treesliceR (version 1.0.3)

CpR_graph: Make a line graph or a grid map of estimated rates of accumulation of a given phylogenetic index.

Description

This function creates a line graph, or a grid map, depicting the estimated rates of accumulation of a given phylogenetic index (e.g., phylogenetic diversity, endemism, etc.), obtained from functions such as CpD(), CpE(), CpB(), or CpB_RW().

Usage

CpR_graph(data, rate = NULL, map = NULL, pal = NULL, qtl = FALSE)

Value

The function returns a ggplot graph.

Arguments

data

data frame. The outputted data frame from a CpR-rate function.

rate

character string. The desired cumulative phylogenetic rate to plot, which can be phylogenetic diversity (CpD), phylogenetic endemism (CpE), phylogenetic B-diversity (CpB), or phylogenetic B-diversity range-weighted (CpB_RW). Default is NULL, but must be filled with "CpD", "CPE", "CpB", or "CpB_RW".

map

spatial data. A grid map containing the assemblages at which the phylogenetic rates were assessed. Default is NULL.

pal

character vector. A vector containing a color palette. If none provided, a default color palette will be used.

qtl

boolean. Should the color palette be displayed according to CpR-rates quantiles? It can be either TRUE or FALSE. Default is FALSE.

Author

Matheus Lima de Araujo

References

See the tutorial on how to use this function on our website.

See Also

Other cumulative phylogenetic rate analysis: CpD(), CpE(), CpB(), CpB_RW(), CpR_sensitivity() Other plotting: CpR_sensitivity_plot().

Examples

# Generate a random tree
tree <- ape::rcoal(20)

# Create a presence-absence matrix
mat <- matrix(sample(c(1,0), 20*10, replace = TRUE), ncol = 20, nrow = 10)
colnames(mat) <- tree$tip.label

# Calculate the CpD for 100 tree slices
CpD_DF <- CpD(tree, n = 100, mat = mat)

# Plot it using the CpR_graph
CpR_graph(CpD_DF, rate = "CpD")