idar (version 1.5)

localdar: Map Local Diversity Area Relationships

Description

Estimates and maps local diversity-area relationships.

Usage

localdar(mippp, mippp.sp = NULL, nx = NULL, ny = NULL, mimark = NULL, idar = "isar", 
            buffer = 0, bfw = NULL, r, cross.idar = FALSE, tree = NULL, traits = NULL, 
            namesmark = NULL, correct.trait.na = TRUE, correct.trait = "mean",
            correct.phylo="mean")
fdismap(comm, traits)
raoDmap(comm, phy = NULL)

Value

If a focal point patternn has been provided by the arguments mippp.sp or mimark, localdar will return a list of marked point patterns (as long as the vector r) with the marks showing the estimation of the selected diversity index for the local community defined by a circle of radius r around each of the points of the focal pattern. If no focal point pattern is provided, it will return a list of maps (as long as the vector r) each with the format im of spatstat, each pixel showing the estimation of the selected diversity index for the local community defined by a circle of radius r around the pixel center.

Arguments

mippp

A multitype (a.k.a. multivariate) marked point pattern. An object with the ppp format of spatstat.

mippp.sp

Univariate point pattern of the focal species. An object with the ppp format of spatstat.

nx

Number of points of the grid along the x axis.

ny

Number of points of the grid along the y axis.

mimark

Character. Name of the focal species in the multitype mippp.

idar

Character. The name of the idar function to be computed. Either "isar", "ipsvar", "ipsrar", "ipsear", "ipscar", "icwmar", "icwmar.O", "iraodar"or "imntdar"

buffer

One of "adapt", i.e., compute an adaptive buffer, or a number indicating the width of a fixed buffer area around the plot border

bfw

An owin object indicating the limits of the buffer area.

r

Vector of distances to compute IDAR(r) functions

cross.idar

Logical. If TRUE, the focal pattern will be excluded form the community being measured.

tree

A phylogenetic tree in phylo format (ape) or a phylogenetic covariance matrix

traits

A data.frame of traits, or a distance matrix among species (in dist or matrix format) computed on a data.frame of traits.

namesmark

Character. If the marks in mippp are within a data.frame, the name of the column with the species names

correct.trait.na

Logical flag indicating whether NA values in the matrix of traits should be "corrected": NA values will be assigned the mean trait value.

correct.trait

Character. Either "mean" or "exclude". Species missing in the data.frame of traits will be assigned mean trait values or will be excluded from the analysis, respectively.

correct.phylo

Character. Either "mean" meaning "include missing species in the tree with a constant mean phylogenetic covariance" or "exclude", meaning "exclude missing species in the tree from the analysis"

comm

A comunity data table (sites x species).

phy

A comunity data table (sites x species).

Author

Marcelino de la Cruz

Details

localdar estimates any of the individual diversity area indices (isar, ipsvar,ipsrar, ipsear, ipscar, icwmar, icwmar.O, iraodar or imntdar) at specific locations, such as the locations of trees of a "focal" point partern or at some grid of points (i.e., "mapping" local diversity area relationships). If no predefined focal point pattern is provided (by the arguments mippp.sp or mimark), localdar will, by default, estimate the selected idar function in a 30 x 30 point-grid and return a map (the size of the grid can be modified by the arguments nx and ny). fdismap and raoDmap are internal functions used by localdar to get the individual componentes of iraoD and FDis, instead of the averages obtained by envelope4idar.

See Also

envelope4idar

Examples

# Map of local species area-relationship [ISAR(r)] in San Francisco plot at r=5 and r= 6 m
  data(SF)
  data(SFphylotree)
  data(SFtraits)

  isarSF <- localdar(SF, r=5:6, namesmark="species")
  
  isarSF
  
  plot(isarSF[[1]])
  
  
# Map of local species area-relationship [ISAR(r)] in San Francisco plot at r=5 and r= 6 m,
# with an adaptive buffer

isarSF <- localdar(SF, r=5:6, namesmark="species",buffer="adapt")



# Map of local species area-relationship [ISAR(r)] in lansing woods at different radii,
# with an fixed  buffer (only for rectangular windows).

data(lansing)
lansing.bfw<- owin(c(0.2,0.8),c(0.2,0.8))
lansing.lsar.bf<-localdar(lansing, r=seq(0.05,0.2,by=0.05), bfw=lansing.bfw)


# Map of local species area-relationship [ISAR(r)] in San Francisco plot at r=5 and r= 6 m,
# with a buffer of 7 m within plot limits

  mibfw<- erosion(SF$win, r=7)

 isarSF <- localdar(SF, r=5:6, namesmark="species", bfw=mibfw)



# Estimate local species area-relationship [ISAR(r)] in the local communities 
#  in circles with radius  r=5 and r= 6 m around the individuals of sp_44

  sp_44_sar <- localdar(SF, r=5:6, namesmark="species", mimark="sp_44")
  sp_44_sar
  plot(sp_44_sar[[1]])
  sp_44_sar[[1]]$marks
  


# Estimate local species area-relationship [ISAR(r)] in the local communities 
#  in circles with radius  r=5 and r= 6 m around the individuals of sp_44
# EXCLUDING the focal species from species counts.

  sp_44_sar <- localdar(SF, r=5:6, namesmark="species", mimark="sp_44", cross.idar=TRUE)
  sp_44_sar
  plot(sp_44_sar[[1]])
  sp_44_sar[[1]]$marks
 
  
  


# Map and estimation of local Phylogenetic Species Variety
local_psvar<-localdar(SF, r=5:6, idar="ipsvar", tree=SFphylotree, namesmark="species")
sp44_psvar <- localdar(SF, r=5:6, idar="ipsvar", tree=SFphylotree, namesmark="species",
                                    mimark="sp_44", buffer="adapt")

# Map and estimation of local Functional Dispersion
local_fdar <- localdar(SF, nx=50, ny=25, r=5:6,  idar="ifdar", traits=SFtraits,
                                 namesmark="species", correct.trait.na=TRUE)
sp44_fdar <- localdar(SF, nx=50, ny=25, r=5:6,  idar="ifdar", traits=SFtraits,
                                  namesmark="species", mimark="sp_44", correct.trait.na=TRUE)


# Map of a local community weighted mean of wood density
# first, put the wood desnsity data as a named vector
 wood.density.vec<-unlist(SFtraits[,  "wood.density", drop=FALSE])
    names(wood.density.vec)<- rownames(SFtraits)
    
local_cwd <- localdar(SF, r=5:6,  idar="icwmar", traits=wood.density.vec,
                                  namesmark="species", correct.trait.na=TRUE)
local_O.cwm <-localdar(SF, r=5:6, idar="icwmar.O", traits=wood.density.vec, 
                                     namesmark="species", correct.trait.na=TRUE)

# Map of Rao's phylogenetic diversity
local_rao<- localdar(SF,  r=5:6, idar="iraodar",  tree=SFphylotree, namesmark="species")
local_O.rao <- localdar(SF, r=5:6, idar="iraodar.O",  tree=SFphylotree, namesmark="species")

# Map of local mean nearest taxon distance 
local_mntd <- localdar(SF, r=5:6, idar="imntdar",  tree=SFphylotree, namesmark="species")