xlof: Flags suspicious using the local outlier factor or...

In specleanr: Detecting Environmental Outliers in Data Analysis Pipelines

Flags suspicious using the local outlier factor or Density-Based Spatial Clustering of Applications with Noise.

Description

Flags suspicious using the local outlier factor or Density-Based Spatial Clustering of Applications with Noise.

Usage

xlof(
  data,
  output,
  minPts,
  exclude = NULL,
  metric = "manhattan",
  mode = "soft",
  pc = FALSE,
  boot = FALSE,
  var,
  pcvar = NULL
)

Arguments

data	Data frame of species records with environmental data
output	Either clean: for data frame with no suspicious outliers or outlier: to return dataframe with only outliers.
minPts	Minimum neighbors around the records.
exclude	Exclude variables that should not be considered in the fitting the one class model, for example x and y columns or latitude/longitude or any column that the user doesn't want to consider.
metric	Distance-based measure to examine the distance between variables. Default manhattan.
mode	Either soft if mean is used or robust if mad is used. Default soft.
pc	Whether principal component analysis will be computed. Default FALSE
boot	Whether bootstrapping will be computed. Default FALSE
var	The variable of concern, which is vital for univariate outlier detection methods
pcvar	Principal component analysis to e used for outlier detection after PCA. Default PC1

Value

Dataframe with or with no outliers.

Examples

data("efidata")

danube <- system.file('extdata/danube.shp.zip', package='specleanr')

db <- sf::st_read(danube, quiet=TRUE)

wcd <- terra::rast(system.file('extdata/worldclim.tiff', package='specleanr'))

refdata <- pred_extract(data = efidata, raster= wcd ,
                       lat = 'decimalLatitude',
                       lon= 'decimalLongitude',
                       colsp = "scientificName",
                      bbox = db,
                       minpts = 10)

lofout <- xlof(data = refdata[["Thymallus thymallus"]], exclude = c("x", "y"),
                output='outlier', metric ='manhattan',
                minPts = 10, mode = "soft")

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