Generate JAGS Code for a Network's Model

Description

Based on the parameters given to a network, the code for each node is generated and all of the node models are pasted into a single JAGS model script.

Usage

writeNetworkModel(network, pretty = FALSE)

Arguments

Author(s)

Jarrod Dalton and Benjamin Nutter

See Also

writeJagsModel, writeJagsFormula

Examples

data(PE, package='HydeNet')
Net <- HydeNetwork(~ wells +
                     pe | wells +
                     d.dimer | pregnant*pe +
                     angio | pe +
                     treat | d.dimer*angio +
                     death | pe*treat,
                     data = PE)

#* Default printing
writeNetworkModel(Net)

#* Something a little easier on the eyes.
writeNetworkModel(Net, pretty=TRUE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(HydeNet)
Loading required package: nnet
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.1.0
Loaded modules: basemod,bugs
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HydeNet/writeNetworkModel.Rd_%03d_medium.png", width=480, height=480)
> ### Name: writeNetworkModel
> ### Title: Generate JAGS Code for a Network's Model
> ### Aliases: writeNetworkModel
> 
> ### ** Examples
> 
> data(PE, package='HydeNet')
> Net <- HydeNetwork(~ wells +
+                      pe | wells +
+                      d.dimer | pregnant*pe +
+                      angio | pe +
+                      treat | d.dimer*angio +
+                      death | pe*treat,
+                      data = PE)
> 
> #* Default printing
> writeNetworkModel(Net)
[1] "model{\n   wells ~ dnorm(3.7942, 0.6305)\n   pe ~ dbern(ilogit(0.5757 * wells + -3.90355))\n   d.dimer ~ dnorm(210.24251 + 68.37938 * pe + 29.29496 * pregnant, 0.03347)\n   pi.pregnant[1] <- 0.9014; pi.pregnant[2] <- 0.0986\n   pregnant ~ dcat(pi.pregnant)\n   pi.angio <- cpt.angio[(pe+1), ]\n   angio ~ dcat(pi.angio)\n   treat ~ dbern(ilogit(1.73354 * angio + 0.01994 * d.dimer + -5.89316))\n   pi.death <- cpt.death[(pe+1), (treat+1), ]\n   death ~ dcat(pi.death)\n}"
Warning messages:
1: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
2: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
3: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
4: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
> 
> #* Something a little easier on the eyes.
> writeNetworkModel(Net, pretty=TRUE)
model{
   wells ~ dnorm(3.7942, 0.6305)
   pe ~ dbern(ilogit(0.5757 * wells + -3.90355))
   d.dimer ~ dnorm(210.24251 + 68.37938 * pe + 29.29496 * pregnant, 0.03347)
   pi.pregnant[1] <- 0.9014; pi.pregnant[2] <- 0.0986
   pregnant ~ dcat(pi.pregnant)
   pi.angio <- cpt.angio[(pe+1), ]
   angio ~ dcat(pi.angio)
   treat ~ dbern(ilogit(1.73354 * angio + 0.01994 * d.dimer + -5.89316))
   pi.death <- cpt.death[(pe+1), (treat+1), ]
   death ~ dcat(pi.death)
}Warning messages:
1: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
2: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
3: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
4: In bind_rows_(x, .id) :
  binding factor and character vector, coercing into character vector
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>