Package: biospheremetrics 1.1.0

Fabian Stenzel

biospheremetrics: Biosphere integrity metrics for LPJmL

Functions to compute Biosphere integrity metrics BioCol and EcoRisk based on output from LPJmL.

Authors:Fabian Stenzel [aut, cre], Jannes Breier [aut], Johanna Braun [aut]

biospheremetrics_1.1.0.tar.gz
biospheremetrics_1.1.0.zip(r-4.7)biospheremetrics_1.1.0.zip(r-4.6)biospheremetrics_1.1.0.zip(r-4.5)
biospheremetrics_1.1.0.tgz(r-4.6-any)biospheremetrics_1.1.0.tgz(r-4.5-any)
biospheremetrics_1.1.0.tar.gz(r-4.7-any)biospheremetrics_1.1.0.tar.gz(r-4.6-any)
biospheremetrics_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
biospheremetrics/json (API)

# Install 'biospheremetrics' in R:
install.packages('biospheremetrics', repos = c('https://pik-piam.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stenzelf/biospheremetrics/issues

On CRAN:

Conda:

3.00 score 2 stars 3 scripts 33 exports 87 dependencies

Last updated from:012b8cc99c. Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING164
source / vignettesOK233
linux-release-x86_64WARNING146
macos-release-arm64WARNING97
macos-oldrel-arm64WARNING97
windows-develWARNING108
windows-releaseWARNING100
windows-oldrelWARNING87
wasm-releaseOK146

Exports:average_nyear_windowcalc_biocolcalc_delta_vcalc_ecoriskcalc_roc_datacalculate_within_biome_diffsclassify_biomesdisaggregate_into_biomesecorisk_combine_hist_and_scen_dataecorisk_cross_tableecorisk_wrapperget_biome_nameslist_outputsplot_biocolplot_biocol_mapplot_biocol_tsplot_biome_averagesplot_biome_internal_distributionplot_biomesplot_ecorisk_cross_tableplot_ecorisk_mapplot_ecorisk_mapsplot_ecorisk_over_time_panelplot_ecorisk_radialplot_ecorisk_radial_panelplot_ecorisk_radial_to_screenplot_globalplot_overtime_to_screenread_calc_biocolread_ecorisk_datareplace_ref_data_with_average_ref_biome_cellroc_plotroc_plot_paper

Dependencies:abindaskpassbitbit64circlizeclassclassIntclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdoParalleldotCall64dplyre1071farverfBasicsfieldsforeachgenericsggplot2GlobalOptionsgluegssgtablehmshttrisobanditeratorsjsonliteKernSmoothlabelinglatticelifecyclelpjmlkitmagrittrmapsMASSmimeopensslpillarpkgconfigprettyunitsprocessxprogressproxypspurrrR6RColorBrewerRcppreadrrlangrnaturalearths2S7scalessfshapespamspatialstablediststringistringrsysterratibbletidyrtidyselecttidyterratimeDatetimeSeriestzdbunitsutf8vctrsviridisLitevroomwithrwkyamlzoo

Computing biospheremetrics

Fabian Stenzel

Rendered frombiospheremetrics.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2024-03-14
Started: 2024-03-14

Readme and manuals

Help Manual

Help pageTopics
Calculate averages (mean) for defined window sizesaverage_nyear_window
Calculate BioColcalc_biocol
Calculates changes in vegetation structure (vegetation_structure_change)calc_delta_v
Calculate the ecosystem change metric EcoRisk between 2 sets of states This function is called by the wrapper function (ecorisk_wrapper), unless you know what you are doing, don't use this function directly.calc_ecorisk
Calculate ROC curve datacalc_roc_data
Calculate ecorisk with each biomes average cellcalculate_within_biome_diffs
Classify biomesclassify_biomes
Averages EcoRisk values across regionsdisaggregate_into_biomes
Create modified EcoRisk data combining two time seriesecorisk_combine_hist_and_scen_data
Create modified EcoRisk data for crosstableecorisk_cross_table
Wrapper for calculating the ecosystem change metric EcoRiskecorisk_wrapper
Get biome namesget_biome_names
List required output files for given metriclist_outputs
Plot absolute BioCol, overtime, maps, and npp into given folderplot_biocol
Plot global map of BioCol to fileplot_biocol_map
Plot absolute BioCol, overtime, maps, and npp into given folderplot_biocol_ts
Plot radial EcoRisk with 4/16 biomesplot_biome_averages
Plot distribution of similarity within biomesplot_biome_internal_distribution
Plot global distribution of lpjml simulated biomesplot_biomes
Plot crosstable showing (dis-)similarity between average biome pixelsplot_ecorisk_cross_table
Plot EcoRisk map to fileplot_ecorisk_map
Plot EcoRisk mapsplot_ecorisk_maps
Plot timeline of EcoRisk variables as panel to file with 4/16 biomesplot_ecorisk_over_time_panel
Plot radial EcoRisk plot to fileplot_ecorisk_radial
Plot radial EcoRisk panel to file with 4/16 biomesplot_ecorisk_radial_panel
Plot radial EcoRisk plot to screenplot_ecorisk_radial_to_screen
Plot global LPJmL arrayplot_global
Plot timeline of EcoRisk variables to screenplot_overtime_to_screen
Calculate BioCol based on file lists from a PNV run and LU run of LPJmL. Do not use this function directly, unless you are instructed to do so, there is a wrapper called calc_biocol() which is for use of endusers.read_calc_biocol
Read in output data from LPJmL to calculate the ecosystem change metric EcoRisk. This function is called by the wrapper function (ecorisk_wrapper), unless you know what you are doing, don't use this function directly.read_ecorisk_data
Create modified EcoRisk data filereplace_ref_data_with_average_ref_biome_cell
Plot ROC curveroc_plot
Plot ROC curveroc_plot_paper
c based on Heyder 2011 eq. 10-13state_diff_global
based on Heyder 2011 eq. 6-9; epsilon case handling from code by Sebastian Ostberg (not documented in papers)state_diff_local