---
title: "Using Bayesian Networks for Inference"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Inference}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(RNetica)
```

```{r all}

###################################################################
##  Inference using the EM-SM algorithm (Almond & Mislevy, 1999).  
## System/Student model
sess <- NeticaSession()
startSession(sess)

EMSMSystem <- ReadNetworks(system.file("sampleNets","System.dne",
                                       package="RNetica"),
                           session=sess)


## Evidence model for Task 1a
EMTask1a <- ReadNetworks(system.file("sampleNets","EMTask1a.dne",
                                     package="RNetica"),
                         session=sess)

## Evidence model for Task 2a
EMTask2a <- ReadNetworks(system.file("sampleNets","EMTask2a.dne",
                                     package="RNetica"),
                         session=sess)

## Task 1a has a footprint of Skill1 and Skill2 (those are the
## referenced student model nodes.  So we want joint the footprint into
## a single clique.
MakeCliqueNode(NetworkFindNode(EMSMSystem, NetworkFootprint(EMTask1a)))
## The footprint for Task2 a is already a clique, so no need to do
## anything. 

## Make a copy for student 1
student1 <- CopyNetworks(EMSMSystem,"student1")
## Monitor nodes for proficiency
student1.prof <- NetworkNodesInSet(student1,"Proficiency")

student1.t1a <- AdjoinNetwork(student1,EMTask1a)
## We are done with the original EMTask1a now
DeleteNetwork(EMTask1a)

## Now add findings
CompileNetwork(student1)
NodeFinding(student1.t1a$Obs1a1) <- "Right"
NodeFinding(student1.t1a$Obs1a2) <- "Right"

student1.probt1a <- JointProbability(student1.prof)

## Done with the observables, absorb them
AbsorbNodes(student1.t1a)
CompileNetwork(student1)
student1.probt1ax <- JointProbability(student1.prof)

## Now Task 2
student1.t2a <- AdjoinNetwork(student1,EMTask2a,"t2a")
DeleteNetwork(EMTask2a)

## Add findings
CompileNetwork(student1)
NodeFinding(student1.t2a$Obs2a) <- "Half"

AbsorbNodes(student1.t2a)
CompileNetwork(student1)
student1.probt1a2ax <- JointProbability(student1.prof)

DeleteNetwork(list(student1, EMSMSystem))
stopSession(sess)
```