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Modified JAGS file architecture

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This commit is contained in:
Corentin Choisy
2025-05-01 00:47:58 +02:00
parent a62a9bac54
commit 079d15b211
6 changed files with 101 additions and 4 deletions
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3
DESCRIPTION
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@ -12,4 +12,5 @@ LazyData: true
RoxygenNote: 7.3.2
Imports:
vcrpart,
rjags
rjags,
dclone

1
NAMESPACE
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@ -4,5 +4,6 @@ export(bpcm)
export(pcm)
export(res_ij)
export(residif)
import(dclone)
import(rjags)
import(vcrpart)

7
R/bpcm.R
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@ -14,6 +14,7 @@
#' @param diag.plots boolean indicating whether the JAGS diagnosis plots should be displayed
#' @return A data.frame containing various model outputs
#' @import rjags
#' @import dclone
#' @export
bpcm <- function(df=NULL,grp=NULL,is.dif=NULL,is.unif=NULL,priors=NULL,param=list(),verbose=T,diag.plots=F) {
@ -121,7 +122,7 @@ bpcm <- function(df=NULL,grp=NULL,is.dif=NULL,is.unif=NULL,priors=NULL,param=lis
if (verbose) {
cat('Initializing Chains...')
}
dclone::parJagsModel(cl,name="mod.jags",data = data,inits = NULL,file = "/home/corentin/Documents/These/Recherche/SPT/src/bpcm",n.chains=n.chains)
dclone::parJagsModel(cl,name="mod.jags",data = data,inits = NULL,file = system.file("jags","bpcm",package="SPT"),n.chains=n.chains)
if (verbose) {
cat('DONE \n')
cat('Applying burn-in iterations...')
@ -231,7 +232,7 @@ bpcm <- function(df=NULL,grp=NULL,is.dif=NULL,is.unif=NULL,priors=NULL,param=lis
if (verbose) {
cat('Initializing Chains...')
}
dclone::parJagsModel(cl,name="mod.jags",data = data,inits = NULL,file = "/home/corentin/Documents/These/Recherche/SPT/src/bpcm_beta",n.chains=n.chains)
dclone::parJagsModel(cl,name="mod.jags",data = data,inits = NULL,file = system.file("jags","bpcm_beta",package="SPT"),n.chains=n.chains)
if (verbose) {
cat('DONE \n')
cat('Applying burn-in iterations...')
@ -356,7 +357,7 @@ bpcm <- function(df=NULL,grp=NULL,is.dif=NULL,is.unif=NULL,priors=NULL,param=lis
if (verbose) {
cat('Initializing Chains...')
}
dclone::parJagsModel(cl,name="mod.jags",data = data,inits = NULL,file = "/home/corentin/Documents/These/Recherche/SPT/src/bpcm_dif",n.chains=n.chains)
dclone::parJagsModel(cl,name="mod.jags",data = data,inits = NULL,file = system.file("jags","bpcm_dif",package="SPT"),n.chains=n.chains)
if (verbose) {
cat('DONE \n')
cat('Applying burn-in iterations...')

23
inst/jags/bpcm Normal file
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@ -0,0 +1,23 @@
model {
for (i in 1:n) {
for (j in 1:p) {
Y[i,j] ~ dcat(prob[i,j,1:K[j]])
}
theta[i] ~ dnorm(0,1)
}
for (i in 1:n) {
for (j in 1:p) {
for (k in 1:K[j] ) {
eta[i,j,k] <- theta[i] - delta[j,k]
psum[i,j,k] <- sum(eta[i,j,1:k])
exp.psum[i,j,k] <- exp(psum[i,j,k])
prob[i,j,k] <- exp.psum[i,j,k] / sum(exp.psum[i,j,1:K[j]])
} } }
for (j in 1:p) {
delta[j,1] <- 0.0
for (k in 2:K[j]) {
delta[j,k] ~ dnorm(m.delta, pr.delta)
}
}
pr.delta <- pow(s.delta, -2)
}

25
inst/jags/bpcm_beta Normal file
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@ -0,0 +1,25 @@
model {
for (i in 1:n) {
for (j in 1:p) {
Y[i,j] ~ dcat(prob[i,j,1:K[j]])
}
theta[i] ~ dnorm(0,1)
}
for (i in 1:n) {
for (j in 1:p) {
for (k in 1:K[j] ) {
eta[i,j,k] <- theta[i] + (beta * Z[i,1]) - delta[j,k]
psum[i,j,k] <- sum(eta[i,j,1:k])
exp.psum[i,j,k] <- exp(psum[i,j,k])
prob[i,j,k] <- exp.psum[i,j,k] / sum(exp.psum[i,j,1:K[j]])
} } }
for (j in 1:p) {
delta[j,1] <- 0.0
for (k in 2:K[j]) {
delta[j,k] ~ dnorm(m.delta, pr.delta)
}
}
beta ~ dnorm(m.beta,pr.beta)
pr.delta <- pow(s.delta, -2)
pr.beta <- pow(s.beta,-2)
}

46
inst/jags/bpcm_dif Normal file
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@ -0,0 +1,46 @@
model {
for (i in 1:n) {
for (j in 1:p) {
Y[i,j] ~ dcat(prob[i,j,1:K[j]])
}
theta[i] ~ dnorm(0, 1)
}
for (i in 1:n) {
for (j in 1:p) {
for (k in 1:K[j] ) {
eta[i,j,k] <- theta[i] + (beta * Z[i,1]) - ( delta[j,k] + Z[i,1]*ifelse(k==1,0,gamma[j,k]) )
psum[i,j,k] <- sum(eta[i,j,1:k])
exp.psum[i,j,k] <- exp(psum[i,j,k])
prob[i,j,k] <- exp.psum[i,j,k] / sum(exp.psum[i,j,1:K[j]])
} } }
for (j in 1:pnodif) {
delta[j,1] <- 0.0
gamma[j,1] <- 0.0
for (k in 2:K[j]) {
delta[j,k] ~ dnorm(m.delta, pr.delta)
gamma[j,k] <- 0.0
}
}
for (j in pnodif1:pnounif) {
delta[j,1] <- 0.0
gamma[j,1] <- 0.0
for (k in 2:K[j]) {
delta[j,k] ~ dnorm(m.delta, pr.delta)
gamma[j,k] ~ dnorm(m.gamma,s.gamma)
}
}
for (j in pnounif1:p) {
delta[j,1] <- 0.0
gamma[j,1] <- 0.0
gamma[j,2] ~ dnorm(m.gamma,pr.gamma)
delta[j,2] ~ dnorm(m.delta, pr.delta)
for (k in 3:K[j]) {
delta[j,k] ~ dnorm(m.delta, pr.delta)
gamma[j,k] <- gamma[j,2]
}
}
beta ~ dnorm(m.beta,pr.beta)
pr.delta <- pow(s.delta, -2)
pr.beta <- pow(s.beta,-2)
pr.gamma <- pow(s.gamma,-2)
}