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Package: biospheremetrics 1.1.1

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_1.1.1.tar.gz
biospheremetrics_1.1.1.zip(r-4.7)biospheremetrics_1.1.1.zip(r-4.6)biospheremetrics_1.1.1.zip(r-4.5)
biospheremetrics_1.1.1.tgz(r-4.6-any)biospheremetrics_1.1.1.tgz(r-4.5-any)
biospheremetrics_1.1.1.tar.gz(r-4.7-any)biospheremetrics_1.1.1.tar.gz(r-4.6-any)
biospheremetrics_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
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:

3.00 score 2 stars 3 scripts 33 exports 87 dependencies

Last updated from:5329e79a5c. Checks:7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	WARNING	177
source / vignettes	OK	235
linux-release-x86_64	WARNING	182
macos-release-arm64	WARNING	85
macos-oldrel-arm64	WARNING	94
windows-devel	WARNING	166
windows-release	WARNING	113
windows-oldrel	WARNING	99
wasm-release	OK	198

Exports:average_nyear_window calc_biocol calc_delta_v calc_ecorisk calc_roc_data calculate_within_biome_diffs classify_biomes disaggregate_into_biomes ecorisk_combine_hist_and_scen_data ecorisk_cross_table ecorisk_wrapper get_biome_names list_outputs plot_biocol plot_biocol_map plot_biocol_ts plot_biome_averages plot_biome_internal_distribution plot_biomes plot_ecorisk_cross_table plot_ecorisk_map plot_ecorisk_maps plot_ecorisk_over_time_panel plot_ecorisk_radial plot_ecorisk_radial_panel plot_ecorisk_radial_to_screen plot_global plot_overtime_to_screen read_calc_biocol read_ecorisk_data replace_ref_data_with_average_ref_biome_cell roc_plot roc_plot_paper

Dependencies:abind askpass bit bit64 circlize class classInt cli clipr codetools colorspace cpp11 crayon curl data.table DBI doParallel dotCall64 dplyr e1071 farver fBasics fields foreach generics ggplot2 GlobalOptions glue gss gtable hms httr isoband iterators jsonlite KernSmooth labeling lattice lifecycle lpjmlkit magrittr maps MASS mime openssl pillar pkgconfig prettyunits processx progress proxy ps purrr R6 RColorBrewer Rcpp readr rlang rnaturalearth s2 S7 scales sf shape spam spatial stabledist stringi stringr sys terra tibble tidyr tidyselect tidyterra timeDate timeSeries tzdb units utf8 vctrs viridisLite vroom withr wk yaml zoo

Computing biospheremetrics

Rendered frombiospheremetrics.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate averages (mean) for defined window sizes	average_nyear_window
Calculate BioCol	calc_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 data	calc_roc_data
Calculate ecorisk with each biomes average cell	calculate_within_biome_diffs
Classify biomes	classify_biomes
Averages EcoRisk values across regions	disaggregate_into_biomes
Create modified EcoRisk data combining two time series	ecorisk_combine_hist_and_scen_data
Create modified EcoRisk data for crosstable	ecorisk_cross_table
Wrapper for calculating the ecosystem change metric EcoRisk	ecorisk_wrapper
Get biome names	get_biome_names
List required output files for given metric	list_outputs
Plot absolute BioCol, overtime, maps, and npp into given folder	plot_biocol
Plot global map of BioCol to file	plot_biocol_map
Plot absolute BioCol, overtime, maps, and npp into given folder	plot_biocol_ts
Plot radial EcoRisk with 4/16 biomes	plot_biome_averages
Plot distribution of similarity within biomes	plot_biome_internal_distribution
Plot global distribution of lpjml simulated biomes	plot_biomes
Plot crosstable showing (dis-)similarity between average biome pixels	plot_ecorisk_cross_table
Plot EcoRisk map to file	plot_ecorisk_map
Plot EcoRisk maps	plot_ecorisk_maps
Plot timeline of EcoRisk variables as panel to file with 4/16 biomes	plot_ecorisk_over_time_panel
Plot radial EcoRisk plot to file	plot_ecorisk_radial
Plot radial EcoRisk panel to file with 4/16 biomes	plot_ecorisk_radial_panel
Plot radial EcoRisk plot to screen	plot_ecorisk_radial_to_screen
Plot global LPJmL array	plot_global
Plot timeline of EcoRisk variables to screen	plot_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 file	replace_ref_data_with_average_ref_biome_cell
Plot ROC curve	roc_plot
Plot ROC curve	roc_plot_paper
c based on Heyder 2011 eq. 10-13	state_diff_global
based on Heyder 2011 eq. 6-9; epsilon case handling from code by Sebastian Ostberg (not documented in papers)	state_diff_local