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see this original post for more details Sequentially multiply matrices from a list by a vector at time t-1 (recursively)

am trying to accomplish the same thing, this time with sublists of matrices contained within a list, which is then matrix multiplied recursively by a list of storage arrays. Additionally, the commented out section in the forloop, I’m trying to place a cap on the resulting 4th row in all resultant list items. Help extending that concept would also be appreciated. thanks

library(plyr)
library(popbio)
library(ggplot2)
library(tidyr)
library(dplyr)
library(reshape2)
library(simpleboot)
library(boot)
library(reshape)
library(vctrs)

# setting seed for replication purposes and creating function to project. replicating with bootstrap
set.seed(123)

# vector of egg survival morts
egg.to.fry.s <- vec_rep(c(seq(from = 0.40, to = 0.89,by=0.01)),10)

# vector of fry survival morts
fry.to.one.s <- vec_rep(c(seq(from = 0.30, to = 0.79,by=0.01)),10)

# one.to.two rates
one.to.two.s <- rbeta(500,5,4)


  A <- lapply(1:500, function(x)  # construct list of matrices
    matrix(c(0, 0, 0, 0,
             0, 0, 0, 0,
             0, 0, 0, 0,
             0, 0, 0, 0), nrow = 4,ncol=4, byrow = TRUE, ))
  
  Anew <- A
  
  for(t in 1:length(Anew)) {
    Anew[[t]][2,1] <- egg.to.fry.s[t]
    Anew[[t]][3,2] <- fry.to.one.s[t]
    Anew[[t]][4,3] <- one.to.two.s[t]
  }
  
  AnewSplit <- split(Anew, rep(1:10, each = 50)) # split list into lists to represent each sim
  
  n <- c(10000,1000,100,10)  # initial vector of abundances
   
  nYears = 50  # define the number of years to project over
  
  allYears <- matrix(0,nrow=4,ncol=nYears+1)  # build a storage array for all abundances
  
  allYears[,1] <- n  # set the year 0 abundance 
  
  allYearsarray<-replicate(10,allYears)
  allYearslist <- alply(allYearsarray,3)
  

  i1 <- length(allYearslist)
  i2 <- 2:51

  # matrix multiply each list of 50 sequentially in AnewSplit * each list in allYears list and each column - 1
  
  for(t in 1:i1) {
    for(j in seq_along(i2)){
    allYearslist[[t]][,i2[j]] <-  AnewSplit[[t]]%*% allYearslist[[t]][,i2[j]-1]
   # allYearslist[4,i1[t]] <- ifelse (allYearslist[4,i1[t]] > 100000, 100000, allYearslist[4,i1[t]])  # to add density dependence to 4th row
    }
  }
user11057680
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1 Answers1

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I believe this to be the correct answer for the loop. The "cap" also appears to be working iteratively.

  i1 <- length(allYearslist)
  i2 <- 2:51

  for(t in 1:i1) {
    for(j in seq_along(i2)){
    allYearslist[[t]][,i2[j]] <-  AnewSplit[[t]][[j]]%*% allYearslist[[t]][,i2[j]-1]
    allYearslist[[t]][4,i2[j]] <- ifelse (allYearslist[[t]][4,i2[j]] > 2000, 2000, allYearslist[[t]][4,i2[j]])  # to add density dependence to 4th row
    }
  }
user11057680
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