tests/full_gradient_test3a_com.R

In npetraco/CRFutil: Handy Utility Functions for Use with CRF and gRbase packages

library(CRFutil)

load("/Users/npetraco/latex/papers/dust/steph_diss/CRFutil/tests/samps.RData")
grphf <- ~A:B + B:C + C:D + D:A
adj   <- ug(grphf, result="matrix")

n.states <- 2
#===================================
# To compare with fit:
com <- make.crf(adj, n.states)
com <- make.features(com)
com <- make.par(com, 12)

# Fill the parameter index matrices with the standard parameterization
# Standard parameterization, one param per node:
for(i in 1:nrow(com$node.par)){
  com$node.par[i,1,1] <- i
}
com$edge.par[[1]][1,1,1] <- 5
com$edge.par[[1]][2,2,1] <- 6
com$edge.par[[2]][1,1,1] <- 7
com$edge.par[[2]][2,2,1] <- 8
com$edge.par[[3]][1,1,1] <- 9
com$edge.par[[3]][2,2,1] <- 10
com$edge.par[[4]][1,1,1] <- 11
com$edge.par[[4]][2,2,1] <- 12
#===================================

#mrf.nll <- function(par, crf, instances, infer.method = infer.chain, ...)
set.seed(1)
w.test <- runif(com$n.par,-1,1)
w.test

com$node.pot
com$edge.pot

com$par.stat <- mrf.stat(com, samps)
com$par.stat
com$gradient
com$nll
com$par

mrf.exact.nll(w.test, com, samps, infer.exact)

com$node.pot
com$edge.pot

com$par.stat
com$gradient
com$nll
com$par


mrf.update(com) # Rescales potentials
com$node.pot
com$edge.pot


infer.exact(com)