Revision 63c8e8a453ea587001e2438a8ce51cf0e1e1675c authored by Charles J. Geyer on 23 March 2009, 00:00:00 UTC, committed by Gabor Csardi on 23 March 2009, 00:00:00 UTC
1 parent b524c08
Raw File
aster.Rout.save

R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.1 (2006-06-01)
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
>  library(aster)
Loading required package: trust
> 
>  set.seed(42)
>  nind <- 25
>  nnode <- 5
>  ncoef <- nnode + 1
> 
>  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
> 
>  phi <- matrix(modmat, ncol = ncoef) %*% beta
>  phi <- matrix(phi, ncol = nnode)
> 
>  theta.origin <- matrix(as.double(0), nind, nnode)
> 
>  aster:::setfam(fam.default())
> 
>  phi.origin <- .C("aster_theta2phi",
+      nind = as.integer(nind),
+      nnode = as.integer(nnode),
+      pred = as.integer(pred),
+      fam = as.integer(fam),
+      theta = as.double(theta.origin),
+      phi = matrix(as.double(0), nind, nnode),
+      PACKAGE = "aster")$phi
> 
>  theta <- .C("aster_phi2theta",
+      nind = as.integer(nind),
+      nnode = as.integer(nnode),
+      pred = as.integer(pred),
+      fam = as.integer(fam),
+      phi = as.double(phi),
+      theta = matrix(as.double(0), nind, nnode))$theta
> 
>  root <- sample(1:3, nind * nnode, replace = TRUE)
>  root <- matrix(root, nind, nnode)
> 
>  x <- raster(theta, pred, fam, root)
>  
>  out0 <- aster(x, root, pred, fam, modmat, type = "unco", method = "trust")
>  out1 <- aster(x, root, pred, fam, modmat, type = "unco", method = "nlm")
>  out2 <- aster(x, root, pred, fam, modmat, type = "unco", method = "CG")
>  out3 <- aster(x, root, pred, fam, modmat, type = "unco", method = "L-B")
> 
>  all.equal(out0$coefficients, out1$coefficients)
[1] TRUE
>  all.equal(out1$coefficients, out2$coefficients)
[1] TRUE
>  all.equal(out2$coefficients, out3$coefficients)
[1] "Mean relative  difference: 2.127142e-08"
>  all.equal(out3$coefficients, out0$coefficients)
[1] "Mean relative  difference: 1.970140e-08"
> 
>  out4 <- aster(x, root, pred, fam, modmat, type = "unco",
+      method = "trust", origin = theta.origin)
>  print(out4$coefficients)
[1] -0.06809277 -0.30705441  0.18624357  0.07757573 -0.37636339 -0.08435995
>  print(out0$coefficients)
[1]  1.62505441 -1.45887674 -0.96557875 -1.61557145 -2.06951057 -0.08435995
> 
>  foo <- as.numeric(out0$origin) +
+      matrix(out0$modmat, ncol = ncoef) %*% out0$coefficients
>  bar <- as.numeric(out4$origin) +
+      matrix(out4$modmat, ncol = ncoef) %*% out4$coefficients
>  all.equal(foo, bar)
[1] TRUE
>  all.equal(phi.origin, out0$origin)
[1] TRUE
> 
>  out0 <- aster(x, root, pred, fam, modmat, type = "cond", method = "trust")
>  out1 <- aster(x, root, pred, fam, modmat, type = "cond", method = "nlm")
>  out2 <- aster(x, root, pred, fam, modmat, type = "cond", method = "CG")
>  out3 <- aster(x, root, pred, fam, modmat, type = "cond", method = "L-B")
> 
>  all.equal(out0$coefficients, out1$coefficients)
[1] TRUE
>  all.equal(out1$coefficients, out2$coefficients)
[1] TRUE
>  all.equal(out2$coefficients, out3$coefficients)
[1] TRUE
>  all.equal(out3$coefficients, out0$coefficients)
[1] TRUE
> 
>  print(out0$coefficients)
[1]  1.74295791 -1.54997014 -1.71291553 -1.72922986 -2.16895832 -0.02625205
> 
> 
back to top