @@ -10,7 +10,7 @@ get_trips <- function(data, config_content) { dataGroup = data, fieldID = "track_id", fieldDate = "date_gmt", - fieldTime = "time_gmt", + fieldTime = "time", fieldLon = "longitude", fieldLat = "latitude", formatDT = "ymd_HMS" From 9e4584a782c6d4a55b1dec113ae470884a6963a6 Mon Sep 17 00:00:00 2001 From: Mario Villasante Date: Fri, 3 Oct 2025 13:18:34 -0700 Subject: [PATCH 6/6] =?UTF-8?q?=E2=8F=AE=EF=B8=8F=20back=20to=20original?= =?UTF-8?q?=20names?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv | 2 +- tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv | 2 +- tests/data/bl_sample_10_percent_5_ids.csv | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv b/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv index b5da930..1fba271 100644 --- a/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv +++ b/tests/data/bl_gps_albatros_guadalupe_10percent_sample.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt_bad,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device 3C4,female,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-02-27,03:20:04,-118.292138,28.884665,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 8A6,male,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-03-03,16:40:03,-121.790533,34.555902,8A6,8A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3A6,female,I,TRUE,28.884478,-118.291855,2014,2014-02-01,12:10:06,-133.201215,41.094273,3A6,3A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS diff --git a/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv b/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv index a8f91b0..f1ed99f 100644 --- a/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv +++ b/tests/data/bl_gps_albatros_guadalupe_20percent_sample.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt_bad,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device 8A6,male,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-04-01,14:50:03,-118.532453,29.145682,8A6,8A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3A6,female,I,TRUE,28.884478,-118.291855,2014,2014-01-28,03:00:06,-134.958717,37.7068,3A6,3A6,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3C4,female,"I,E,C",TRUE,28.884333,-118.291915,2014,2014-03-30,06:50:04,-118.292263,28.884442,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS diff --git a/tests/data/bl_sample_10_percent_5_ids.csv b/tests/data/bl_sample_10_percent_5_ids.csv index 17e831f..7852c53 100644 --- a/tests/data/bl_sample_10_percent_5_ids.csv +++ b/tests/data/bl_sample_10_percent_5_ids.csv @@ -1,4 +1,4 @@ -bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time_gmt,longitude,latitude,track_id,original_track_id,time_gmt_bad,argos_quality,common_name,site_name,colony_name,device +bird_id,sex,breed_stage,breed_status,lat_colony,lon_colony,season,date_gmt,time,longitude,latitude,track_id,original_track_id,time_gmt,argos_quality,common_name,site_name,colony_name,device 0A7,female,"E,C",TRUE,28.884888348810662,-118.291460434131,2014,2014-03-08,10:20:04,-116.468395,29.959652,0A7,0A7,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 0A7,female,"E,C",TRUE,28.884888348810662,-118.291460434131,2014,2014-03-03,08:11:06,-130.037593,40.550637,0A7,0A7,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS 3C4,female,"I,E,C",TRUE,28.88462085881453,-118.29206212098563,2014,2014-02-11,14:10:10,-118.318125,29.587763,3C4,3C4,NA,NA,Laysan albatross,Mexico,Isla Guadalupe,GPS