Package index • IASDT.R

Package info

IASDT.R IASDT.R-package: IASDT.R: Modelling the distribution of invasive alien plant species in Europe

Prepare species distribution data

gbif_process() gbif_download() gbif_read_chunk() gbif_species_data(): Process GBIF occurrence data for the IASDT

easin_process() easin_taxonomy() easin_download() easin_plot(): Process EASIN data for the IASDT

elter_process(): Process eLTER data for the IASDT

naps_process() naps_distribution() naps_plot() naps_standardisation(): Process and map Naturalized Alien Plant Species (NAPS) data for the IASDT

get_species_name(): Get species name or information of an IASDT species ID

Prepare abiotic data

clc_process(): Process Corine Land Cover (CLC) data for the IASDT

chelsa_variables: Detailed information on CHELSA climate variables

chelsa_process() chelsa_prepare() chelsa_project(): Process CHELSA Climate Data for the IASDT

efforts_process() efforts_request() efforts_download() efforts_summarize() efforts_split() efforts_plot(): Process GBIF sampling effort data for the IASDT

railway_intensity(): Calculate railway intensity based on OpenStreetMap data

road_intensity(): Calculate road intensity per grid cell

river_length(): Calculate the length of rivers in each Strahler order per grid cell

bioreg_process(): Process biogeographical regions dataset

wetness_index_process(): Download and Process Topographic Wetness Index Data

soil_density_process(): Retrieve and project soil bulk density data

Modelling functions

Functions for preparing data, running the models, and postprocessing of model outputs

Data preparation

Prepare input data and scripts for fitting Hmsc-HPC on GPU

mod_cv_prepare(): Prepare spatial-block cross-validation folds for spatial analysis

prepare_knots(): Prepare knot locations for Hmsc GPP models

mod_prepare_data() mod_prepare_hpc(): Prepare initial models for model fitting with Hmsc-HPC

mod_slurm() mod_slurm_refit(): Prepare SLURM scripts for Hmsc-HPC model fitting

mod_fit_windows(): Fit Hmsc-HPC models on UFZ Windows Server

mod_cv_fit(): Prepare cross-validated Hmsc models for HPC fitting

install_hmsc_windows(): Install Hmsc-HPC in a python virtual environment on Windows

solve1() solve2() solve2vect() fast_pnorm() exp_neg_div(): helper C++ functions for fast matrix computations

fit_sdm_models(): Species Distribution Modelling Workflow for Single-Species Models

Model postprocessing

Postprocessing model outputs, including checking for convergence, making spatial predictions, evaluation, and plotting.

coda_to_tibble(): Convert a Coda object to a tibble with specified parameter transformations

trim_hmsc(): Trim an Hmsc Model Object by Removing Specified Components

mod_get_posteriors(): Combines posteriors exported by Hmsc-HPC into an Hmsc object

mod_merge_chains() mod_merge_chains_cv(): Merge model chains into Hmsc and coda objects

mod_summary(): Summary of Hmsc model parameters

rc_prepare_data() rc_plot_species() rc_plot_species_all() rc_plot_sr(): Prepare and plot response curve data for Hmsc models

predict_latent_factor(): Draws samples from the conditional predictive distribution of latent factors

plot_latent_factor(): Plot spatial variation in site loadings of HMSC models

predict_hmsc(): Calculates predicted values from a fitted Hmsc model

predict_maps() predict_maps_cv(): Predict habitat suitability of Hmsc models

plot_prediction(): Plot species and level of invasion predictions as JPEG files using ggplot2

mod_cv_evaluate(): Cross-validation Model Evaluation and Plotting

mod_cv_evaluate_plot(): Plot Evaluation Results for Cross-Validated Hmsc Models

mod_cv_merge_predictions(): Merge Cross-Validation Predictions and Generate Summary Maps

mod_postprocess_1_cpu() mod_prepare_tf() mod_postprocess_2_cpu() mod_postprocess_cv_1_cpu() mod_postprocess_cv_2_cpu(): Model pipeline for post-processing fitted Hmsc models

plot_evaluation(): Generate plots for the explanatory power of Hmsc models

mod_heatmap_beta() mod_heatmap_omega(): Heatmaps for the beta and omega parameters of the Hmsc model

convergence_plot() convergence_alpha() convergence_rho() convergence_beta_ranges(): Plot model convergence of a selected model

convergence_plot_all(): Plot model convergence of multiple modelling alternatives

variance_partitioning_compute() variance_partitioning_plot(): Computes and visualise variance partitioning of Hmsc models

plot_gelman() plot_gelman_alpha() plot_gelman_beta() plot_gelman_omega() plot_gelman_rho(): Plot Gelman-Rubin-Brooks