Package: hibiiscus 0.1

Richard Cornford

hibiiscus: Modelling framework for hierachical ecological impact analysis

This package uses principles of hierarchical modelling to assess the impacts of land use and land-use intensity on ecological communities. Data and modelling approach originate from the PREDICTS framework and are adapted for use with alternative land-use categories (legends), integration of additional ecological data, modelling with frequentist and Bayesian approaches, and extended model evaluation.

Authors:Richard Cornford [aut, cre], Martin Jung [aut]

hibiiscus_0.1.tar.gz
hibiiscus_0.1.zip(r-4.7-any)hibiiscus_0.1.zip(r-4.6-any)hibiiscus_0.1.zip(r-4.5-any)
hibiiscus_0.1.tgz(r-4.6-any)hibiiscus_0.1.tgz(r-4.5-any)
hibiiscus_0.1.tar.gz(r-4.7-any)hibiiscus_0.1.tar.gz(r-4.6-any)
hibiiscus_0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hibiiscus/json (API)

# Install 'hibiiscus' in R:

install.packages('hibiiscus', repos = c('https://iiasa.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/iiasa/hibiiscus/issues

Pkgdown/docs site:https://iiasa.github.io

On CRAN:

ecological-modelling impact-analysis land-use meta-analysis predicts

2.70 score 3 scripts 28 exports 24 dependencies

Last updated from:49f112111a. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	235
source / vignettes	OK	380
linux-release	NOTE	196
macos-release	NOTE	163
macos-oldrel	NOTE	150
windows-devel	NOTE	143
windows-release	NOTE	202
windows-oldrel	NOTE	241
wasm-release	OK	166

Exports:hib_calc_aoa hib_calc_div_between hib_calc_div_within hib_calc_site_contrasts hib_create_db hib_create_lu_legend hib_cv_model hib_filter_sites hib_filter_species hib_fit_brms hib_fit_inla hib_fit_lme4 hib_join_site_contrasts hib_join_sites hib_join_species hib_load hib_project_model hib_save hib_set_lu_legend hib_update_db HibCV HibDatabase HibLULegend HibModelBRMS HibModelINLA HibModelLME4 HibProjection prep_globiom

Dependencies:assertthat cli cpp11 crayon dplyr generics glue lifecycle magrittr pillar pkgconfig purrr R6 Rcpp rlang stringi stringr terra tibble tidyr tidyselect utf8 vctrs withr

Basic usage

1. Load package and PREDICTS-like data | 2. Filter data to remove sites in Oceania | 3. Condense land-use categories | 4. Correct measurements for sampling effort, calculate total abundance per site and Bray-curtis dissimilarity between sites (within studies). | 5. Fit a simple model of (rescaled) total abundance in response to land-use, and a simple model of Bray-Curtis dissimilarity. | 6. Cross-validate the fitted model, using both Random, and geographically blocked folds. | 7. Model projection | 8. Data-integration example

Rendered frombasic_use.Rmdusingknitr::rmarkdown

Last update: 2026-10-30
Started: 2026-10-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
hib_calc_aoa: Calculate the Area-of-Applicability.	hib_calc_aoa
Calculate between-site (within study) diversity metrics	hib_calc_div_between
Calculate within-site diversity metrics	hib_calc_div_within
hib_calc_site_contrasts: Calculate differences between sites for a range of environmental variables.	hib_calc_site_contrasts
hib_create_db: Create a 'HibDatabase' object from input files	hib_create_db
hib_create_lu_legend: Create a 'new' land-use legend.	hib_create_lu_legend
hib_cv_model: Cross-validate a fitted hibiiscus mixed-effects model	hib_cv_model
hib_filter_sites: Filter the database object by site-linked variables	hib_filter_sites
hib_filter_species: Filter the database object by species-linked features.	hib_filter_species
hib_fit_brms: Fit a brms style mixed-effects model	hib_fit_brms
hib_fit_inla: Fit an INLA mixed-effects model	hib_fit_inla
hib_fit_lme4: Fit an lme4 style mixed-effects model	hib_fit_lme4
hib_join_site_contrasts: Join external site-contrast information to a HibDatabase object	hib_join_site_contrasts
hib_join_sites: Join external site information to a HibDatabase object	hib_join_sites
hib_join_species: Join external species information to a HibDatabase object	hib_join_species
hib_load: Load Hib___ objects.	hib_load
hib_project_model: Project a hibiiscus mixed-effects model	hib_project_model
hib_save: Save Hib___ objects.	hib_save
hib_set_lu_legend: Set a 'HibLULegend' as the LU legend in a 'HibDatabase'	hib_set_lu_legend
hib_update_db: Update an existing 'HibDatabase' with further data	hib_update_db
HibCV	HibCV
HibDatabase	HibDatabase
HibLULegend	HibLULegend
HibModelBRMS	HibModelBRMS
HibModelINLA	HibModelINLA
HibModelLME4	HibModelLME4
HibProjection	HibProjection
prep_globiom: Prepare GLOBIOM output for projection.	prep_globiom