treesliceR (version 1.0.3)

CpR_sensitivity_plot: 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")

Value

The function returns a ggplot graph.

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".

Author

Matheus Lima de Araujo

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")