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: v3.3.1...v3.3.2

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 #125

Full Changelog: v3.3.0...v3.3.1

v3.3.0

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 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

v3.2.0...v3.3.0

v3.2.0

Major

• Use the new GeoPressureAPI pressurepath entry point for geopressurepath_create()
• Update to GeoPressureAPI v2 for geopressure_timeseries() 732d1a0
• Fix major bug 05c3203
• Migrate from httrto httr2
• Fix major bug with saving enviremnt variable in param 9bcbf79
• Add functions speed2bearing() and windsupport() fe244f6
• Use interpolated stap_id for flight instead of 0 d7491c2
• Create edge_add_wind() 36412dc
• Create path2elevation() using GeoPressureAPI to compute ground elevation from a path

Minor

• Add workers argument in graph_create() e1ce458
• Add codemeta.json 4f7f7bc
• Add project status badge ecd8f61
• Fix leaflet tile provider with Stadia change 8d9bd15
• Add WORDLIST for spelling package.
• Remove the use of ind in path f7b38e1
• Read temperature sensor 1752465
• Only download wind data for non-existing file by default (instead of all flights) b6a2c41
• Remove pressurepath2altitude() now computed in pressurepath_create()

Full Changelog

v3.1.0...v3.2.0

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: v3.0.0...v3.1.0

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 b69c2a2
• Review all tests and example
• Review all functions names and parameters

v2.8-beta

Major

• Run request in parrallel with 100 workers c650785
• Improvement following revision: Approximation of distance 6f41625
• Improvement following revision: Single removal of nodes 1df06e7

Minor

• Fix bug for .deg 73eb5da
• Fix bug for simulation with multiple starting location (unknown equipement) 3abac39
• Use of utils.R file for functions used at several location
• Fix bug cf09893

Full Changelog

v2.7-beta...v2.8-beta

v2.7-beta

Major

• Major fix in the computation of the marginal map bd1103f

Minor

• Improve graph_download_wind() #54
• Geopressureviz function in #52
• Replace isoutliar with `isoutlier in #43
• Use assertthat in #46 and #47
• Typo of equipement and retrival in #48
• Various minor fixes

Full Changelog

v2.6-beta...v2.7-beta

v2.6-beta

Major

• add windspeed download function graph_download_wind()

Minor

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

Full Changelog

v2.5-beta...v2.6-beta

v2.5-beta

Major

• Migration of all the vignette and data used for the vignette in GeoPressureManual bda0f78
• Read Migrate Technology data (should not be breaking change, but some significant changes) #23
• Add logis function in flight_prob() 6e1a8f0

Minor

• Read Avonet data as package data c5c8d80
• Update of r-lib/actions to v2 3382fb9
• 8720b6e
• Improvement of GeoPressureViz 97be49d 964b558
• Add checks and warning in functions
• Preparation of the code for CRAN

Full Changelog

v2.4-beta...v2.5-beta