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:Jakob Jentschke [aut, cre], FVA BW, Abt. Waldschutz [cph, fnd]

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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'))

Peer review:

Bug tracker:https://github.com/jjentschke/barrks/issues

On CRAN:

5.58 score 19 scripts 144 downloads 52 exports 36 dependencies

Last updated 18 days agofrom:af8f8835ad. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winOKNov 04 2024
R-4.5-linuxOKNov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winOKNov 04 2024
R-4.3-macOKNov 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.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-07-10
Started: 2024-06-13

Model customization

Rendered frommodel-customization.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-07-10
Started: 2024-06-13

Station data

Rendered fromstations.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-07-10
Started: 2024-06-13

The BSO model

Rendered frombso.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-07-10
Started: 2024-06-13

Use a storage

Rendered fromstorage.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-07-10
Started: 2024-06-13

Readme and manuals

Help Manual

Help pageTopics
Analyse a phenologyanalyse.phenology
Analyse a BSO generated phenologyanalyse.phenology.bso
Get 'barrks' default color palettesbarrks_colors
Load sample databarrks_data
Get 'barrks' default legend labelsbarrks_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 phenologybso_translate_phenology
Make a numeric generations raster categoricalcategorize_generations_rst
Create a data frame of day lengthscreate_daylength_df
Create day length rasterscreate_daylength_rst
Create phenological events (onset/diapause/mortality)create_diapause create_events create_mortality create_onset
Create a data frame of sunrises and sunsetscreate_suntimes_df
Create rasters that indicate sunrise and sunsetcreate_suntimes_rsts
Get the beetles developmentget_development get_development_df get_development_rst
Get generationsget_generations get_generations_df get_generations_rst get_hibernating_generations_df get_hibernating_generations_rst
Get (preprocessed) input dataget_input_data
Get onset, diapause or mortalityget_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 modelslist_models
Get a phenology modelmodel
Combine different (sub-)modelsmodel_combine
Use BSOmodel.bso.apply
Customize BSOmodel.bso.customize
Use CHAPYmodel.chapy.apply
Customize CHAPYmodel.chapy.customize
Use the Jönnson modelmodel.joensson.apply
Customize the Jönsson modelmodel.joensson.customize
Use the Lange modelmodel.lange.apply
Customize the Lange modelmodel.lange.customize
Use PHENIPS-Climmodel.phenips_clim.apply
Customize PHENIPS-Climmodel.phenips_clim.customize
Use PHENIPSmodel.phenips.apply
Customize PHENIPSmodel.phenips.customize
Use RITYmodel.rity.apply
Customize RITYmodel.rity.customize
Get model parametersparams
Central function to calculate a phenologybso_phenology phenology
Plot a development diagramplot_development_diagram
Get phenology propertiesproperties prop_dates prop_filial_generations prop_first_date prop_hatched_generations prop_last_date prop_sister_broods prop_stations prop_year
Save/load a phenologyload_phenology save_load_phenology save_phenology
Work with stationsstations stations_assign stations_cells stations_create stations_names