enmpa (version 0.2.1)

plot_niche_signal: Plot Niche Signal results

Description

Plots to interpret results from niche_signal tests (Cobos & Peterson (2022) doi:10.17161/bi.v17i.15985).

Usage

plot_niche_signal(niche_signal_list, statistic = "mean",
                  variables = NULL, ellipses = FALSE, level = 0.99,
                  breaks = "Sturges", main = "", xlab = NULL, ylab = NULL,
                  h_col = "lightgray", h_cex = 0.8, lty = 2, lwd = 1,
                  l_col = c("blue", "black"), e_col = c("black", "red"),
                  pch = 19, pt_cex = c(1.3, 0.8), pt_col = c("black", "red"),
                  ...)
plot_niche_signal_univariate(niche_signal_univariate_list, statistic = "mean",
                             breaks = "Sturges", main = "", xlab = NULL,
                             ylab = "Frequency", h_col = "lightgray",
                             h_cex = 0.8, lty = 2, lwd = 1,
                             l_col = c("blue", "black"), ...)
plot_niche_signal_permanova(niche_signal_permanova_list, variables = NULL,
                           ellipses = FALSE, level = 0.99, main = "",
                           xlab = NULL, ylab = NULL,
                           e_col = c("black", "red"), lty = 2, lwd = 1,
                           pch = 19, pt_cex = c(1.3, 0.8),
                           pt_col = c("black", "red"), ...)

Value

A plot.

Arguments

niche_signal_list

list of results from niche_signal.

statistic

(character) name of the statistic for which results will be explored when results come for univariate analysis. Default = "mean". Options are: "mean", "median", "SD", and "range".

variables

(character) name of variables to used in plots when results come from analysis using the permanova method. The default, NULL, uses the first two variables.

ellipses

(logical) whether to use ellipses to represent all and positive data when results come from PERMANOVA. The default, FALSE, plots points instead.

level

(numeric) value from 0 to 1 representing the limit of the ellipse to be plotted. Default = 0.99.

breaks

breaks in the histogram as in hist. Default = "Sturges".

main

(character) title for plot. Default = "".

xlab

(character) x axis label. Default = NULL. For results from PERMANOVA, appropriate variable names are used.

ylab

(character) y axis label. Default = NULL. For univariate results, the default turn into "Frequency". For results from PERMANOVA, appropriate variable names are used.

h_col

a color to be used to fill the bars of histograms. Default = "lightgray".

h_cex

(numeric) value by which plotting text and symbols should be magnified relative to the default in histograms. Default = 0.8.

lty

(numeric) line type. See options in par. Default = 2. A vector of length = 2 can be used, in order, all and positive.

lwd

(numeric) line width. See options in par. Default = 1. A vector of length = 2 can be used, in order, all and positive.

l_col

line color for observed value of positives and confidence intervals. Default = c("blue", "black").

e_col

color of ellipse lines for all and positive data. Default = c("black", "red").

pch

point type. See options in points. Default = 19. A vector of length = 2 can be used, in order, all and positive.

pt_cex

(numeric) value by which points will be magnified. Values for all and positive points are recommended. Default = c(1.3, 0.8).

pt_col

color for points. Values for all and positive points are recommended. Default = c("black", "red").

...

other plotting arguments to be used.

niche_signal_univariate_list

list of results from niche_signal_univariate.

niche_signal_permanova_list

list of results from niche_signal_permanova.

Examples

# Load species occurrences and environmental data.
data("enm_data", package = "enmpa")
head(enm_data)

# Detection of niche signal using an univariate non-parametric test
sn_bio1 <- niche_signal(data = enm_data,
                        variables = "bio_1",
                        condition = "Sp",
                        method = "univariate")

plot_niche_signal(sn_bio1, variables = "bio_1")

sn_bio12 <- niche_signal(data = enm_data,
                         variables = "bio_12",
                         condition = "Sp",
                         method = "univariate")

plot_niche_signal(sn_bio12, variables = "bio_12")