Description Usage Arguments Author(s) Examples
This function draws mixing plot for the estimated parameters, the parameter's general means, and the sigma.
1 |
x |
Object of class HMSC |
toplot |
A character string defining whether the mixing plot should be drawn for parameter in "paramX", "means", or "sigma". Any unambiguous variation of wording used in this argument is accepted. |
param |
A vector of one ("means" when using |
add |
Logical. Whether a new plot ( |
... |
Graphical arguments passed to this function. |
F. Guillaume Blanchet
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | desc<-cbind(1,scale(1:50),scale(1:50)^2)
dataBase<-communitySimulH(desc,nsp=20)
#=================================
### Formatting data and parameters
#=================================
formdata<-as.HMSCdata(dataBase$data$Y,desc,Ypattern="sp",interceptX=FALSE)
formparam<-as.HMSCparam(formdata,dataBase$param$param,means=dataBase$param$means,sigma=dataBase$param$sigma)
formpriors<-as.HMSCprior(formparam,rep(0,length(formparam$means)),0,length(formparam$means),diag(length(formparam$means)))
#===========================================================================================================
### Building model using a linear modelling approach (currently 2000 iterations takes about 1 minute to run)
#===========================================================================================================
modelLinear<-hmscH(formdata,formparam,formpriors,niter=200,nburn=100)
#___________________
#### Community Sigma
#___________________
par(mfrow=c(3,3),mar=c(1,3,3,1))
for(i in 1:3){
for(j in 1:3){
mixing(modelLinear,toplot="sigma",param=c(i,j),col="red",xlab="Sites",ylab="Sigma",las=1)
abline(h=formparam$sigma[i,j],col=c("red"),lwd=3)
title(paste("Community Sigma",i,"-",j))
}
}
#__________________
### Community means
#__________________
mixing(modelLinear,toplot="means",param=1,ylim=range(modelLinear$model$means),xlab="Sites",ylab="Means",las=1)
title("Community means")
mixing(modelLinear,toplot="means",param=2,add=TRUE,col="blue",xlab="Sites",ylab="Means",las=1)
mixing(modelLinear,toplot="means",param=3,add=TRUE,col="red",xlab="Sites",ylab="Means",las=1)
abline(h=formparam$means,col=c("black","blue","red"),lwd=3)
#_____________________________
### Parameter for each species
#_____________________________
par(mfrow=c(5,4),mar=c(1,3,2,1))
for(i in 1:20){
mixing(modelLinear,toplot="paramX",param=c(i,1),ylim=range(modelLinear$model$paramX[i,,]),xlab="Sites",ylab="paramX",las=1,xaxt="n")
title(paste("Species",i))
mixing(modelLinear,toplot="paramX",param=c(i,2),add=TRUE,col="blue")
mixing(modelLinear,toplot="paramX",param=c(i,3),add=TRUE,col="red")
abline(h=formparam$paramX[i,],col=c("black","blue","red"),lwd=3)
}
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