occSimpFilter: Runs tests and validates data

In occTest: Characterizing and Filtering Species Occurrence Data

Runs tests and validates data

Description

Runs tests and validates data

Usage

occSimpFilter(
  spOcc,
  env,
  speciesName = "My species",
  x = "x",
  y = "y",
  date = NULL,
  isoCountry = NULL,
  classification = "majority",
  filterCols = TRUE
)

Arguments

spOcc	data.frame. Object with the coordinate data.
env	raster or rasterStack. Environmental data (e.g. typically climatic).
speciesName	character. Name of the species.
x	name of the field with the coordinate x. Default 'x'
y	name of the field with the coordinate y. Default 'y'
date	name of the field with the values of the reported timestamp of the record. Default NULL
isoCountry	name of the field with the values of the reported country of the record. Default NULL
classification	character. Indicates the thresholds philosophy applied to classify errors in occurrence data. Possible values 'strict','relaxed','custom'
filterCols	logical. Should only the initial input columns be retained in the output (the filtered dataframe)?

Value

a list of two. First element is a data.frame with profiled occurrence records with their associated profiled labels. Second element is a dataframe with all outputs of the analysis implemented.

Note

The majority of function parameters can be adjusted but we provide default values.
We recommend those default values if the user is to use the geospatial data included in the package.
but this automatic implementation (occTest + occFilter) missses some analysis to increase speed.

Author(s)

Josep M Serra-Diaz ([e-mail])

Examples

### THIS IS A CUT DOWN  EXAMPLE 
### visit vignetteXtra-occTest for more info
#load environmental raster
library (raster)
library (sf)
library (occTest)
#load occurrence data
occData <- read.csv (system.file('ext/exampleOccData.csv',package = 'occTest'))
#load environmental raster
renv <- raster (system.file('ext/AllEnv.tif',package = 'occTest'))
#load elevation raster
dem <- raster (system.file('ext/DEM.tif',package = 'occTest'))
#load settings
settings <- readRDS (system.file('ext/exSettings.rds',package = 'occTest'))
#run occTest
out = occTest(sp.name='MyFake species',
             sp.table = occData,ntv.ctry = 'ESP',inv.ctry = 'FRA',
             tableSettings = settings$tableSettings,
             writeoutSettings = settings$writeoutSettings,
             analysisSettings = settings$analysisSettings,
             r.env = renv,r.dem=dem)
#filter
occFilter(out)

occTest documentation built on Nov. 18, 2022, 5:07 p.m.