plot_PAM_geo {biosurvey}R Documentation

Plot of PAM indices in geography

Description

Plot of PAM indices in geography

Usage

plot_PAM_geo(PAM, index = "RI", master_selection = NULL,
             region_border = TRUE, mask_border = FALSE,
             selection_type = NULL, selection_number = 1,
             col_pal = NULL, border = NULL, col_sites = NULL,
             col_pre = NULL, pch_sites = 16, pch_pre = 16)

Arguments

PAM

object of class base_PAM.

index

(character) code for the index to be plotted. Options are: "RI" (Richness), "RIN" (Richness normalized), "DF" (Dispersion field), or "MCC" (Mean composition covariance). Default = "RI".

master_selection

master_selection object derived from functions random_selection, uniformG_selection, uniformE_selection, or EG_selection.

region_border

(logical) whether to add region border to the plot. Default = TRUE.

mask_border

(logical) whether to add mask border to the plot. Ignored if mask is not present in master_selection. Default = FALSE.

selection_type

(character) Type of selection depending on the function used to select sites. The options available are "random" (random_selection), "G" (uniformG_selection), "E" (uniformE_selection), and "EG" (EG_selection).

selection_number

(numeric) number of selection to be plotted. Default = 1.

col_pal

color palette function to be used in defining colors for the index to be plotted. The default, NULL, uses a simple color blind friendly palette similar to viridis, purplow. Warmer colors indicate higher values.

border

color for cell borders of the PAM grid. The default, NULL, does not plot any border.

col_sites

color for selected sites. The default, NULL, uses a red color to represent selected sites.

col_pre

color for preselected sites. The default, NULL, uses a purple color to represent preselected sites. Ignored if preselected sites are not present in master_selection.

pch_sites

(numeric) integer specifying a symbol when plotting points of selected sites. Default = 16.

pch_pre

(numeric) integer specifying a symbol when plotting points of preselected sites. Default = 16. Ignored if preselected sites are not present in master_selection.

Value

A plot of index represented in geography. Selected sites are added if master_selection is defined.

Examples

# Data
data("b_pam", package = "biosurvey")

# Plotting
plot_PAM_geo(b_pam, index = "RI")

# You can add a legend with
legend_bar(position = "bottomleft", col = purplow(8), title = "Richness",
           labels = c("Low", "High"))

[Package biosurvey version 0.1.1 Index]