optimal_threshold: Optimize threshold for clean data extraction.

In specleanr: Detecting Environmental Outliers in Data Analysis Pipelines

Optimize threshold for clean data extraction.

Description

Optimize threshold for clean data extraction.

Usage

optimal_threshold(
  refdata,
  outliers,
  var_col = NULL,
  warn = FALSE,
  verbose = FALSE,
  plotsetting = list(plot = FALSE, group = NULL),
  cutoff = 0.6
)

Arguments

refdata	dataframe. Species data frame from precleaned analysis.
outliers	datacleaner. Datacleaner output with outliers flagged in multidetect function.
var_col	string. A column with species names if dataset for species is a dataframe not a list. See pred_extract for extracting environmental data.
warn	logical. If TRUE, warning on whether absolute outliers obtained at a low threshold is indicated. Default TRUE.
verbose	logical. If true, then messages about the outlier flagging will be displayed.
plotsetting	list. to show plot of loess fitted function with local and global maxima (optimal threshold and clean data). The list had two parameters. 1) plot to indicate the plot and group to provide the plot title.
cutoff	numeric. Ranging from 0.5 to 0.8 indicating the cutoff to initiate the LOESS model to optimize the identification of absolute outliers.

Value

Either a list or dataframe of cleaned records for multiple species.

specleanr documentation built on Nov. 26, 2025, 1:07 a.m.