mapcomp: Map Comparison procedure.

In chgigot/epiphy: Analysis of Plant Disease Epidemics

Map Comparison procedure.

Description

mapcomp performs a spatial pattern analysis based on the calculation of a formal distance (the Hellinger distance) between the density map of count or incidence data, and the density map of sampling effort. Statistical tests of spatial homogeneity are based on permutations across sampling sites and on valuable properties of the Hellinger distance.

Usage

mapcomp(data, ...)

## S3 method for class 'data.frame'
mapcomp(
  data,
  delta,
  bandwidth,
  nperm = 100,
  edge_correction = FALSE,
  threads = 1,
  verbose = TRUE,
  ...
)

## S3 method for class 'matrix'
mapcomp(
  data,
  delta,
  bandwidth,
  nperm = 100,
  edge_correction = FALSE,
  threads = 1,
  verbose = TRUE,
  ...
)

## S3 method for class 'count'
mapcomp(
  data,
  delta,
  bandwidth,
  nperm = 100,
  edge_correction = FALSE,
  threads = 1,
  verbose = TRUE,
  ...
)

## S3 method for class 'incidence'
mapcomp(
  data,
  delta,
  bandwidth,
  nperm = 100,
  edge_correction = FALSE,
  threads = 1,
  verbose = TRUE,
  ...
)

Arguments

data	A data frame or a matrix with only three columns: the two first ones must be the x and y coordinates of the sampling units, and the last one, the corresponding disease intensity observations. It can also be a count or an incidence object.
...	Additional arguments to be passed to other methods.
delta	Mesh size of the grid over the geographical domain of the sampling units used to compute the integral Hellinger distance between the probability density function of observations and the probability density function of sampling effort.
bandwidth	Bandwidth parameter for smoothing. It allows to test the spatial extent of heterogeneity if any.
nperm	Number of random permutations to assess probabilities.
edge_correction	Apply edge correction to account for the fact that bordering points intrinsically suffer from a lack of neighboring observation sites. FALSE by default.
threads	Number of threads to perform the computations.
verbose	Explain what is being done (TRUE by default).

Value

An object of class mapcomp, which is a list containing the following components:

data	The input data.
coord	The coordinates and normalized intensity for each point of the full grid.
object	The class of data.
bandwidth	The bandwidth parameter.
stat, pval	The statistic and corresponding p-value (see references for more details).

References

Lavigne C, Ricci B, Franck P, Senoussi R. 2010. Spatial analyses of ecological count data: A density map comparison approach. Basic and Applied Ecology. 11:734–742.

Examples

set.seed(123)
my_res <- mapcomp(codling_moths, delta = 1, bandwidth = 11,
                  edge_correction = FALSE, nperm = 20)
my_res
plot(my_res)

set.seed(123)
my_count <- count(codling_moths, mapping(x = xm, y = ym))
my_res <- mapcomp(my_count, delta = 1, bandwidth = 11,
                  edge_correction = FALSE, nperm = 20)
my_res
plot(my_res, bins = 10)

chgigot/epiphy documentation built on Nov. 20, 2023, 1:13 p.m.