R/createAge.R

In IPMbook: Functions and Data for the Book 'Integrated Population Models'

# Section 4.5.1.1

# p 80 of MS dated 2020-11-13

# Create a matrix x[i,t] which indicates the age class at time t
# for each individual i, based on the occasion of first capture, f, and
# age at first capture.

# Function to create the age matrix
createAge <- function(f, age, nyears, mAge=2){
  # Checks and fixes for input data -----------------------------
  stopifnotEqualLength(f, age)
  f <- round(f)
  stopifNegative(f, allowNA=FALSE, allowZero=FALSE)
  age <- round(age)
  stopifNegative(age, allowNA=FALSE, allowZero=FALSE)
  nyears <- round(max(nyears))
  if(nyears < max(f))
    stop("The value of 'f' cannot exceed 'nyears'", call.=FALSE)
  mAge <- round(max(mAge))
  stopifNegative(mAge, allowNA=FALSE, allowZero=FALSE)
  # --------------------------------------------------------------
  
  a <- matrix(NA, nrow=length(f), ncol=nyears)
  k <- c(1:mAge, rep(mAge, nyears))
  for (i in 1:length(f)){
    a[i,f[i]:(nyears)] <- k[age[i]:(nyears-f[i]+age[i])]
  }
  return(a[, 1:(nyears - 1)])
}