env_grid_filter: Filter occurrences in environmental space

In naturaList: Classify Occurrences by Confidence Levels in the Species ID

Filter occurrences in environmental space

Description

Filter the occurrence with the most realible species identification in the environmental space. This function is based in the function envSample provided by Varela et al. (2014) and were adapted to the naturaList package to select the occurrence with the most realible species identification in each environmental grid.

Usage

env_grid_filter(
  occ.cl,
  env.data,
  grid.res,
  institution.code = "institutionCode",
  collection.code = "collectionCode",
  catalog.number = "catalogNumber",
  year = "year",
  date.identified = "dateIdentified",
  species = "species",
  identified.by = "identifiedBy",
  decimal.latitude = "decimalLatitude",
  decimal.longitude = "decimalLongitude",
  basis.of.record = "basisOfRecord",
  media.type = "mediaType",
  occurrence.id = "occurrenceID"
)

Arguments

occ.cl	data frame with occurrence records information already classified by classify_occ function.
env.data	data frame with rows for occurrence observation and columns for each environmental variable
grid.res	numeric vector. Each value represents the width of each bin in the scale of the environmental variable. The order in this vector is assumed to be the same order in the of the variables in the env.data data frame.
institution.code	column name of occ.cl with the name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
collection.code	column name of occ.cl with The name, acronym, code, or initials identifying the collection or data set from which the record was derived.
catalog.number	column name of occ.cl with an identifier (preferably unique) for the record within the data set or collection.
year	Column name of occ.cl the four-digit year in which the Event occurred, according to the Common Era Calendar.
date.identified	Column name of occ.cl with the date on which the subject was determined as representing the Taxon.
species	column name of occ with the species names.
identified.by	column name of occ.cl with the name of who determined the species.
decimal.latitude	column name of occ.cl latitude in decimal degrees.
decimal.longitude	column name of occ.cl longitude in decimal degrees.
basis.of.record	column name with the specific nature of the data record. See details.
media.type	column name of occ.cl with the media type of recording. See details.
occurrence.id	column name of occ with link or code for the occurrence record. See in Darwin Core Format

Value

Data frame with the same columns of occ.cl.

References

Varela et al. (2014). Environmental filters reduce the effects of sampling bias and improve predictions of ecological niche models. *Ecography*. 37(11) 1084-1091.

See Also

classify_occ

Examples

## Not run: 
library(naturaList)
library(tidyverse)

data("cyathea.br")
data("speciaLists")
data("r.temp.prec")

occ <- cyathea.br %>%
  filter(species == "Cyathea atrovirens")

occ.cl <- classify_occ(occ, speciaLists, spec.ambiguity = "is.spec")

# temperature and precipitaion data
env.data <- raster::extract(
  r.temp.prec,
  occ.cl[,c("decimalLongitude", "decimalLatitude")]
) %>% as.data.frame()

# the bins for temperature has 5 degrees each and for precipitation has 100 mm each
grid.res <- c(5, 100)

occ.filtered <- env_grid_filter(
  occ.cl,
  env.data,
  grid.res
)


## End(Not run)

naturaList documentation built on May 29, 2024, noon