fauna_pam: Get a presence-absence matrix

In faunabr: Explore Catálogo Taxônomico da Fauna do Brasil Database

Get a presence-absence matrix

Description

Get a presence-absence matrix of species based on its distribution (brazilian states and/or countries) according to Fauna do Brasil.

Usage

fauna_pam(data, by_state = TRUE, by_country= 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_faunabr function or generated by either select_fauna or subset_fauna functions
by_state	(logical) get occurrences by State. Default = TRUE
by_country	(logical) get occurrences by countries. 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 (by State and/or country)

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

Examples

#Test function
data("fauna_data") #Load fauna e Funga do Brasil data
#Select native species of mammals with occurrence only in Brazil
br_mammals <- select_fauna(data = fauna_data,
                           include_subspecies = FALSE, phylum = "all",
                           class = "Mammalia",
                           order = "all", family = "all",
                           genus = "all",
                           lifeForm = "all", filter_lifeForm = "in",
                           habitat = "all", filter_habitat = "in",
                           states = "all", filter_states = "in",
                           country = "BR", filter_country = "only",
                           origin = "all", taxonomicStatus = "valid")
#Get presence-absence matrix in states
pam_mammals <- fauna_pam(data = br_mammals, by_state = TRUE,
                         by_country = FALSE,
                         remove_empty_sites = TRUE,
                         return_richness_summary = TRUE,
                         return_spatial_richness = TRUE,
                         return_plot = TRUE)

faunabr documentation built on Nov. 5, 2025, 7:26 p.m.