MapPlot — MapPlot • SpatDiv

Map Spatialized Communities

MapPlot(x, ...)

# S3 method for Accumulation
MapPlot(
  x,
  Order,
  NeighborHood,
  AllowJitter = TRUE,
  Nbx = 128,
  Nby = 128,
  Contour = TRUE,
  Palette = grDevices::topo.colors(128, alpha = 1),
  Contournlevels = 10,
  Contourcol = "dark red",
  Points = FALSE,
  pch = 20,
  Pointcol = "black",
  ...,
  CheckArguments = TRUE
)

# S3 method for fv
MapPlot(
  x,
  spCommunity,
  ReferenceType = "",
  r = median(x$r),
  AllowJitter = TRUE,
  Nbx = 128,
  Nby = 128,
  Contour = TRUE,
  Palette = grDevices::topo.colors(128, alpha = 1),
  Contournlevels = 10,
  Contourcol = "dark red",
  Points = FALSE,
  pch = 20,
  Pointcol = "black",
  ...,
  CheckArguments = TRUE
)

Arguments

x: An object to map.
...: Further parameters.
Order: The order of diversity, i.e. the value of $q$.
NeighborHood: The neighborhood size, i.e. the number of neighbors or the distance to consider.
AllowJitter: If TRUE, duplicated points are jittered to avoid their elimination by the kriging procedure.
Nbx: The number of columns (pixels) of the resulting map, 128 by default.
Nby: The number of rows (pixels) of the resulting map, 128 by default.
Contour: If TRUE, contours are added to the map.
Palette: The color palette of the map.
Contournlevels: The number of levels of contours.
Contourcol: The color of the contour lines.
Points: If TRUE, the points that brought the data are added to the map.
pch: The symbol used to represent points.
Pointcol: The color of the points.
CheckArguments: If TRUE (default), the function arguments are verified. Should be set to FALSE to save time in simulations for example, when the arguments have been checked elsewhere.
spCommunity: A spatialized community (A wmppp.object with PointType values as species names.)
ReferenceType: The point type used to calculate the function values. The default value is "", i.e. all point types, but it will generate an error if the actual reference type is different.
r: The distance at which the function value must be considered. The default value is the median distance used to calculate the function values.

Value

An autoKrige object that can be used to produce alternative maps.

Details

Maps of interpolated values from points of a spatialized community (a wmppp.object) are produced. x may be:

an "Accum" object produced e.g. by the function DivAccum. A map of diversity of the chosen order within the chosen neighborhoods of points is obtained by kriging.
an fv object produced by a distance-based measure of spatial structure, such as dbmss:Mhat, with individual values. Then a map of the local value of the function is produced, following (Getis and Franklin 1987) .

Examples

# Generate a random community
spCommunity <- rSpCommunity(1, size=50, S=10)
# Calculate the species accumulation curve
accum <- DivAccum(spCommunity, q.seq=c(0,1), n.seq=4, Individual=TRUE)
# Plot the local richness, accumulated up to 5 individuals.
MapPlot(accum, Order=0, NeighborHood=5)
#> [using ordinary kriging]


# Generate a random community
spCommunity <- rSpCommunity(1, size=50, S=3, Species = paste0("sp",1:3))
library("dbmss")
#> Loading required package: spatstat.explore
#> Loading required package: spatstat.data
#> Loading required package: spatstat.geom
#> spatstat.geom 3.2-1
#> Loading required package: spatstat.random
#> spatstat.random 3.1-5
#> Loading required package: nlme
#> spatstat.explore 3.2-1
M_i <- Mhat(spCommunity, ReferenceType = "sp1", Individual = TRUE)
MapPlot(M_i, spCommunity, ReferenceType = "sp1", r=0.2, Points=TRUE)
#> [using ordinary kriging]