# 4. Obtaining a Presence-Absence Matrix

One way of organizing biodiversity data is by using presence-absence matrices (PAMs), where a one represents the presence of species j in cell i, and a zero indicates absence. From a PAM, we can estimate a variety of metrics related to biodiversity patterns, including richness, range size, and composition. For a comprehensive list of biodiversity metrics, refer to the PAM_indices function in the biosurvey package.

## Loading data

Before you begin, use the `load_faunabr` function to load the data. For more detailed information on obtaining and loading the data, please refer to 1. Getting started with faunabr

    library(faunabr)
    library(terra)
    #Folder where you stored the data with the function get_faunabr()
    #Load data
    bf <- load_faunabr(data_dir = my_dir,
                       data_version = "latest",
                       type = "short") #short version
    #> Loading version 1.3

## Getting a presence-absence matrix

The `fauna_pam()` function facilitates the utilization of species distribution information in Fauna do Brazil to generate a PAM. Each site represents a brazilian state or a country. In addition to the PAM, the function also provides a summary and a SpatVector containing the number of species in each site.

As an example, lets obtain a PAM consisting of all mammal species natives to Brazil:

    #Select native species of mammals with confirmed occurrence in Brazil
    br_mammals <- select_fauna(data = bf,
                               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 = "in",
                               origin = "all", taxonomicStatus = "valid")

    #Get presence-absence matrix in states and countries
    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)

    #Visualize (as tibble) the PAM for the first 5 species and 7 sites
    tibble::tibble(pam_mammals$PAM[1:7, 1:5])
    #> # A tibble: 7 × 5
    #>   states `Platyrrhinus aurarius` `Kannabateomys amblyonyx` `Callicebus lucifer` `Cerradomys maracajuensis`
    #>   <fct>                    <dbl>                     <dbl>                <dbl>                      <dbl>
    #> 1 AM                           1                         0                    1                          0
    #> 2 ES                           0                         1                    0                          0
    #> 3 MG                           0                         1                    0                          1
    #> 4 PR                           0                         1                    0                          0
    #> 5 RJ                           0                         1                    0                          0
    #> 6 RS                           0                         1                    0                          0
    #> 7 SC                           0                         1                    0                          0

Since return_richness_summary is set to TRUE, the function also returns a data frame containing the number of species per site.

    #Visualize (as tibble) the richness summary table
    tibble::tibble(pam_mammals$Richness_summary[1:7,])
    #> # A tibble: 7 × 3
    #> states   richness
    #>   <fct>     <dbl>
    #> 1 AM          225
    #> 2 ES          120
    #> 3 MG          188
    #> 4 PR          116
    #> 5 RJ          133
    #> 6 RS          105
    #> 7 SC          101

If return_spatial_richness is set to TRUE, the function will return a SpatVector containing the number of species per site. Additionally, when return_plot is also set to TRUE, the function returns a plot.