Reference

All functions

JSDM_bino_pro()

Run jSDM_binomial_probit from jSDM package and plot results for some species. Plots can be display and/or save.

PCA_or_tSNE_on_pro_pres_est()

Run PCA or tSNE on pixels with as coordinates, probabilities of presence of species. Plot Axis 1 vs axis 2, axis 2 vs axis 3 and dendrogram. Possibility to hide plot and save it in .png.

create_sf_forest()

Create sf object of forest with minimal altitude and percentage of forest

create_sf_moist_forest()

Create sf object of moist forest according to FAO's criteria. MAP >=1500 mm <5 months where precipitations < 100 mm

data_JSDM()

Create dataframe with values of each variable on each site

extract_var_JSDM()

Extract layers and create power wanted of each variable

knn_interpolation_jSDM()

Interpole alpha and all latent variables with knn algorithm. Then save interpolation on disk in output folder.

max_min_species_group()

Get species with estimated probabilities of presence highest for each group. Same thing with lowest probabilities.

plot_HCA_EM_Kmeans()

Display plots in 2 & 3D with number of groups set and a choosen method. Possibility to hide 2D plots and save it.

plot_RGB_group_by_color()

Create plots with coordinates from dimensional reduction algorithm and plot pixel group with multiple colors. Plot can be hide and/or save.

plot_pres_est_one_species()

Plot presence absence and estimated probabilities of presence for one species. Possibility to save plots

plot_prob_pres_interp()

Create plot with probabilities of presence interpolated for a choosen species. Plot can be hide and/or save in plot folder

plot_species_richness()

Plot species richnessobserved and estimated probabilities of presence for all sites. Possibility to save plots

plot_species_richness_interpolated()

Create plot with species richness with optional sf border.

prob_est_species_forest()

Create tif files with probabilities of presences for each species on a given area. Results are save in output/theta

reproject_sf_stars()

Reproject shapefile, stars or terra object with right EPSG

sensitivity()

Process Sensitivity (species rightly predicted as present) on inventory sites.

shiny()

Create shiny output

specificity()

Process Specificity (species rightly predicted as absent) on inventory sites.