plot_occurrences: S3 Methods for plot and mapview

In caretSDM: Build Species Distribution Modeling using 'caret'

S3 Methods for plot and mapview

Description

This function creates different plots depending on the input.

Usage

plot_occurrences(i, spp_name = NULL, pa = TRUE)

plot_grid(i)

plot_predictors(i, variables_selected = NULL)

plot_scenarios(i, variables_selected = NULL, scenario = NULL)

plot_predictions(
  i,
  spp_name = NULL,
  scenario = NULL,
  id = NULL,
  ensemble = TRUE,
  ensemble_type = "mean_occ_prob"
)

mapview_grid(i)

mapview_occurrences(i, spp_name = NULL, pa = TRUE)

mapview_predictors(i, variables_selected = NULL)

mapview_scenarios(i, variables_selected = NULL, scenario = NULL)

mapview_predictions(
  i,
  spp_name = NULL,
  scenario = NULL,
  id = NULL,
  ensemble = TRUE,
  ensemble_type = "mean_occ_prob"
)

plot_background(i, variables_selected = NULL)

plot_niche(
  i,
  spp_name = NULL,
  variables_selected = NULL,
  scenario = NULL,
  id = NULL,
  ensemble = TRUE,
  ensemble_type = "mean_occ_prob",
  raster = FALSE
)

Arguments

i	Object to be plotted. Can be a input_sdm, but also occurrences or sdm_area.
spp_name	A character with species to be plotted. If NULL, the first species is plotted.
pa	Boolean. Should pseudoabsences be plotted together? (not implemented yet.)
variables_selected	A character vector with names of variables to be plotted.
scenario	description
id	The id of models to be plotted (only used when ensemble = FALSE). Possible values are row names of get_validation_metrics(i).
ensemble	Boolean. Should the ensemble be plotted (TRUE)? Otherwise a prediction will be plotted
ensemble_type	Character of the type of ensemble to be plotted. One of: "mean_occ_prob", "wmean_AUC" or "committee_avg"
raster	Should the niche be extrapolated to a raster covering all possibe values in the environmental space?

Details

We implemented a bestiary of plots to help visualizing the process and results. If you are not familiar with mapview, consider using it to better visualize maps.

Value

The plot or mapview desired.

Author(s)

Luíz Fernando Esser ([e-mail]) https://luizfesser.wordpress.com

See Also

WorldClim_data

caretSDM documentation built on Aug. 29, 2025, 5:17 p.m.