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Plot Taxonomic Rarefaction Curve

Source: R/plot_rarefaction.R
plot_rarefaction.Rd

Visualises a rarefaction curve with confidence intervals using ggplot2. Accepts output from rarefaction_taxonomic().

Usage

plot_rarefaction(
  rare_result,
  title = NULL,
  xlab = "Sample Size (individuals)",
  ylab = NULL,
  ci_color = "steelblue",
  line_color = "darkblue"
)

Arguments

rare_result

A data frame returned by rarefaction_taxonomic().

title

Optional plot title. If NULL, an automatic title is generated based on the index used.

xlab

Label for the x-axis (default: "Sample Size (individuals)").

ylab

Label for the y-axis. If NULL, determined from the index.

ci_color

Fill color for the confidence interval ribbon (default: "steelblue").

line_color

Color of the mean line (default: "darkblue").

Value

A ggplot object.

Details

The plot shows the mean diversity value at each sample size as a solid line, surrounded by a shaded ribbon representing the bootstrap confidence interval. A vertical dashed line marks the total sample size (full data).

Requires the ggplot2 package.

See also

rarefaction_taxonomic() for computing the rarefaction curve.

Examples

# \donttest{
comm <- c(sp1 = 10, sp2 = 5, sp3 = 8, sp4 = 2, sp5 = 3)
tax <- data.frame(
  Species = paste0("sp", 1:5),
  Genus   = c("G1", "G1", "G2", "G2", "G3"),
  Family  = c("F1", "F1", "F1", "F2", "F2"),
  stringsAsFactors = FALSE
)
rare <- rarefaction_taxonomic(comm, tax, index = "shannon", n_boot = 50)
plot_rarefaction(rare)

# }