R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> 
>  library(aster)
Loading required package: trust
>  library(numDeriv)
> 
>  # needed because of the change in R function "sample" in R-devel
>  suppressWarnings(RNGversion("3.5.2"))
> 
>  set.seed(42)
> 
>  nind <- 25
>  nnode <- 5
>  ncoef <- nnode + 1
> 
>  famlist <- fam.default()
>  fam <- c(1, 1, 2, 3, 3)
>  pred <- c(0, 1, 1, 2, 3)
> 
>  modmat <- array(0, c(nind, nnode, ncoef))
>  modmat[ , , 1] <- 1
>  for (i in 2:nnode)
+      modmat[ , i, i] <- 1
>  modmat[ , , ncoef] <- rnorm(nind * nnode)
> 
>  beta <- rnorm(ncoef) / 10
> 
>  theta <- matrix(modmat, ncol = ncoef) %*% beta
>  theta <- matrix(theta, ncol = nnode)
> 
>  root <- sample(1:3, nind * nnode, replace = TRUE)
>  root <- matrix(root, nind, nnode)
> 
>  x <- raster(theta, pred, fam, root)
>  
>  out <- mlogl(beta, pred, fam, x, root, modmat, deriv = 2,
+      type = "conditional")
> 
>  my.value <- 0
>  for (j in 1:nnode) {
+      ifam <- fam[j] 
+      k <- pred[j]
+      if (k > 0)
+          xpred <- x[ , k]
+      else
+          xpred <- root[ , j]
+      for (i in 1:nind)
+          my.value <- my.value -
+              sum(x[i, j] * theta[i, j] -
+              xpred[i] * famfun(famlist[[ifam]], 0, theta[i, j]))
+  }
>  all.equal(out$value, my.value)
[1] TRUE
> 
>  foo <- function(beta) {
+      stopifnot(is.numeric(beta))
+      stopifnot(is.finite(beta))
+      mlogl(beta, pred, fam, x, root, modmat, type = "conditional")$value
+  }
> 
>  g <- grad(foo, beta)
>  all.equal(g, out$gradient)
[1] TRUE
> 
>  h <- hessian(foo, beta)
>  all.equal(h, out$hessian)
[1] TRUE
> 
>  ##########
> 
>  objfun <- function(beta) {
+      out <- mlogl(beta, pred, fam, x, root, modmat, deriv = 1,
+          type = "conditional")
+      result <- out$value
+      attr(result, "gradient") <- out$gradient
+      return(result)
+  }
>  out1 <- nlm(objfun, beta, fscale = nind)
> 
>  ##########
> 
>  objfun <- function(beta) {
+      out <- mlogl(beta, pred, fam, x, root, modmat, deriv = 2,
+          type = "conditional")
+      result <- out$value
+      attr(result, "gradient") <- out$gradient
+      attr(result, "hessian") <- out$hessian
+      return(result)
+  }
>  out <- nlm(objfun, beta, fscale = nind)
>  all.equal(out1$minimum, out$minimum)
[1] TRUE
>  all.equal(out1$estimate, out$estimate, tolerance = 1e-4)
[1] TRUE
> 
>  ########## expected Fisher information ##########
> 
>  aster:::setfam(fam.default())
> 
>  fout <- .C(aster:::C_aster_fish_cond,
+      nind = as.integer(nind),
+      nnode = as.integer(nnode),
+      ncoef = as.integer(ncoef),
+      pred = as.integer(pred),
+      fam = as.integer(fam),
+      beta = as.double(out$estimate),
+      root = as.double(root),
+      x = as.double(x),
+      modmat = as.double(modmat),
+      fish = matrix(as.double(0), ncoef, ncoef))
> 
>  mout <- mlogl(out$estimate, pred, fam, x, root, modmat,
+      deriv = 2, type = "conditional")
> 
>  aster:::setfam(fam.default())
> 
>  theta <- .C(aster:::C_aster_mat_vec_mult,
+     nrow = as.integer(nind * nnode),
+     ncol = as.integer(ncoef),
+     a = as.double(modmat),
+     b = as.double(out$estimate),
+     c = matrix(as.double(0), nind, nnode))$c
>  ctau <- .C(aster:::C_aster_theta2ctau,
+      nind = as.integer(nind),
+      nnode = as.integer(nnode),
+      pred = as.integer(pred),
+      fam = as.integer(fam),
+      theta = as.double(theta),
+      ctau = matrix(as.double(0), nind, nnode))$ctau
>  tau <- .C(aster:::C_aster_ctau2tau,
+      nind = as.integer(nind),
+      nnode = as.integer(nnode),
+      pred = as.integer(pred),
+      fam = as.integer(fam),
+      root = as.double(root),
+      ctau = as.double(ctau),
+      tau = matrix(as.double(0), nind, nnode))$tau
>  psiDoublePrime <- .C(aster:::C_aster_theta2whatsis,
+      nind = as.integer(nind),
+      nnode = as.integer(nnode),
+      pred = as.integer(pred),
+      fam = as.integer(fam),
+      deriv = as.integer(2),
+      theta = as.double(theta),
+      result = matrix(as.double(0), nind, nnode))$result
> 
>  my.hessian <- theta * NaN
>  my.fish <- theta * NaN
> 
>  for (i in 1:nind) {
+      for (j in 1:nnode) {
+          k <- pred[j]
+          if (k > 0) {
+              my.hessian[i, j] <- x[i, k] * psiDoublePrime[i, j]
+              my.fish[i, j] <- tau[i, k] * psiDoublePrime[i, j]
+          } else {
+              my.hessian[i, j] <- root[i, j] * psiDoublePrime[i, j]
+              my.fish[i, j] <- root[i, j] * psiDoublePrime[i, j]
+          }
+      }
+  }
> 
>  modmat <- matrix(as.double(modmat), ncol = ncoef)
>  my.hessian <- as.numeric(my.hessian)
>  my.fish <- as.numeric(my.fish)
>  my.hessian <- t(modmat) %*% diag(my.hessian) %*% modmat
>  my.fish <- t(modmat) %*% diag(my.fish) %*% modmat
> 
>  all.equal(my.hessian, mout$hessian)
[1] TRUE
>  all.equal(my.fish, fout$fish)
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
  0.277   0.012   0.281