localdar: Map Local Diversity Area Relationships
In idar: Individual Diversity-Area Relationships
localdar R Documentation
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)
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).
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.
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.
Author(s)
Marcelino de la Cruz marcelino.delacruz@urjc.es
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")
idar documentation built on Jan. 5, 2023, 5:10 p.m.
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| localdar | R Documentation |
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)
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 |
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 |
tree |
A phylogenetic tree in |
traits |
A data.frame of traits, or a distance matrix among species (in |
namesmark |
Character. If the marks in |
correct.trait.na |
Logical flag indicating whether |
correct.trait |
Character. Either |
correct.phylo |
Character. Either |
comm |
A comunity data table (sites x species). |
phy |
A comunity data table (sites x species). |
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.
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.
Author(s)
Marcelino de la Cruz marcelino.delacruz@urjc.es
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")
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