tests/LLvsPLL_wierd_triange_test2.R

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

library(CRFutil)

# Graph formula:
grphf <- ~A:B:C
adj   <- ug(grphf, result="matrix")

n.states <- 2
fitc <- make.crf(adj, n.states)
fitc <- make.features(fitc)
fitc <- make.par(fitc, 6)

# Parameterization:
fitc$node.par[1,1,] <- 1
fitc$node.par[2,1,] <- 2
fitc$node.par[3,1,] <- 2
fitc$edge.par[[1]][1,1,1] <- 3
fitc$edge.par[[1]][2,2,1] <- 3
fitc$edge.par[[2]][1,1,1] <- 2
fitc$edge.par[[2]][2,2,1] <- 4
fitc$edge.par[[3]][1,1,1] <- 5
fitc$edge.par[[3]][2,2,1] <- 6

s1<-1
s2<-2
f0 <- function(y){ as.numeric(c((y==1),(y==2)))}    # Feature function

configs <- rbind(
  c(1,1,1),
  c(1,2,1),
  c(2,2,1),
  c(2,2,2)
)

# Make up a test parameter vector:
theta <- c(1,2,3,4,5,6)
fitc$par <- theta
make.pots(parms=fitc$par, crf = fitc, rescaleQ=F, replaceQ=T, format = "regular", printQ=T)

fitc$node.pot
fitc$edge.pot

fitc$node.par
fitc$edge.par

# Check: get the parameter vector back?
make.par.from.potentials(fitc)

#
gr.info <- make.gRbase.potentials(crf = fitc, node.names = c("A","B","C"), state.nmes = c(1,2))

xn <- 1
cn <- 1
conditional.config.energy2(    config = configs[xn,], condition.element.number = cn, crf=fitc, ff=f0, printQ=FALSE)
conditional.config.energy(     config = configs[xn,], condition.element.number = cn, crf=fitc, ff=f0, printQ=FALSE)
conditional.config.energy.old( config = configs[xn,], condition.element.number = cn,
                           adj.node.list = fitc$adj.nodes,
                           edge.mat = fitc$edges,
                           one.lgp = gr.info$node.energies,
                           two.lgp = gr.info$edge.energies,
                           ff = f0,
                           printQ = F)