Stephen D. Gregory - CJS is fast in TMB

A popular way to estimate life-history rates, such as survival, reproduction and movement rates, is using Cormack Jolly Seber (CJS) models cast in state-space equations. These models vary in complexity, but generally build on two fairly simple equations representing state and observation processes:

$z_{i, t} \sim Bernoulli (z_{i, t - 1}, φ)$

$y_{i, t} \sim Bernoulli (z_{i, t}, p)$

The first equation is known as the state process and allows for the estimation of the transition rate, here survival $φ$ , from the state $z$ of individual $i$ and time $t$ from their state at time $t - 1$ . The second equation is known as the observation process and allows for the estimation of the recapture or resighting rate $p$ of the individual in state $z$ at time $t$ .

I’ve used CJS models in a number of capacities (see ), and for each I’ve written my own model in OpenBUGS, JAGS, Stan or nimble, and used Bayesian inference. However, Bayesian inference relies on sampling the parameter space using Monte-Carlo Markov Chains (MCMC), which can be time-consuming (despite ever-efficient algorithms and computation).

Recently, I attended fantastic Template Model Builder training given by Anders Nielsen. It is promoted as a fast and flexible language for inference, whether frequentist or Bayesian.

I thought that it might be nice to write a simple CJS model in TMB, following the excellent examples by Olivier Gimenez, and in native R too.

Here is my try…

Data simulation

We first build a function to simulate data from a multi-event (juvenile and adult) capture-recapture (CJS) model:

simul <- function(
    n_individuals = 1000,
    n_occasions = 3, # release, first sighting, second sighting
    n.states = 3, # juvenile, adult, dead
    phi = 0.7,
    psi = 0.8,
    p = 0.3) { 
  
  # state matrix
  phi_state <- matrix(c(
    
    0, phi, 1 - phi,
    0, psi, 1 - psi,
    0, 0, 1
    
  ), nrow = n.states, byrow = TRUE)
  
  # observation matrix 
  phi_obs <- matrix(c(
    
    0, 0, 1,
    0, p, 1 - p,
    0, 0, 1
    
  ), nrow = n.states, byrow = TRUE)
  
  # empty capture history list of matrices
  ch <- ch_true <- matrix(NA, 
                          nrow = n_individuals, 
                          ncol = n_occasions)
  
  # always seen at release
  ch[, 1] <- ch_true[, 1] <- 1
  
  # fill CH
  for (i in 1:n_individuals) {
    for (o in 2:n_occasions) {
      # state transition
      state_p <- rmultinom(n = 1, 
                           size = 1, 
                           prob = phi_state[ch_true[i, o - 1], ])
      ch_true[i, o] <- which(state_p == 1)
      # observation transition
      event_p <- rmultinom(n = 1, 
                           size = 1, 
                           prob = phi_obs[ch_true[i, o], ])
      ch[i, o] <- which(event_p == 1)
    } # o
  } # i
  
  # return
  return(list("ch" = ch, "ch.true" = ch_true))
  
}

Likelihood function in native `R`

First, we need a small function to protect the log from “exploding” (thanks, Olivier Gimenez):

logprot <- function(v) {
  eps <- 2.2204e-016
  u <- log(eps) * (1 + vector(length = length(v)))
  index <- (v > eps)
  u[index] <- log(v[index])
  return(u)
}

Then the likelihood (take the time to compare this function to the data simulation function - they’re similar!):

cjs <- function(b, ch) { 
  
  # R version of the TMB function below - not used here 
  multvecmat <- function(A, B) {
    nrowb <- nrow(B)
    ncolb <- ncol(B)
    C <- vector("numeric", length = ncolb)
    for (i in 1:ncolb) {
      C[i] <- 0
      for (k in 1:nrowb) {
        C[i] <- C[i] + A[k] * B[k, i]
      }
    }
    return(C)
  }
  
  # parameters
  n_individuals <- nrow(ch)
  n_occasions <- ncol(ch)
  
  # transforms
  phi <- plogis(b[1])
  psi <- plogis(b[2])
  p <- plogis(b[3])
  
  # state matrix
  A <- matrix(c(
    0, phi, 1 - phi,
    0, psi, 1 - psi,
    0, 0, 1
  ), nrow = 3, byrow = TRUE)
  
  # observation matrix
  B <- matrix(c(
    0, 0, 1,
    0, p, 1 - p,
    0, 0, 1
  ), nrow = 3, byrow = TRUE)
  
  # log likelihood
  l <- 0
  for (i in 1:n_individuals) {
    foo <- c(1, 0, 0)
    for (j in 2:n_occasions) {
      foo <- (foo %*% A) * B[, ch[i, j]]
    }
    l <- l + logprot(sum(foo))
  }
  
  # negative loglikelihood
  l <- -l
  
  # return
  return(l)
  
}

Likelihood function in `TMB`

Now, let me try and write the same thing in TMB:

tmb_model <- "

// capture-recapture model
#include <TMB.hpp>

/* implement the vector - matrix product */
template<class Type>
vector<Type> multvecmat(vector<Type> A, matrix<Type> B) {
  int nrowb = B.rows();
  int ncolb = B.cols(); 
  vector<Type> C(ncolb);
  for (int i = 0; i < ncolb; i++) {
    C(i) = Type(0);
    for (int k = 0; k < nrowb; k++) {
      C(i) += A(k) * B(k, i);
    }
  }
  return C;
}

template<class Type>
Type objective_function<Type>::operator() () {

  // data
  DATA_IMATRIX(ch);
  int n_individuals = ch.rows();  
  int n_occasions = ch.cols();
  // DATA_VECTOR(fii);
  
  // parameters
  PARAMETER_VECTOR(b);
  
  // transformations
  int npar = b.size();
  vector<Type> par(npar);
  for (int i = 0; i < npar; i++) {
    par(i) = Type(1.0) / (Type(1.0) + exp(-b(i)));
  }
  Type phi = par(0);
  Type psi = par(1);
  Type p = par(2);
  
  // observation matrix
  matrix<Type> A(3, 3);
  A(0, 0) = Type(0.0);
  A(0, 1) = phi;
  A(0, 2) = Type(1.0) - phi;
  A(1, 0) = Type(0.0);
  A(1, 1) = psi;
  A(1, 2) = Type(1.0) - psi;
  A(2, 0) = Type(0.0);
  A(2, 1) = Type(0.0);
  A(2, 2) = Type(1.0);
  
  // observation matrix
  matrix<Type> B(3, 3);
  B(0, 0) = Type(0.0);
  B(0, 1) = Type(0.0);
  B(0, 2) = Type(1.0);
  B(1, 0) = Type(0.0);
  B(1, 1) = p;
  B(1, 2) = Type(1.0) - p;
  B(2, 0) = Type(0.0);
  B(2, 1) = Type(0.0);
  B(2, 2) = Type(1.0);
  
  // likelihood
  Type ll;
  Type nll;
  for (int i = 0; i < n_individuals; i++) {
    vector<Type> foo(3);
    foo(0) = Type(1.0);
    foo(1) = Type(0.0);
    foo(2) = Type(0.0);
    for (int j = 1; j < n_occasions; j++) {
      foo = multvecmat(foo, A) * vector<Type> (B.col(ch(i, j)));
    }
    ll += log(sum(foo));
  }
  
  // negative loglikelihood
  nll = -ll;
  
  // return
  return nll;
  
}"

Then, we write the code to disk, compile and load it, which requires the R package TMB:

write(tmb_model, file = "cjs_tmb.cpp")

library(TMB)
if (!file.exists("cjs_tmb.dll")) compile("cjs_tmb.cpp")
dyn.load(dynlib("cjs_tmb"))

Estimation

With that done, let’s see how estimates from the two approaches compare and their speed:

# data simulation
raw_data <- simul(
  n_individuals = 10000,
  phi = 0.6,
  psi = 0.9,
  p = 0.2
)

# initial parameter values
b <- runif(3, -1, 1)

# extract the data
ch <- raw_data$ch

# R - using optim
tic <- Sys.time()
faa <- optim(par = b, 
             fn = cjs, 
             gr = NULL, 
             hessian = TRUE, 
             ch, 
             method = "BFGS")
r_time <- (Sys.time() - tic)
r_ests <- round(plogis(faa$par), digits = 3)
names(r_ests) <- c("phi", "psi", "p")
print(r_ests)

  phi   psi     p 
0.625 0.880 0.195

# TMB - using optim
tic <- Sys.time()
obj <- MakeADFun(data = list(ch = ch - 1), # subtract 1 for indexing from 0
                 parameters = list(b = b), 
                 DLL = "cjs_tmb",
                 silent = TRUE)
opt <- do.call("optim", obj)
tmb_time <- (Sys.time() - tic)
tmb_ests <- round(plogis(opt$par), digits = 3)
names(tmb_ests) <- c("phi", "psi", "p")
print(tmb_ests)

  phi   psi     p 
0.625 0.880 0.195

# clean up
dyn.unload(dynlib("cjs_tmb"))

Warning: 3 external pointers will be removed

unlink("cjs_tmp.*")

# print times
print(r_time)

Time difference of 9.823374 secs

print(tmb_time)

Time difference of 0.09974098 secs

Conclusion

It looks like it works and could be a useful tool for running sensitivity analyses…

Reuse

https://creativecommons.org/licenses/by/4.0/

Citation

BibTeX citation:

@online{d. gregory2023,
  author = {D. Gregory, Stephen},
  title = {CJS Is Fast in {TMB}},
  date = {2023-03-10},
  url = {https://stephendavidgregory.github.io/posts/cjs-tmb-is-fast},
  langid = {en}
}

For attribution, please cite this work as:

D. Gregory, Stephen. 2023. “CJS Is Fast in TMB.” March 10, 2023. https://stephendavidgregory.github.io/posts/cjs-tmb-is-fast.