CpR_sensitivity_plot: Make a plot of the sensitivity analysis evaluated under...

In treesliceR: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time

Make a plot of the sensitivity analysis evaluated under cumulative phylogenetic rate functions

Description

This function generates a plot of the sensitivity analysis calculated for a given cumulative phylogenetic rate (CpR) assessed through the CpR_sensitivity() function.

Usage

CpR_sensitivity_plot(sst_output, rate = NULL, stc = "mean")

Arguments

sst_output	data frame. The outputted data frame from the CpR_sensitivity() function.
rate	character string. The desired phylogenetic index rate to display. It can be filled with "CpD", "CPE", "CpB", or "CpB_RW".
stc	character string. A statistical measure to summarize the phylogenetic rates and create the plot, which could be filled with "mean", "var", "median", "sd", "min", and "max". Default is "mean".

Value

The function returns a ggplot graph.

Author(s)

Matheus Lima de Araujo [e-mail]

References

Users can use the CpR_sensitivity_plot() function for plotting sensitivity analysis outputs.

See Also

CpR sensitivity analysis: CpR_sensitivity().

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(tree, n = 100, mat = mat)

# Create a vector of number of slices
vec <- c(25, 50, 75, 100, 125, 150)

# Calculate the sensitivity of the CpD
Sens_out <- CpR_sensitivity(tree, vec, mat, rate = "CpD", samp = 5)

# Plot the sensitity analysis
CpR_sensitivity_plot(Sens_out, rate = "CpD", stc = "mean")

treesliceR documentation built on Sept. 11, 2024, 8:47 p.m.