NEWS.md

In Rafnuss/GeoPressureR: Global Positioning by Atmospheric Pressure

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$param_name. The structure of the param has been reorganised: this named list stored inside of tag and graph stores parameters used during the building of tag and graph. We standardized this structure as param${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

• replace species_name by scientific_name
• crop date UTC
• fix new variable name in netcdf

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

Major

• Use the new GeoPressureAPI pressurepath entry point for geopressurepath_create()
• Update to GeoPressureAPI v2 for geopressure_timeseries() https://github.com/Rafnuss/GeoPressureR/pull/103/commits/732d1a02cc241dc7d2dde3401c8747fa860650c6
• Fix major bug https://github.com/Rafnuss/GeoPressureR/pull/103/commits/05c3203ef1588bbc1f769050377cadf5f1aadcbd
• Migrate from httrto httr2
• Fix major bug with saving environment variable in param https://github.com/Rafnuss/GeoPressureR/commit/9bcbf790a7de133448c738db272bf136dc831f8f
• Add functions speed2bearing() and windsupport() https://github.com/Rafnuss/GeoPressureR/commit/fe244f6057db14b6a286c0a77aaaef4c5ec0152c
• Use interpolated stap_id for flight instead of 0 https://github.com/Rafnuss/GeoPressureR/commit/d7491c2a5580c9eeafe598935933727489590a75
• Create edge_add_wind() https://github.com/Rafnuss/GeoPressureR/commit/36412dc8f0fd061798a701ca632766dbe6f069c8
• Create path2elevation() using GeoPressureAPI to compute ground elevation from a path

Minor

• Add workers argument in graph_create() https://github.com/Rafnuss/GeoPressureR/commit/e1ce45882809e1fd3da0e8feb2ff80ac70f2bf8b
• Add codemeta.json https://github.com/Rafnuss/GeoPressureR/pull/105/commits/4f7f7bce8875b4af59db3fc1ce403d41d6317469
• Add project status badge https://github.com/Rafnuss/GeoPressureR/pull/105/commits/ecd8f61ec49dcd376748e54d19dfb2000675d302
• Fix leaflet tile provider with Stadia change https://github.com/Rafnuss/GeoPressureR/pull/106/commits/8d9bd159874deb87d61907ea14911eca12877038
• Add WORDLIST for spelling package.
• Remove the use of ind in path https://github.com/Rafnuss/GeoPressureR/commit/f7b38e1c1b06666f590df394395d7db387f2565a
• Read temperature sensor https://github.com/Rafnuss/GeoPressureR/commit/17524658a5f49466a211ea5bfbfc34c523b09a47
• Only download wind data for non-existing file by default (instead of all flights) https://github.com/Rafnuss/GeoPressureR/commit/b6a2c41420bef2354a9ace640adffcb4e79e1aa1
• Remove pressurepath2altitude() now computed in pressurepath_create()

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v3.1.0...v3.2.0

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

Minor

• fix flight and avonet database #10
• fix #9

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.1-beta...v2.2-beta

GeoPressureR v2.1-beta

Major

• Graph Addition of wind: https://raphaelnussbaumer.com/GeoPressureR/articles/wind-graph.html
• Movement model function: converting airspeed/groundspeed to probability.

Minor

• Minor correction of existing code
• cleaning of name, variable and file saved for more consistency
• Update to GeoPressureAPI v2.1

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.0-beta...v2.1-beta

GeoPressureR v2.0-beta

What's Changed

• Add vignette and code for light geopositioning in #4
• minor language changes by @jsocolar in #7

New Contributors

• @jsocolar made their first contribution in #7

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v1.1-beta...v2.0-beta

GeoPressureR v1.1-beta

Full Changelog

https://github.com/Rafnuss/GeoPressureR/commits/v1.1-beta

Rafnuss/GeoPressureR documentation built on April 17, 2025, 12:58 p.m.