specleanr (version 1.0.0)

ecological_ranges: Check for environmental outliers using species optimal ranges.

Description

Check for environmental outliers using species optimal ranges.

Usage

ecological_ranges(
  data,
  var,
  output = "outlier",
  species = NULL,
  optimumSettings = list(optdf = NULL, optspcol = NULL, mincol = NULL, maxcol = NULL,
    ecoparam = NULL, direction = NULL),
  minval = NULL,
  maxval = NULL,
  lat = NULL,
  lon = NULL,
  ecoparam = NULL,
  direction = NULL,
  pct = 80,
  checkfishbase = FALSE,
  mode = NULL,
  warn = TRUE
)

Value

Dataframe with or with no outliers.

Arguments

data

Dataframe with environmental predictors for a species or multiple species.

var

Environmental parameter considered in flagging suspicious outliers.

output

output Either clean: for dataframe with no suspicious outliers or outlier: to retrun dataframe with only outliers.

species

The species should be indicated if the minimum minval and maximum values maxval are provided.

optimumSettings

A list of optimal parameters are provided mostly when multiple species are examined.

• optdf: is the dataframe with species optimal values (min, max, or ecoparam). This dataset can be generated from literature for different species.

• optspcol: Is the column with species names in the optdf dataset.

• mincol: Is the column name in the optdf with minimum values.

• maxcol: Is the column name in the optdf with maximum values.

• ecoparam: If in the optdf the minimum and maximum values are not found, then the the column with ecoparam should be provided.

• direction: If ecoparam is provided in the optdf, then column for direction should be provided.

minval, maxval

Minimum and maximum values (ranges) for a particular that are used to flag out values outside the ranges.

lat, lon

If the checkfishbase and mode are set, then the columns for latitude longitude should be provided.

ecoparam

This parameter is used only when the lower bound (minimum) and upper bound maximum or ranges are absent. For example, if only minimum value is present for a particular species, then ecoparam is set and the direction is provided whether lower, greater, equal, less/equal or greater/equal the ecoparam value provided.

direction

This indicates if the provided ecological threshold ecoparam or ranges is greater than greater, less than less, equal equal, less or equal le or greater or equal ge. Íf the minimum and maximum values are known, then the ecoparam and direction should not be used.

pct

The percentage similarity of the species name provided by the user and the one in FishBase. Only fish species names are checked with Fishbase but other taxa can be checked using taxize package.

checkfishbase

Either TRUE to check for both temperatures temp and latitudinal or geographical ranges geo. If the checkfishbase is set to TRUE then the mode parameter must be set to either geo or temp. This function applies for only fish species.

mode

Either geo or temp for latitudinal ranges or temperature ranges respectively. See thermal_ranges or geo_ranges on how to obtain the data.

warn

Either TRUE to return warning messages or FALSE for no warning messages. the defualt is FALSE:

Examples

if (FALSE) {

data("efidata")
data("jdsdata")

datafinal <- match_datasets(datasets = list(jds = jdsdata, efi=efidata),
                            lats = 'lat',
                            lons = 'lon',
                            species = c('speciesname','scientificName'),
                            date = c('Date', 'sampling_date'),
                            country = c('JDS4_site_ID'))

efidata <- check_names(data = datafinal, colsp='species', pct=90, merge=TRUE)

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)

saldata <- refdata[["Thymallus thymallus"]]
#1. checking the annual maean temperature (bio1) are within the ranges in FishBase
salmotherange <- thermal_ranges(x = "Salmo trutta")

sdatatemp <- ecological_ranges(data = saldata, var = 'bio1', species = "Salmo trutta",
                              checkfishbase = TRUE, mode = 'temp', output = 'outlier')
#zero record no outliers
#====
#2. geographical ranges: latitude longitude
#geo ranges in fishbase
salgeorange <- geo_ranges(data = "Salmo trutta")
sdatageo <- ecological_ranges(data = saldata, lat = 'y', lon = 'x', output = 'outlier',
                              species = "Salmo trutta",
                              checkfishbase = TRUE, mode = 'geo')
#3. GENERAL LITERATURE RANGES
#======
#1. when the min and and max are provided
#multiple FALSE SHOULD BE SET
#3.1: If only the minimum value is present: assuming minimum temperature is 6, varible: bio1
#direction less than 6.0 is outlier and greater is not
sdata <- ecological_ranges(data = saldata, ecoparam = 6.0, var = 'bio1',
                           direction = 'greater' )
#3.2
sdata2 <- ecological_ranges(data = saldata, var = 'bio1', minval = 2,
                            maxval = 24, species = "Salmo trutta" )

#4. Multiple TRUE
#the optimal parameters should be provided in a dataframe format with min max, or ecoparam
#4.1 optimal dataset

optdata <- data.frame(species= c("Salmo trutta", "Abramis brama"),
                      mintemp = c(6, 1.6),maxtemp = c(20, 21),
                      meantemp = c(8.5, 10.4), #ecoparam
                      direction = c('greater', 'greater'))

#parameter used is annual mean temperature (WORLDCLIM)
#provide the column with species names in the environment dataset
#set optimal list parameter
#
# #optimal parameters
sdata3 <- ecological_ranges(data = saldata, species = 'Salmo trutta',
                            var = 'bio1', output = "outlier",
                            optimumSettings = list(optdf = optdata,maxcol = "maxtemp",
                                                   mincol ="mintemp",optspcol = "species"))
#
#
#only one ecological parameter (ecoparam is provided) and direction
sdata4 <- ecological_ranges(data = saldata, species = 'Salmo trutta', var = 'bio1',
                            output = "outlier",
                            optimumSettings = list(optdf = optdata,
                                                   ecoparam = "meantemp",
                                                   optspcol = "species",
                                                   direction= "direction"))
}