MapPlot: MapPlot

In EricMarcon/SpatDiv: Spatially Explicit Measures of Diversity

MapPlot

Description

Map Spatialized Communities

Usage

MapPlot(x, ...)

## S3 method for class '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 class '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.

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 \insertCiteGetis1987SpatDiv.

Value

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

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)

# Generate a random community
spCommunity <- rSpCommunity(1, size=50, S=3, Species = paste0("sp",1:3))
library("dbmss")
M_i <- Mhat(spCommunity, ReferenceType = "sp1", Individual = TRUE)
MapPlot(M_i, spCommunity, ReferenceType = "sp1", r=0.2, Points=TRUE)

EricMarcon/SpatDiv documentation built on May 25, 2023, 12:54 p.m.