GeoPressureR - v3.4.0

Moderate

• Fix major issue of most_likely_path with computation of probability r…

Minor

• Update path$ind in geopressureviz as path changes
• Add pruning of the graph after filtering graph by airspeed.

Full Changelog: https://github.com/Rafnuss/GeoPressureR/compare/v3.3.4...v3.4.0

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss 2 months ago

GeoPressureR - v3.3.4

Moderate

• Make geolight_map() work for non-regular light data

Minor

• Add reading of BAS tags and PRESTAG tag
• deprecate cds api token as parameter
• deprecate *_update()
• Increase timeout for downloading wind

Full Changelog: https://github.com/Rafnuss/GeoPressureR/compare/v3.3.3...v3.3.4

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss 2 months ago

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/Rafnuss/GeoPressureR/compare/v3.3.2...v3.3.3

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss 4 months ago

GeoPressureR - v3.3.2

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss 5 months ago

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss 5 months ago

GeoPressureR - v3.3.0

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
• Improvement of tag_label_auto() with post-processing step
• Create path2twilight.R and Add twilight_line in plot_twilight

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss 7 months ago

GeoPressureR - v3.2.0

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 enviremnt 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/v3.2.0...v3.1.0

Full Changelog

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss about 1 year ago

GeoPressureR - v3.1.0

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss over 1 year ago

GeoPressureR - v2.8-beta

Major

• Run request in parrallel with 100 workers c650785925344461ac17ecdd3fdc09dc40443a9b
• Improvement following revision: Approximation of distance 6f4162501a6e6bf2e721e09da23aac6c836033d4
• Improvement following revision: Single removal of nodes 1df06e7892e36871a6a220cb2458bc3d4f1d5529

Minor

• Fix bug for .deg 73eb5dadbdf3226df3dd807254630e5dbaba23bb
• Fix bug for simulation with multiple starting location (unknown equipement) 3abac396055d3c114e312df5f9d36a64af9bebec
• Use of utils.R file for functions used at several location
• Fix bug cf0989376934cafc3016f37a0a163e56243c2dcc

Full Changelog

https://github.com/Rafnuss/GeoPressureR/compare/v2.7-beta...v2.8-beta

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss over 1 year ago

GeoPressureR - v3.0.0

Guiding principles of v3

This new version consists of a significant revamp of the entire code centered 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 labeling #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 ploting 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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss over 1 year ago

GeoPressureR - v2.7-beta

Major

• Major fix in the computation of the marginal map bd1103fda0c5b4e3c0f218ee7bcf3fbc69dc6123

Minor

• Improve graph_download_wind() #54
• Geopressureviz function in https://github.com/Rafnuss/GeoPressureR/pull/52
• Replace isoutliar with `isoutlier in https://github.com/Rafnuss/GeoPressureR/pull/43
• Use assertthat in https://github.com/Rafnuss/GeoPressureR/pull/46 and https://github.com/Rafnuss/GeoPressureR/pull/47
• Typo of equipement and retrival in https://github.com/Rafnuss/GeoPressureR/pull/48
• Various minor fixes

Full Changelog

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss over 2 years ago

GeoPressureR - v2.6-beta

Major

• add windspeed download function graph_download_wind()

Minor

• fixes for reading pam data
• various fixes (see https://github.com/Rafnuss/GeoPressureR/pull/42)

Full Changelog

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss over 2 years ago

GeoPressureR - v2.5-beta

Major

• Migration of all the vignette and data used for the vignette in GeoPressureManual bda0f7898dd9e6b8d9d786ce56ae3e5ec422c935
• Read Migrate Technology data (should not be breaking change, but some significant changes) #23
• Add logis function in flight_prob() 6e1a8f0e93d82ec2a9bccce404cdb59fcc218277

Minor

• Read Avonet data as package data c5c8d807f9a7e13a49e3d1565a7b3beffb58022f
• Update of r-lib/actions to v2 3382fb9b7b9970f1c102cf9aabf3a6b06b5d505e
• 8720b6e6032f910f0c702e649a907dcf10bc2258
• Improvement of GeoPressureViz 97be49de4ed6c309b16e23fbedde1d618ae0a04c 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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss over 2 years ago

GeoPressureR - v2.4-beta

Major

• Accept request over water and display warning message. See https://github.com/Rafnuss/GeoPressureR/pull/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 https://github.com/Rafnuss/GeoPressureR/issues/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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss almost 3 years ago

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss about 3 years ago

GeoPressureR - v2.2-beta

Major

• New function geopressure_map2path with return of index of lat-lon option
• New function geopressure_ts_path to compute mulitple 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 databse (https://github.com/Rafnuss/GeoPressureR/issues/10)
• fix https://github.com/Rafnuss/GeoPressureR/issues/9

Full Changelog

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss about 3 years ago

GeoPressureR - v2.1-beta

What's Changed

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 GeoPresureAPI v2.1

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss about 3 years ago

GeoPressureR - v2.0-beta

What's Changed

• Add vignette and code for light geopositioning by @Rafnuss in https://github.com/Rafnuss/GeoPressureR/pull/4
• minor language changes by @jsocolar in https://github.com/Rafnuss/GeoPressureR/pull/7

New Contributors

• @jsocolar made their first contribution in https://github.com/Rafnuss/GeoPressureR/pull/7

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss about 3 years ago

GeoPressureR - v1.1-beta

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

Biosphere - Avian Monitoring and Analysis - R
Published by Rafnuss about 3 years ago