Changelog • GeoPressureR

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_threshold parameter 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 a stap_elev 2060790
Add other type of pressurepath in interim 8d7f1d1

Minor

Plenty of small fixes and minor improvements 834155e, 152c6e7, 54aa995, 3a5ff95, 6eedd83, 8797533, 1e68260

Full Changelog: https://github.com/Rafnuss/GeoPressureR/compare/v3.3.1…v3.3.2

GeoPressureR v3.3.1

Major update

[Update of param structure to function_name $param_name](https://github.com/Rafnuss/GeoPressureR/commit/2235e9ec0bceef3b49d8e1887a309b2048353552). The structure of the param has been reorganised: this named list stored inside of tag and graph stores parameters used during the building of tag and graph. We standardized this structure as param$ {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.

Minor

New Contributors

@PabloCapilla made their first contribution in https://github.com/Rafnuss/GeoPressureR/pull/125

Full Changelog: https://github.com/Rafnuss/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 (https://github.com/Rafnuss/GeoPressureR/pull/123/commits/d11f8cc4774b4c91c27318c43d438823b681066e, https://github.com/Rafnuss/GeoPressureR/pull/123/commits/85ffe940ec46af8cd56592c2d641f25d19712129)
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 ECMF 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, improve print
Change default map height
fix plot_twilight() for twl_offset
update all actions

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v3.2.0…v3.3.0

GeoPressureR v3.2

GeoPressureR v3.1

Major

Update to GeoPressureAPI v2, using thr_mask in geopressure_map_mismatch() and splitting keep_mse_mask.
Adjust computation of ground speed to account for grid resolution.

Minor

Use negative indexing for known
remove trailing / to default directories.
documentations and minor fixes.

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v3.0.0…v3.1.0

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 tag instead of pam)
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 tag and pressurepath without 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 raster to terra #59
New label scheme with test and messaging for troubleshooting #67 #73 #83
Create tag_update() and pressurepath_update()
Review the structure of a path and edges.

Minor

Formulate graph as a HMM #68
Simplified workflow #69
Use of cli for message.
Create graph_shortestpath https://github.com/Rafnuss/GeoPressureR/commit/b69c2a21b784f598b03822e940c02c216114e9f9
Review all tests and example
Review all functions names and parameters

GeoPressureR v2.7-beta

Major

Major fix in the computation of the marginal map https://github.com/Rafnuss/GeoPressureR/commit/bd1103fda0c5b4e3c0f218ee7bcf3fbc69dc6123

Minor

Improve graph_download_wind() #54
GeoPressureViz function in #52
Replace isoutliar with isoutlier in #43
Use assertthat in #46 and #47
Typo of equipment and retrieval in #48
Various minor fixes

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.6-beta…v2.7-beta

GeoPressureR v2.6-beta

Major

add windspeed download function graph_download_wind()

Minor

fixes for reading pam data
various fixes (see #42)

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.5-beta…v2.6-beta

GeoPressureR v2.5-beta

Major

Migration of all the vignette and data used for the vignette in GeoPressureManual https://github.com/Rafnuss/GeoPressureR/commit/bda0f7898dd9e6b8d9d786ce56ae3e5ec422c935
Read Migrate Technology data (should not be breaking change, but some significant changes) #23
Add logis function in flight_prob() https://github.com/Rafnuss/GeoPressureR/commit/6e1a8f0e93d82ec2a9bccce404cdb59fcc218277

Minor

Read Avonet data as package data https://github.com/Rafnuss/GeoPressureR/commit/c5c8d807f9a7e13a49e3d1565a7b3beffb58022f
Update of r-lib/actions to v2 https://github.com/Rafnuss/GeoPressureR/commit/3382fb9b7b9970f1c102cf9aabf3a6b06b5d505e
https://github.com/Rafnuss/GeoPressureR/commit/8720b6e6032f910f0c702e649a907dcf10bc2258
Improvement of GeoPressureViz https://github.com/Rafnuss/GeoPressureR/commit/97be49de4ed6c309b16e23fbedde1d618ae0a04c https://github.com/Rafnuss/GeoPressureR/commit/964b558913de7f7b6ef9915fc9cc41fc0b3dd0d3
Add checks and warning in functions
Preparation of the code for CRAN

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.4-beta…v2.5-beta

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 https://github.com/Rafnuss/GeoPressureR/commit/696566e8041e90d04e3e01d7d84ef299660bab6e
Compute groundspeed in parallel in graph creation https://github.com/Rafnuss/GeoPressureR/commit/b1466c737a66c740e2f6a35bcdbc19d9f5aebfd1

Minor

minor fixes for sta_id=0 or NA
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

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.3-beta…v2.4-beta

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 https://github.com/Rafnuss/GeoPressureR/commit/5acfb136b8cac49d3cfd9633ce9a0a81ccc9b252
Major update in the data location to avoid being loaded when using the package. Move all data to inst/extdata to avoid having them loaded with https://github.com/Rafnuss/GeoPressureR/commit/65c8f8062cf07fb1471c9f15f6f08757d00951df
Add more information on various dataset to be able to load in GeoPressureViz
Change to the graph https://github.com/Rafnuss/GeoPressureR/commit/4aeed9ab77c8efe15b2da591247700d0ebb0cb5f

Minor

Multiple test file and add covr
Optimize sta_pam()
Re-write find_twilights
Create function graph_path2edge
Add energy figure
Multiple improvement on GeoPressureViz
Add citation and contribution file
use 100 character width
Add link to GeoPressureTemplate

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.2-beta…v2.3-beta

GeoPressureR v2.2-beta

Major

New function geopressure_map2path with return of index of lat-lon option
New function geopressure_ts_path to compute multiple geopressure_ts function on a full path
Update GeoPressureViz (https://rafnuss.shinyapps.io/GeoPressureViz/) to accept geopressure_ts_path output