Published

May 15, 2025

Modified

March 31, 2026

Function Reference

This page documents all custom R functions used across the BIODYNAMICS vegetation co-occurrence project. The repo is part of the BIODYNAMICS project — see Methods & Overview for the full pipeline context.

Function categories

The project is implemented in R and driven by a {targets} reproducible pipeline. Functions are organised into the following categories:

Category	Role
Community	Pollen data extraction, reshaping, filtering, taxonomic classification
Abiotic	Environmental predictor retrieval, collinearity reduction, interpolation
Modelling	jSDM fitting, spatial MEMs, model evaluation, variance partitioning
Time	Age handling, temporal interpolation, sample alignment
Utility	Pipeline helpers, configuration, quality checks, visualisation

Each function is documented with roxygen2 and its page is auto-generated by R/03_Supplementary_analyses/Document_functions.R. After adding or editing a function, re-run that script and re-render the site to keep this page up to date.

All functions

add_age_column_from_rownames()

add_age_to_samples()

add_dataset_name_column_from_rownames()

add_model_evaluation()

assemble_data_to_fit()

binarize_community_data()

check_and_prepare_data_for_fit()

check_and_report_missing_taxa()

check_data_sample_ids_n()

check_min_n_cores()

check_presence_of_vegvault()

classify_taxonomic_resolution()

combine_classification_tables()

evaluate_jsdm()

extract_data_from_vegvault()

filter_by_n_samples()

filter_community_by_n_cores()

filter_constant_taxa()

filter_non_plantae_taxa()

filter_rare_taxa()

fit_hmsc_model()

fit_jsdm_model()

get_abiotic_data()

get_active_config()

get_age_from_string()

get_anova()

get_aux_classification_table()

get_better_model_based_on_fit()

get_community_data()

get_community_taxa()

get_coords()

get_dataset_name_from_string()

get_pollen_sum()

get_predictor_collinearity()

get_random_structure_for_model()

get_sample_ages()

get_scale_id_from_store()

get_significant_associations()

get_spatial_window()

get_species_association()

get_taxa_classification()

get_taxa_without_classification()

interpolate_community_data()

interpolate_data()

make_classification_table()

make_community_data_long()

make_community_proportions()

make_env_formula()

make_hmsc_model()

plot_network_metrics_by_age()

prepare_coords_for_fit()

prepare_data_for_fit()

replace_na_community_data_with_zeros()

run_pipeline()

save_progress_visualisation()

scale_abiotic_for_fit()

scale_spatial_for_fit()

select_n_taxa()

transform_to_proportions()

verify_sjsdm_setup()

Code coverage

Tests are written with {testthat} and coverage is measured with {covr}. Coverage is computed per function and aggregated across the project.

Current coverage:

Full interactive coverage report: