Modified JAGS file architecture

DESCRIPTION

@@ -12,4 +12,5 @@ LazyData: true
 RoxygenNote: 7.3.2
 Imports:
     vcrpart,
-    rjags
+    rjags,
+    dclone

NAMESPACE

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

R/bpcm.R

@@ -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...')

inst/jags/bpcm

@@ -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)
+}

inst/jags/bpcm_beta

@@ -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)
+}

inst/jags/bpcm_dif

@@ -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)
+}