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Comparative plots of species accumulation curves

Source: R/compare_SAC.R
compare_SAC.Rd

creates comparative plots of two species accumulation curves from information contained in lists obtained with the function selected_sites_SAC.

Usage

compare_SAC(SAC_selected_sites, element_1, element_2, col_mean1 = "blue",
            col_CI1 = "lightblue", col_mean2 = "gray15",
            col_CI2 = "gray65", lty1 = 1, lty2 = 2,
            alpha_mean = 0.9, alpha_CI = 0.3,
            xlab = "Number of sites", ylab = "Species",
            line_for_multiple = TRUE, add_legend = TRUE, ...)

Arguments

SAC_selected_sites

nested list of "specaccum" objects obtained with function selected_sites_SAC.

element_1

(numeric or character) index of position or character indicator of the first element (type of selection) in SAC_selected_sites to be plotted. Character options are: "random", "E", "G", "EG".

element_2

(numeric or character) index of position or character indicator of the second element (type of selection) in SAC_selected_sites to be plotted. Character options are: "random", "E", "G", "EG".

col_mean1

(character) color for mean value of curve in element_1; default = "blue".

col_CI1

(character) color for confidence interval region for the curve in element_1; default = "lightblue".

col_mean2

(character) color for mean value of curve in element_2; default = "gray15".

col_CI2

(character) color for confidence interval region for the curve in element_2; default = "gray65".

lty1

type of line for element_1. See lty in par.

lty2

type of line for element_2. See lty in par.

alpha_mean

(numeric) alpha level for line representing the mean, values from 0 to 1; default = 0.9. Values close to 0 increase transparency.

alpha_CI

(numeric) alpha level for the region representing the confidence interval; default = 0.3.

xlab

(character) label for x-axis of plot; default = "Number of sites".

ylab

(character) label for y-axis of plot; default = "Species".

line_for_multiple

(logical) whether to plot SACs only as lines when multiple objects are in one or more of the internal lists in SAC_selected_sites. Default = TRUE.

add_legend

(logical) whether to add default legend to plot; default = TRUE.

...

other arguments to be passed to plot method for objects of class "specaccum".

Value

A comparative plot of two species "specaccum" objects done based on what is defined in element_1 and element_2.

Examples

# Data
b_pam <- read_PAM(system.file("extdata/b_pam.rds",
                              package = "biosurvey"))
m_selection <- read_master(system.file("extdata/m_selection.rds",
                                       package = "biosurvey"))

# Subsetting base PAM according to selections
sub_pam_all <- subset_PAM(b_pam, m_selection, selection_type = "all")

SACs <- selected_sites_SAC(PAM_subset = sub_pam_all, selection_type = "all")

compare_SAC(SAC_selected_sites = SACs, element_1 = 1, element_2 = 2)