swh:1:snp:bbee81fcdc4b36c131a8db323aa6b1ea43209e9a
Tip revision: 1cc05f63437c1a519a5bdc24b3cc669980d81d48 authored by Charles J. Geyer on 13 May 2019, 18:20:03 UTC
version 1.0-3
version 1.0-3
Tip revision: 1cc05f6
newpickle.R
library(aster)
data(radish)
pred <- c(0,1,2)
fam <- c(1,3,2)
### need object of type aster to supply to penmlogl and pickle
aout <- aster(resp ~ varb + fit : (Site * Region + Block + Pop),
pred, fam, varb, id, root, data = radish)
### model matrices for fixed and random effects
modmat.fix <- model.matrix(resp ~ varb + fit : (Site * Region),
data = radish)
modmat.blk <- model.matrix(resp ~ 0 + fit:Block, data = radish)
modmat.pop <- model.matrix(resp ~ 0 + fit:Pop, data = radish)
rownames(modmat.fix) <- NULL
rownames(modmat.blk) <- NULL
rownames(modmat.pop) <- NULL
idrop <- match(aout$dropped, colnames(modmat.fix))
idrop <- idrop[! is.na(idrop)]
modmat.fix <- modmat.fix[ , - idrop]
nfix <- ncol(modmat.fix)
nblk <- ncol(modmat.blk)
npop <- ncol(modmat.pop)
### try newpickle
sigma.start <- c(1, 1)
alpha.start <- aout$coefficients[match(colnames(modmat.fix),
names(aout$coefficients))]
cee.start <- rep(0, nblk + npop)
alphaceesigma.start <- c(alpha.start, cee.start, sigma.start)
foo <- newpickle(alphaceesigma.start, fixed = modmat.fix,
random = list(modmat.blk, modmat.pop), obj = aout)
names(foo)