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
b_pam <- read_PAM(system.file("extdata/b_pam.rds",
                              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"))