- 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
- 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
- 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.
- @PabloCapilla made their first contribution in #125
Full Changelog: https://github.com/Rafnuss/GeoPressureR/compare/v3.3.0...v3.3.1
- 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.
- 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
https://github.com/Rafnuss/GeoPressureR/compare/v3.2.0...v3.3.0
- 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
httrtohttr2 - Fix major bug with saving environment variable in param https://github.com/Rafnuss/GeoPressureR/commit/9bcbf790a7de133448c738db272bf136dc831f8f
- Add functions
speed2bearing()andwindsupport()https://github.com/Rafnuss/GeoPressureR/commit/fe244f6057db14b6a286c0a77aaaef4c5ec0152c - Use interpolated
stap_idfor flight instead of0https://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
- Add
workersargument ingraph_create()https://github.com/Rafnuss/GeoPressureR/commit/e1ce45882809e1fd3da0e8feb2ff80ac70f2bf8b - Add
codemeta.jsonhttps://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
WORDLISTforspellingpackage. - Remove the use of
indin 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 inpressurepath_create()
https://github.com/Rafnuss/GeoPressureR/compare/v3.1.0...v3.2.0
- Update to GeoPressureAPI v2, using
thr_maskingeopressure_map_mismatch()and splittingkeep_mse_mask. - Adjust computation of ground speed to account for grid resolution.
- Use negative indexing for
known - remove trailing
/to default directories. - documentations and minor fixes.
https://github.com/Rafnuss/GeoPressureR/compare/v3.0.0...v3.1.0
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.
- 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.
- Formulate graph as a HMM #68
- Simplified workflow #69
- Use of
clifor message. - Create
graph_shortestpathhttps://github.com/Rafnuss/GeoPressureR/commit/b69c2a21b784f598b03822e940c02c216114e9f9 - Review all tests and example
- Review all functions names and parameters
- Major fix in the computation of the marginal map https://github.com/Rafnuss/GeoPressureR/commit/bd1103fda0c5b4e3c0f218ee7bcf3fbc69dc6123
- Improve
graph_download_wind()#54 - GeoPressureViz function in #52
- Replace
isoutliarwithisoutlierin #43 - Use
assertthatin #46 and #47 - Typo of equipment and retrieval in #48
- Various minor fixes
https://github.com/Rafnuss/GeoPressureR/compare/v2.6-beta...v2.7-beta
- add windspeed download function
graph_download_wind()
- fixes for reading pam data
- various fixes (see #42)
https://github.com/Rafnuss/GeoPressureR/compare/v2.5-beta...v2.6-beta
- 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
logisfunction inflight_prob()https://github.com/Rafnuss/GeoPressureR/commit/6e1a8f0e93d82ec2a9bccce404cdb59fcc218277
- Read Avonet data as package data https://github.com/Rafnuss/GeoPressureR/commit/c5c8d807f9a7e13a49e3d1565a7b3beffb58022f
- Update of
r-lib/actionsto 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
https://github.com/Rafnuss/GeoPressureR/compare/v2.4-beta...v2.5-beta
- 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 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
https://github.com/Rafnuss/GeoPressureR/compare/v2.3-beta...v2.4-beta
- 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/extdatato 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
- 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
https://github.com/Rafnuss/GeoPressureR/compare/v2.2-beta...v2.3-beta
- 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 (https://rafnuss.shinyapps.io/GeoPressureViz/) to accept
geopressure_ts_pathoutput
- fix flight and avonet database #10
- fix #9
https://github.com/Rafnuss/GeoPressureR/compare/v2.1-beta...v2.2-beta
- Graph Addition of wind: https://raphaelnussbaumer.com/GeoPressureR/articles/wind-graph.html
- Movement model function: converting airspeed/groundspeed to probability.
- Minor correction of existing code
- cleaning of name, variable and file saved for more consistency
- Update to GeoPressureAPI v2.1
https://github.com/Rafnuss/GeoPressureR/compare/v2.0-beta...v2.1-beta
- Add vignette and code for light geopositioning in #4
- minor language changes by @jsocolar in #7
- @jsocolar made their first contribution in #7
https://github.com/Rafnuss/GeoPressureR/compare/v1.1-beta...v2.0-beta