Package: barrks 1.0.1
Jakob Jentschke
barrks: Calculate Bark Beetle Phenology Using Different Models
Calculate the bark beetle phenology based on raster data or point-related data. There are multiple models implemented for two bark beetle species. The models can be customized and their submodels (onset of infestation, beetle development, diapause initiation, mortality) can be combined. The following models are available in the package: PHENIPS-Clim (first-time release in this package), PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>, RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>, CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>, BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>, Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>, Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>. The package may be expanded by models for other bark beetle species in the future.
Authors:
barrks_1.0.1.tar.gz
barrks_1.0.1.zip(r-4.5)barrks_1.0.1.zip(r-4.4)barrks_1.0.1.zip(r-4.3)
barrks_1.0.1.tgz(r-4.4-any)barrks_1.0.1.tgz(r-4.3-any)
barrks_1.0.1.tar.gz(r-4.5-noble)barrks_1.0.1.tar.gz(r-4.4-noble)
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barrks.pdf |barrks.html✨
barrks/json (API)
NEWS
# Install 'barrks' in R: |
install.packages('barrks', repos = c('https://jjentschke.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jjentschke/barrks/issues
Last updated 2 days agofrom:af8f8835ad. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 04 2024 |
R-4.5-win | OK | Nov 04 2024 |
R-4.5-linux | OK | Nov 04 2024 |
R-4.4-win | OK | Nov 04 2024 |
R-4.4-mac | OK | Nov 04 2024 |
R-4.3-win | OK | Nov 04 2024 |
R-4.3-mac | OK | Nov 04 2024 |
Exports:barrks_colorsbarrks_databarrks_labelsbso_get_flight_dfbso_get_flight_rstbso_get_individuals_dfbso_get_individuals_rstbso_phenologybso_plot_flight_diagrambso_plot_stage_diagrambso_translate_phenologycategorize_generations_rstcreate_daylength_dfcreate_daylength_rstcreate_diapausecreate_mortalitycreate_onsetcreate_suntimes_dfcreate_suntimes_rstsget_development_dfget_development_rstget_diapause_dfget_diapause_rstget_generations_dfget_generations_rstget_hibernating_generations_dfget_hibernating_generations_rstget_input_dataget_mortality_dfget_mortality_rstget_onset_dfget_onset_rstlist_modelsload_phenologymodelmodel_combineparamsphenologyplot_development_diagramprop_datesprop_filial_generationsprop_first_dateprop_hatched_generationsprop_last_dateprop_sister_broodsprop_stationsprop_yearsave_phenologystations_assignstations_cellsstations_createstations_names
Dependencies:bitbit64clicliprcpp11crayondplyrfansigenericsgluehmslifecyclelubridatemagrittrpillarpkgconfigprettyunitsprogresspurrrR6rbibutilsRcppRdpackreadrrlangstringistringrterratibbletidyselecttimechangetzdbutf8vctrsvroomwithr
Example: Model comparison
Rendered frommodel-comparison.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-07-10
Started: 2024-06-13
Model customization
Rendered frommodel-customization.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-07-10
Started: 2024-06-13
Station data
Rendered fromstations.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-07-10
Started: 2024-06-13
The BSO model
Rendered frombso.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-07-10
Started: 2024-06-13
Use a storage
Rendered fromstorage.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-07-10
Started: 2024-06-13
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Analyse a phenology | analyse.phenology |
Analyse a BSO generated phenology | analyse.phenology.bso |
Get 'barrks' default color palettes | barrks_colors |
Load sample data | barrks_data |
Get 'barrks' default legend labels | barrks_labels |
Get flight of individuals (BSO only) | bso_get_flight bso_get_flight_df bso_get_flight_rst |
Get individuals (BSO only) | bso_get_individuals bso_get_individuals_df bso_get_individuals_rst |
Plot a flight diagram (BSO only) | bso_plot_flight_diagram |
Plot a stage diagram (BSO only) | bso_plot_stage_diagram |
Translate BSO generated phenology | bso_translate_phenology |
Make a numeric generations raster categorical | categorize_generations_rst |
Create a data frame of day lengths | create_daylength_df |
Create day length rasters | create_daylength_rst |
Create phenological events (onset/diapause/mortality) | create_diapause create_events create_mortality create_onset |
Create a data frame of sunrises and sunsets | create_suntimes_df |
Create rasters that indicate sunrise and sunset | create_suntimes_rsts |
Get the beetles development | get_development get_development_df get_development_rst |
Get generations | get_generations get_generations_df get_generations_rst get_hibernating_generations_df get_hibernating_generations_rst |
Get (preprocessed) input data | get_input_data |
Get onset, diapause or mortality | get_diapause get_diapause_df get_diapause_rst get_events get_mortality get_mortality_df get_mortality_rst get_onset get_onset_df get_onset_rst |
List all models | list_models |
Get a phenology model | model |
Combine different (sub-)models | model_combine |
Use BSO | model.bso.apply |
Customize BSO | model.bso.customize |
Use CHAPY | model.chapy.apply |
Customize CHAPY | model.chapy.customize |
Use the Jönnson model | model.joensson.apply |
Customize the Jönsson model | model.joensson.customize |
Use the Lange model | model.lange.apply |
Customize the Lange model | model.lange.customize |
Use PHENIPS-Clim | model.phenips_clim.apply |
Customize PHENIPS-Clim | model.phenips_clim.customize |
Use PHENIPS | model.phenips.apply |
Customize PHENIPS | model.phenips.customize |
Use RITY | model.rity.apply |
Customize RITY | model.rity.customize |
Get model parameters | params |
Central function to calculate a phenology | bso_phenology phenology |
Plot a development diagram | plot_development_diagram |
Get phenology properties | properties prop_dates prop_filial_generations prop_first_date prop_hatched_generations prop_last_date prop_sister_broods prop_stations prop_year |
Save/load a phenology | load_phenology save_load_phenology save_phenology |
Work with stations | stations stations_assign stations_cells stations_create stations_names |