tests/pseudo_grad_tests4.R

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

library(CRFutil)

# Graph formula for Slayer field:
grphf <- ~A:B+A:C+A:D+A:E+B:C+B:D+B:E+C:D+D:E

# Check the graph:
gp <- ug(grphf, result = "graph")
dev.off()
iplot(gp)

# Adjacenty matrix:
adj <- ug(grphf, result="matrix")

# Define states and feature function:
s1 <- 1
s2 <- 2
f  <- function(y){ as.numeric(c((y==s1),(y==s2))) }

# Make up random potentials and return a CRF-object
num.samps   <- 100
n.states    <- 2
slay    <- sim.field.random(adjacentcy.matrix=adj, num.states=n.states, num.sims=num.samps, seed=1)
samps       <- slay$samples
known.model <- slay$model
mrf.sample.plot(samps)

pot.info <- make.gRbase.potentials(known.model, node.names = gp@nodes)
s1<-1
s2<-2
f0 <- function(y){ as.numeric(c((y==1),(y==2)))}    # Feature function

en.result <- array(0, c(num.samps*ncol(samps),5))
count <- 1
for(i in 1:num.samps) {
  for(j in 1:ncol(samps)) {
    samp.num <- i
    elem.num <- j
    ce1 <- conditional.config.energy2(config = samps[samp.num,], condition.element.number = elem.num, crf = known.model, ff = f0)
    ce2 <- conditional.config.energy(config= samps[samp.num,],condition.element.number = elem.num,adj.node.list= known.model$adj.nodes,edge.mat= known.model$edges,one.lgp= pot.info$node.energies,two.lgp= pot.info$edge.energies,ff= f0,printQ= F)
    en.result[count,] <- c(i,j,ce1,ce2,ce1-ce2)
    count <- count + 1
  }
}
en.result
en.result[,5]
hist(en.result[,5])
plot(1:length(en.result[,5]),en.result[,5], ylab="Difference between formulas", xlab="Config index")