BIODYNAMICS - Vegetation Co-occurrence

This is a project to study the co-occurrence of vegetation across space and time.

The repo is part of the BIODYNAMICS project.

See detailed description of the project for more information.

The latest information are always available on the project website.

Functions

This project is coded in R and uses {targets} pipeline to run the analysis.

Documentation of individual functions

Each function used in the project is documented using the roxygen2 package. Here we present the list of functions used in the project:

add_age_column_from_rownames()

add_age_to_samples()

add_dataset_name_column_from_rownames()

add_model_evaluation()

check_and_prepare_data_for_fit()

check_presence_of_vegvault()

classify_taxonomic_resolution()

extract_data_from_vegvault()

fit_hmsc_model()

get_abiotic_data()

get_active_config()

get_age_from_string()

get_better_model_based_on_fit()

get_community_data()

get_community_taxa()

get_coords()

get_dataset_name_from_string()

get_pollen_sum()

get_random_structure_for_model()

get_sample_ages()

get_significant_associations()

get_species_association()

get_taxa_classification()

interpolate_community_data()

interpolate_data()

make_classification_table()

make_community_data_long()

make_hmsc_model()

prepare_data_for_fit()

replace_na_community_data_with_zeros()

save_progress_visualisation()

select_n_taxa()

transform_to_proportions()

Code coverage

In order to check issues during the development of the code, we are writing test using the {testthat} package. Then we are using the {covr} package to check the code coverage. The code coverage is calculated for each function and the overall code coverage is calculated as well.

Current code coverage is:

The full interactive report of the {covr} package can be found here: