Get a presence-absence matrix

Source: R/get_pam.R

Get a presence-absence matrix of species based on its distribution (states, biomes and vegetation types) according to Flora e Funga do Brasil.

get_pam(data, by_biome = TRUE, by_state = TRUE,
               by_vegetation = FALSE, remove_empty_sites = TRUE,
               return_richness_summary = TRUE,
               return_spatial_richness = TRUE,
               return_plot = TRUE)

Arguments

data

(data.frame) a data.frame imported with the load_florabr function or generated by either select_species or subset_species functions

by_biome

(logical) get occurrences by biome. Default = TRUE

by_state

(logical) get occurrences by State. Default = TRUE

by_vegetation

(logical) get occurrences by vegetation type. Default = FALSE

remove_empty_sites

(logical) remove empty sites (sites without any species) from final presence-absence matrix. Default = TRUE

return_richness_summary

(logical) return a data.frame with the number of species in each site. Default = TRUE

return_spatial_richness

(logical) return a SpatVector with the number of species in each site. Default = TRUE

return_plot

(logical) plot map with the number of species in each site. Only works if return_spatial_richness = TRUE. Default = TRUE

Value

If return_richness_summary and/or return_spatial_richness is set to TRUE, return a list with:

  • PAM: the presence-absence matrix (PAM)

  • Richness_summary: a data.frame with the number of species in each site

  • Spatial_richness: a SpatVector with the number of species in each site (only by State and biome)

If return_richness_summary and return_spatial_richness is set to FALSE, return a presence-absence matrix

References

Flora e Funga do Brasil. Jardim Botânico do Rio de Janeiro. Available at: http://floradobrasil.jbrj.gov.br/

Examples

data("bf_data") #Load Flora e Funga do Brasil data
#Select endemic and native species of trees with occurrence only in Amazon
am_trees <- select_species(data = bf_data,
                          include_subspecies = FALSE,
                          include_variety = FALSE,
                          kingdom = "Plantae",
                          group = "All", subgroup = "All",
                          family = "All", genus = "All",
                          lifeForm = "Tree", filter_lifeForm = "only",
                          habitat = "All", filter_habitat = "in",
                          biome = "Amazon",
                          filter_biome = "only",
                          state = "All", filter_state = "and",
                          vegetation = "All",
                          filter_vegetation = "in",
                          endemism = "Endemic", origin = "Native",
                          taxonomicStatus = "Accepted",
                          nomenclaturalStatus = "All")
#Get presence-absence matrix
pam_am <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
                 by_vegetation = FALSE, remove_empty_sites = TRUE,
                 return_richness_summary = TRUE,
                 return_spatial_richness = TRUE,
                 return_plot = TRUE)