Allow collapseMatrix to collapse non-adjacent stages & remove rearrangeMatrix about rage HOT 5 CLOSED

matU[is.na(matU)]=0
matF[is.na(matF)]=0
matC[is.na(matC)]=0

matA=matU+matF+matC
matDim=dim(matA)[1]
dorm=dorm

out = data.frame("Survival"=NA,"Progression"=NA,"Retrogression"=NA,"Reproduction"=NA,"Clonality"=NA,"GoDorm"=NA,"StayDorm"=NA,"Awake"=NA,
                 "SurvivalSSD"=NA,"ProgressionSSD"=NA,"RetrogressionSSD"=NA,"ReproductionSSD"=NA,"ClonalitySSD"=NA,"GoDormSSD"=NA,"StayDormSSD"=NA,"AwakeSSD"=NA)

#Extracting SSD corrected vital rate values
SSD=eigen.analysis(matA)$stable.stage
f=colSums(matF)
out$Reproduction=mean(f)
out$ReproductionSSD=mean(f*SSD)
c=colSums(matC)
out$Clonality=mean(c)
out$ClonalitySSD=mean(c*SSD)

#Preparing survival-independent matrix to calculate survival and dormancy
uDistrib=matrix(NA,ncol=matDim,nrow=matDim)
u=colSums(matU)
out$Survival=mean(u[which(!(1:matDim)%in%dorm)])
out$SurvivalSSD=mean((u[which(!(1:matDim)%in%dorm)])*SSD[which(!(1:matDim)%in%dorm)])
if (length(dorm)>0) {
  out$StayDorm=mean(u[dorm])
  out$StayDormSSD=mean((u[dorm])*(SSD[dorm]))
}

#Making matrix for transitions conditional on survival
for (j in which(u>0)) uDistrib[,j]=matU[,j]/u[j]
UPrime=uDistrib
UPrime[is.na(UPrime)]=0

#Extracting proxy to individual progressive growth rate
UPrimeGrowth=UPrime
UPrimeGrowth[upper.tri(UPrime, diag = T)]=NA
UPrimeGrowth[matDim,matDim]=UPrime[matDim,matDim]  #Putting back the last element of stasis bc there is likely growth on the top of class
out$Progression=mean(colSums(UPrimeGrowth,na.rm=T)[which(!(1:matDim)%in%dorm)])
out$ProgressionSSD=mean(colSums(UPrimeGrowth,na.rm=T)[which(!(1:matDim)%in%dorm)]*(SSD[which(!(1:matDim)%in%dorm)]))

#Extracting proxy to individual retrogressive growth rate
UPrimeShrinkage=UPrime
UPrimeShrinkage[lower.tri(UPrime, diag = T)]=NA
out$Retrogression=mean(colSums(UPrimeShrinkage,na.rm=T)[which(!(1:matDim)%in%dorm)])
out$RetrogressionSSD=mean((colSums(UPrimeShrinkage,na.rm=T)[which(!(1:matDim)%in%dorm)])*(SSD[which(!(1:matDim)%in%dorm)]))

if (length(dorm)>0) {
  
  #Extracting proxy to going into dormancy
  UPrimeGoDorm=UPrime
  UPrimeGoDorm[upper.tri(UPrime, diag = T)]=NA
  UPrimeGoDorm[matDim,matDim]=UPrime[matDim,matDim]  #Putting back the last element of stasis bc there is likely growth on the top of class
  out$GoDorm=mean(colSums(UPrimeGrowth,na.rm=T)[dorm])
  out$GoDormSSD=mean(colSums(UPrimeGrowth,na.rm=T)[dorm]*(SSD[dorm]))
  
  #Extracting proxy to awaking from dormancy
  UPrimeAwake=UPrime
  UPrimeAwake[lower.tri(UPrime, diag = T)]=NA
  out$Awake=mean(colSums(UPrimeAwake,na.rm=T)[dorm])
  out$AwakeSSD=mean((colSums(UPrimeAwake,na.rm=T)[dorm])*(SSD[dorm]))
}  

return(out)  

list(propStages = propStage,
     preRepStages = preRep,
     repStages = Rep,
     postRepStages = postRep)