SAMPLE: Executing this function runs all the steps of the SAMPLE...

In SAMPLE: Estimate Sampling Effort for Species Occurrence Rates

Executing this function runs all the steps of the SAMPLE pipeline.

Description

Only the input dataframe is required to run SAMPLE, all the other arguments have default values that can be adjusted (but it is not necessary to do so). To obtain the same output as in the example file, remember to set.seed(812) after importing the dataset. Alternatively, SAMPLE can be run using separate functions. To do so, please refer to RunPerm() for the first step of this process.

Usage

SAMPLE(input, output_N = file.path(tempdir(), "Results"), replicates = 50,
  stability_thresh = 2, success_points = 10, diff = 1)

Arguments

input	Input dataframe (a dataframe object).
output_N	Prefix, optionally including a path, used for the output (a character; default is "Results" in the R session's temporary directory). A prefix without a path also writes to the temporary directory.
replicates	Number of permutation replicates to perform (an integer; default replicates=50).
success_points	Number of successive (mean) prevalence rates that are below a threshold (see parameter stability_thresh) used to define stability (an integer; default success_points = 10).
stability_thresh	Threshold used to define stability (an integer). This value will be divided by the square root of the number of replicates (a float; default stability_thresh = 2.0).
diff	Difference between absolute minimum and maximum values among the all the means used to set the stability threshold (a float; default diff = 1.0).

Value

A text file (.txt) with the output values of the analysis, and a PDF file with the generated plots from the analysis.

Examples

data("coral_symbionts")
set.seed(812)
output_prefix <- file.path(tempdir(), "Example")
SAMPLE(input = coral_symbionts,
  output_N = output_prefix,
  replicates = 50,
  stability_thresh = 2,
  success_points = 10,
  diff = 1)
unlink(paste0(output_prefix, ".pdf"))
unlink(paste0(output_prefix, ".txt"))

SAMPLE documentation built on Sept. 15, 2026, 5:09 p.m.