Example Dataset for a Custom Study Area

Description

An example of the format needed to provide custom areas for calculate_bias

Usage

area_example

Format

An object of class sf (inherits from data.frame) with 2 rows and 1 columns.

Examples

data(area_example)

Borneo

Description

The outline of Borneo, as example data for the user-defined study area option of calculate_bias. From https://www.naturalearthdata.com.

Usage

borneo

Format

An object of class sf (inherits from data.frame) with 1 rows and 3 columns.

Examples

data(borneo)

Evaluating Sampling Bias in Species Distribution Data

Description

The major function of the package, calculating the bias effect of sampling bias due to geographic structures, such as the vicinity to cities, airports, rivers and roads. Results are projected to space, and can be compared numerically.

Usage

calculate_bias(
  x,
  gaz = NULL,
  res = 1,
  buffer = NULL,
  restrict_sample = NULL,
  terrestrial = TRUE,
  inp_raster = NULL,
  mcmc_rescale_distances = 1000,
  mcmc_iterations = 1e+05,
  mcmc_burnin = 20000,
  mcmc_outfile = NULL,
  prior_q = c(1, 0.01),
  prior_w = c(1, 1),
  plot_raster = FALSE,
  verbose = FALSE,
  run_null_model = FALSE,
  use_hyperprior = TRUE
)

Arguments

Details

The default gazetteers delivered with the package are simplified from http://www.naturalearthdata.com/downloads/. They include major features, and for small scale analyses custom gazetteers should be used.

For computational convenience, the gazetteers are cropped to the extent of the point occurrence data sets. To account for the fact, that, relevant structures might lay directly outside this extent, but still influencing the distribution of samples in the study area, the buffer option, gives the area, around the extent that should be included in the distance calculation.

Visit https://github.com/azizka/sampbias/wiki for more information on distance calculation and the algorithm behind sampbias.

Value

An object of the S3-class ‘sampbias’, which is a list including the following objects:

Note

Check https://github.com/azizka/sampbias/wiki for a tutorial on sampbias.

See Also

summary.sampbias is.sampbias plot.sampbias

Examples

  #simulate data
  x <- data.frame(species = rep(sample(x = LETTERS, size = 5), times = 20),
                   decimalLongitude = runif(n = 100, min = 0, max = 20),
                   decimalLatitude = runif(n = 100, min = -4, max = 4))

  out <- calculate_bias(x, terrestrial = TRUE, buffer = 0)
  summary(out)
  plot(out)
  
  
  

Distance Rasters from a List of Geographic Gazetteers

Description

Creates a list of distances rasters based on a list of geographic gazetteers, as SpatVector objects, and a template SpatRaster, indicating the desired extent and resolution.

Usage

dis_rast(gaz, ras, buffer = NULL)

Arguments

Value

a list of SpatRaster objects of the same length as gaz. The values in each raster correspond to the planar geographic distance to the next feature in gaz, given the resolution of ras

Note

Check https://github.com/azizka/sampbias/wiki for a tutorial on sampbias.

See Also

calculate_bias

Examples

#create raster for resolution and extent
ras <- terra::rast(terra::ext(-5,5,-4,4), res = 1)

#create point gazeteer
pts <- data.frame(long = runif(n = 5, min = -5, max = 5),
                  lat = runif(n = 5, min = -4, max = 4),
                  dat = rep("A", 5))

pts <- terra::vect(pts, geom = c("long", "lat"))

lin <- as.matrix(data.frame(long = seq(-5, 5, by = 1),
                  lat = rep(2, times = 11)))
lin <- terra::vect(lin, type = "line")

gaz <- list(point.structure = pts, lines.strucutre = lin)

out <- dis_rast(gaz, ras)

Equal Area Raster

Description

An example for an global equal area raster (in Behrmann projection) for the format needed for a custom grid provided to calculate_bias.

Usage

ea_raster

Format

An object of class PackedSpatRaster of length 1.

Examples

data(ea_raster)
ea_raster <- terra::unwrap(ea_raster)

Detailed Example for a Custom Study Area

Description

An example of the format needed to provide custom areas for calculate_bias based on a publicly available set of global ecoregions.

Usage

ecoregion_example

Format

An object of class sf (inherits from data.frame) with 7 rows and 22 columns.

Source

https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world

Examples

data(ecoregion_example)

Is Method for Class sampbias

Description

Check class of sampbias objects.

Usage

## S3 method for class 'sampbias'
is(object, class2 = "sampbias")

Arguments

Details

With two arguments, tests whether object can be treated as from class2. With one argument, returns all the super-classes of this object's class.

Value

The function returns a logical indicating whether the object is a is of the class sampbias.

Examples

  #simulate data
  occ <- data.frame(species = rep(sample(x = LETTERS, size = 5), times = 10),
                   decimalLongitude = runif(n = 50, min = 12, max = 20),
                   decimalLatitude = runif(n = 50, min = -4, max = 4))

  out <- calculate_bias(x = occ, terrestrial = TRUE)
  is(out)

Mapping Projected Bias Effects

Description

A plotting function to visualize the effect of accessibility bias caused by different biasing factors in space.

Usage

map_bias(x, gaz = NULL, sealine = TRUE, type = "sampling_rate")

Arguments

Value

A series of R plots based on ggplot2.

See Also

calculate_bias, project_bias

Examples

  #simulate data
  occ <- data.frame(species = rep(sample(x = LETTERS, size = 5), times = 10),
                   decimalLongitude = runif(n = 50, min = 12, max = 20),
                   decimalLatitude = runif(n = 50, min = -4, max = 4))

  out <- calculate_bias(x = occ, terrestrial = TRUE)
  proj <- project_bias(out)
  map_bias(proj)

Plotting the Posterior Estimates of the Bias Weights

Description

Plotting method for class sampbias, generating a box-whiskers-plot showing the bias weights for all biasing factors indicating the effect strength for each gazetteer provided to calculate_bias.

Usage

## S3 method for class 'sampbias'
plot(x, ...)

Arguments

Value

A plot

See Also

calculate_bias, summary.sampbias

Examples

  #simulate data
  occ <- data.frame(species = rep(sample(x = LETTERS, size = 5), times = 10),
                   decimalLongitude = runif(n = 50, min = 12, max = 20),
                   decimalLatitude = runif(n = 50, min = -4, max = 4))

  out <- calculate_bias(x = occ, terrestrial = TRUE)
  summary(out)
  plot(out)

Projecting Bias Effects in Space

Description

Uses the the estimated bias weights from a sampbias object to project the bias through space, using the same raster as used for the distance calculation.#'

Usage

project_bias(x, factors = NULL)

Arguments

Value

A raster stack, with the same length as the number of biasing factors used in calculate_bias. The names indicate the factors included for each layer.

See Also

calculate_bias, summary.sampbias

Examples

  #simulate data
  occ <- data.frame(species = rep(sample(x = LETTERS, size = 5), times = 10),
                   decimalLongitude = runif(n = 50, min = 12, max = 20),
                   decimalLatitude = runif(n = 50, min = -4, max = 4))

  out <- calculate_bias(x = occ, terrestrial = TRUE)
  proj <- project_bias(out)

Summary Method for Class sampbias

Description

Summary method for objects of the class sampbias.

Usage

## S3 method for class 'sampbias'
summary(object, ...)

Arguments

Value

Summary printed to screen.

See Also

calculate_bias is.sampbias plot.sampbias

Examples

  #simulate data
  occ <- data.frame(species = rep(sample(x = LETTERS, size = 5), times = 10),
                   decimalLongitude = runif(n = 50, min = 12, max = 20),
                   decimalLatitude = runif(n = 50, min = -4, max = 4))

  out <- calculate_bias(x = occ, terrestrial = TRUE)
  summary(out)