GeoPressureR v3.5.1
Minor
- Labeling / Quiet behavior: Fix missing quiet checks in labeling paths
- Remove experimental lifecycle badge from trainset
Full Changelog: https://github.com/GeoPressure/GeoPressureR/compare/v3.5.0...v3.5.1
GeoPressureR v3.5.0
New functions related to light
- Add tag_stap_daily() to build stap from twilight midpoints and add read_stap() to validate/read stap files
- Add map_add_mask_water() for water masking and mask water pixels in plot.map() filtering
- Create geolight_fit_location(), refactor geolight mapping pipeline, and modularize geolight map flow
- Create twilight calibration plotting (plot_twl_calib)
Minor fixes
- Make stap filtering robust to missing columns
- Fix missing known lat/lon edge case
- Restrict merged path columns in pressurepath creation
- Move ecmwfr and ncdf4 to Suggests with runtime checks
- Use vapply and memory-focused cleanups, opt pass 1, opt pass 2
- Refine messaging / remove multiline cli text
- Switch formatting/lint workflow to air+jarl (follow-up fixes)
- Refactor plot.tag() dispatch/modularity
- Refactor plot.map() args/path plotting
- Refactor plot_path() customization/static mode
- Improve plot_graph_movement() options and annotations / visual polish
Full Changelog: https://github.com/GeoPressure/GeoPressureR/compare/v3.4.5...v3.5.0
GeoPressureR v3.4.5
Main
- Add ability to not read a sensor file with
file= "" - Improve the computation of the decimal of stap_id during flight in
find_stap() - Remove bearing value of 0 when no movement and Normalize bearing to 0-360 degrees in path2edge
- Add twl_time_tolerance parameter to time series functions
- Improving tag_create: fix issue with multiple col and Simplify the approach avoiding memory error
- Switch from lintr+styler to air+jarl link
Minor fixes
- Remove unused ‘directory’ argument from tag_create_dataframe
- Refactor trainset_read to use trainset_read_raw helper
- Remove
timeoutin pressurepath_create, geopressure_timeseries() and path2elevation() - Add fix for migratech “invalid” keyword in file
- Fix issue when migratech deg file has no pressure
- Refine twilight threshold calculation logic
- Swap point colors in plot_tag_twilight function
- Refactor test setup to use temporary extdata directory
- Improve messaging 1 2, 3
GeoPressureR v3.4.4
What’s Changed
Refactored wind
filepath argument to accept bothstap_idandtag_id.[1] [2] [3] [4] [5] [6] [7] [8]Enhanced the
print.graphandprint.tag[1] [2] [3] Improved CLI section headers to include the relevant id in several workflow functions, providing better context for the user. [1] [2] [3]Added an
assert_tagparameter togeopressuretemplate_config[1] [2] [3] [4] Added an assertion for scientific_name type early in bird_create to ensure input validity, and removed a redundant assertion later in the function. [1] [2]Updated progress messages and clarified output in several places. [1] [2] Improved handling of return values in error cases for geopressuretemplate_graph. [1] [2] Cleaned up and clarified documentation and comments, including removal of outdated references and minor formatting fixes. [1] [2]
Fixed a logical error in plot_path_leaflet when checking the interp field.
Ensured likelihood maps are retrieved and displayed more clearly in graph_create.
Added a Year: 2022 field to the DESCRIPTION file.
Full Changelog: https://github.com/GeoPressure/GeoPressureR/compare/v3.4.3...v3.4.4
GeoPressureR v3.4.3
Moderate
Memory Optimization on Graph Creation
- Replaced the use of
geospherefunctions with custom memory-efficient implementations for distance and bearing calculations. - Improved graph creation by introducing distance filtering before distance calculation and adding progress messages for better user feedback.
- Added cleanup steps (
rmandgc) in theedge_add_windfunction to free memory by removing unused variables and closing netCDF files.
Minor
- Use an interp=1 by default in geopressureviz
- Temporarily set default era5_dataset to land
- Removed redundant retry logic in
httr2requests across multiple functions (geopressure_map_mismatch,geopressure_timeseries) to simplify the code (f227a90).
Full Changelog: https://github.com/GeoPressure/GeoPressureR/compare/v3.4.2...v3.4.3
GeoPressureR v3.3.3
Minor
- Minor fixes of plot_path
- Minor fix on plot_twilight
- Minor edits on docs and website
Full Changelog: https://github.com/GeoPressure/GeoPressureR/compare/v3.3.2...v3.3.3
GeoPressureR v3.3.2
Major update
- Change the computation of distance of edges in the graph by removing the fix that added 1 resolution to the distance to account for large grid square and short flight distance. Instead, add warning message in case there might be such an issue (flight distance < grid resolution) ddbd07d.
- Add
zero_speed_thresholdparameter that allow to encourage bird to stay at the same location. This is typically the case for short flight that don’t seems to affect the position. Quite similar to astap_elev2060790 - Add other type of pressurepath in interim 8d7f1d1
GeoPressureR v3.3.1
Major update
-
Update of param structure to
function_name$param_name. The structure of the param has been reorganised: this named list stored inside of tag and graph stores parameters used during the building of tag and graph. We standardized this structure as param{function_name}{argument_name}. See the migration instructions in the GeoPressureR wiki. This will mean you’ll need to update your config.yml structure - sorry for that. - Add geopressuretemplate() functions. The main improvement is related to the use of a single function to run the entire workflow: geopressuretemplate. Read more about this in the corresponding chapter of the GeoPressureManual.
New Contributors
- @PabloCapilla made their first contribution in #125
Full Changelog: https://github.com/GeoPressure/GeoPressureR/compare/v3.3.0...v3.3.1
GeoPressureR v3.3
Major
- Read all sensors type and allow reading sensor without pressure
assert_pressure = FALSE(d11f8cc, 85ffe94) - Update to ecmwfr v2. Change to cds_token. We use the Climate Data Store to download the wind data during the flight. They have recently updated their infrastructure and their login procedure has changed. You’ll need an ECMWF login with an Access Token. See updated procedure in the chapter Trajectory with wind of the GeoPressureManual.
- Improvement of tag_label_auto() with post-processing step. Based on a simple classification of prolonged high activity, migratory flight classification was often not very performant, e.g. when a bird was gliding during the flight. I have now added a post-processing step in the automatic classification to fix this. Read more in the detail section of tag_label_auto()..
- Create path2twilight.R and Add twilight_line in plot_twilight. You can now compute the theoretical twilight of a path, or more interestingly, of a pressurepath. It’s also used in pressurepath_create(), returning a column with sunrise and sunset. Its original purpose was to be able to check the twilight labeling by comparing it to a path generated, e.g., with GeoPressureViz. See the last section of the light map chapter for more info.
Minor
- Fix issue with tag_plot_twilight() when twilight was not yet computed
- Update documentation of windsupport/drift
- Make twilight works with NA in light
- Add type to path as attribute
- Accept known as list and convert it if so
- Fix bug in compute_known in geolight_map()
- Improve progress_bar, remove extra
\f, improveprint - Change default map height
- fix plot_twilight() for twl_offset
- update all actions
GeoPressureR v3.2
Major
- Use the new GeoPressureAPI pressurepath entry point for
geopressurepath_create() - Update to GeoPressureAPI v2 for
geopressure_timeseries()https://github.com/GeoPressure/GeoPressureR/pull/103/commits/732d1a02cc241dc7d2dde3401c8747fa860650c6 - Fix major bug https://github.com/GeoPressure/GeoPressureR/pull/103/commits/05c3203ef1588bbc1f769050377cadf5f1aadcbd
- Migrate from
httrtohttr2 - Fix major bug with saving environment variable in param 9bcbf790
- Add functions
speed2bearing()andwindsupport()fe244f60 - Use interpolated
stap_idfor flight instead of0d7491c2a - Create
edge_add_wind()36412dc8 - Create
path2elevation()using GeoPressureAPI to compute ground elevation from a path
Minor
- Add
workersargument ingraph_create()e1ce4588 - Add
codemeta.jsonhttps://github.com/GeoPressure/GeoPressureR/pull/105/commits/4f7f7bce8875b4af59db3fc1ce403d41d6317469 - Add project status badge https://github.com/GeoPressure/GeoPressureR/pull/105/commits/ecd8f61ec49dcd376748e54d19dfb2000675d302
- Fix leaflet tile provider with Stadia change https://github.com/GeoPressure/GeoPressureR/pull/106/commits/8d9bd159874deb87d61907ea14911eca12877038
- Add
WORDLISTforspellingpackage. - Remove the use of
indin path f7b38e1c - Read temperature sensor 17524658
- Only download wind data for non-existing file by default (instead of all flights) b6a2c414
- Remove
pressurepath2altitude()now computed inpressurepath_create()
GeoPressureR v3.1
Major
- Update to GeoPressureAPI v2, using
thr_maskingeopressure_map_mismatch()and splittingkeep_mse_mask. - Adjust computation of ground speed to account for grid resolution.
GeoPressureR v3.0
Guiding principles of v3
This new version consists of a significant revamp of the entire code centred around these themes:
- Name more general than SOI sensors (e.g., use
taginstead ofpam) - Focus the workflow on pressure sensor (but still allows for acceleration or light data)
- Update the notion of graph into State-Space Model notations (e.g. probability -> likelihood)
- More memory efficient (store minimum graph info) while minimizing computational expense of the “slow” functions
- Shorter workflow #69
- Ease of labelling #67
- Reproducibility and long-term storage with
param. - Use of S3 class object with print and plot generic function.
- Compatible with pipe
|>or%>% - Use of cli for message and progress bar.
- Be able to update
tagandpressurepathwithout re-computing everything. - See #55 for details on the functions named change
- See the migration wiki for a small guide to transition from v2.
Major
- Use of GeoPressureR object:
tag,graph,param,bird - Many new plot functions including update of
geopressureviz() - Transition from
rastertoterra#59 - New label scheme with test and messaging for troubleshooting #67 #73 #83
- Create
tag_update()andpressurepath_update() - Review the structure of a path and edges.
GeoPressureR v2.6-beta
Minor
- fixes for reading pam data
- various fixes (see #42)
GeoPressureR v2.4-beta
Major
- Accept request over water and display warning message. See #15
- Add logging of error and return JSON file of the request in case of error for troubleshooting
- Change downloading and reading of geotiff file to work on windows. See #16
- Remove the artificial increase of flight duration at the creation of graph 696566e8
- Compute groundspeed in parallel in graph creation b1466c73
Minor
- minor fixes for
sta_id=0orNA - minor fixes in
geopressureviz() - add dummy graph test to improve coverage.
- compute windspeed for short flight happening during the same hour
- typos, code readability and
stlyer
GeoPressureR v2.3-beta
Major
- Major fix of wind computation bearing to angle and m/s -> km/h
- Major fix of twilight uncertainty using kernel density. The gamma fitting was very wrong 5acfb136
- Major update in the data location to avoid being loaded when using the package. Move all data to
inst/extdatato avoid having them loaded with 65c8f806 - Add more information on various dataset to be able to load in GeoPressureViz
- Change to the graph 4aeed9ab
Minor
- Multiple test file and add
covr - Optimize
sta_pam() - Re-write
find_twilights - Create function graph_path2edge
- Add energy figure
- Multiple improvements on GeoPressureViz
- Add citation and contribution file
- use 100 character width
- Add link to GeoPressureTemplate
GeoPressureR v2.2-beta
Major
- New function
geopressure_map2pathwith return of index of lat-lon option - New function
geopressure_ts_pathto compute multiplegeopressure_tsfunction on a full path - Update GeoPressureViz (demo app) to accept
geopressure_ts_pathoutput
GeoPressureR v2.1-beta
Major
- Graph Addition of wind: https://geopressure.org/GeoPressureR/articles/wind-graph.html
- Movement model function: converting airspeed/groundspeed to probability.
GeoPressureR v2.0-beta
New Contributors
- @jsocolar made their first contribution in #7