pred_extract: Preliminary data cleaning including removing duplicates,...

In specleanr: Detecting Environmental Outliers in Data Analysis Pipelines

Preliminary data cleaning including removing duplicates, records outside a particular basin, and NAs.

Description

Preliminary data cleaning including removing duplicates, records outside a particular basin, and NAs.

Usage

pred_extract(
  data,
  raster,
  lat = NULL,
  lon = NULL,
  bbox = NULL,
  colsp,
  minpts = 10,
  mp = TRUE,
  rm_duplicates = TRUE,
  na.rm = TRUE,
  na.inform = FALSE,
  list = TRUE,
  merge = FALSE,
  verbose = FALSE,
  warn = FALSE,
  coords = FALSE
)

Arguments

data	dataframe. Data frame with multiple species or only one species for checking records with no coordinates, duplicates, and check for records that fall on land, sea, country or city centroids, and geographical outliers(Zzika et al., 2022).
raster	raster. Environmental layers from different providers such as WORLDCLIM (), Hydrogaphy90m (), CHELSA, Copernicus ().
lat, lon	coordinates. variable for latitude and longitude column names.
bbox	sf or vector. Object of class 'shapefile' If only a particular basin is considered. Bounding box vector points can also be provided in the form "c(xmin, ymin, xmax, ymax)". xmin is the minimum longitude, ymin is the minimum latitude, xmax is the maximum longitude and xmax is the minimum latitude.
colsp	string. variable already in the data that determine the groups to considered when extracting data.
minpts	numeric. Minimum number of records for the species after removing duplicates and those within a particular basin.
mp	logical. If TRUE, then number of minimum records minpts should be provided to allow dropping groups with less records. This is significant if species distribution are going to be fitted.
rm_duplicates	logical TRUE if the duplicates will removed based species coordinates and names. Default TRUE.
na.rm	logical If TRUE, the missing values will be discarded after data extracted. DEFAULT TRUE.
na.inform	logical If TRUE, the missing values will be discarded after data extracted and message will be returned. DEFAULT FALSE.
list	logical. If TRUE the a list of multiple species data frames will be generated and FALSE for a dataframe of species data sets. Default TRUE
merge	logical. To add the other columns in the species data after data extraction. Default TRUE.
verbose	logical. if TRUE message and warnings will be produced. Default TRUE.
warn	logical. indicating to whether to show implementation warning or not. Default FALSE.
coords	logical. If TRUE, the original coordinates are also returned attached on the extracted dataset. Default FALSE.

Value

dataframe or list of precleaned data sets for single or multiple species.

Examples

data("efidata")

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

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

#Get environmental data

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

referencedata <- pred_extract(data = efidata,
                          raster= worldclim ,
                          lat ="decimalLatitude",
                          lon = 'decimalLongitude',
                          colsp = 'scientificName',
                          bbox = danubebasin,
                          list= TRUE, #list will be generated for all species
                          minpts = 7, merge=TRUE)

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