## This is the R output generated duing the Tegrity recording (with a
   few now fixed RNetica bugs edited out).
Tegrity Recording is available at:
https://tegr.it/y/1ijsr


R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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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.
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[Workspace loaded from ~/.RData]

> library(RNetica)
Netica 5.04 Win (AF), (C) 1992-2012 Norsys Software Corp.

The license being used is +Course/FloridaSU/Ex15-05-30,120,310/(security part removed).

> ?MutalInfo
No documentation for "MutalInfo" in specified packages and libraries:
you could try "??MutalInfo"
> ?MutualInfo
> irt5 <- ReadNetworks(paste(library(help="RNetica")$path,
+                            "sampleNets","IRT5.dne",
+                            sep=.Platform$file.sep))
> 
> irt5
<Netica BN: IRT5 > 
> irt5.theta <- NetworkFindNode(irt5,"Theta")
> irt5.theta
<Discrete Node: Theta > 
> irt5.x <- NetworkFindNode(irt5,paste("Item",1:5,sep="_"))
> irt5.x
$Item_1
<Discrete Node: Item_1 > 

$Item_2
<Discrete Node: Item_2 > 

$Item_3
<Discrete Node: Item_3 > 

$Item_4
<Discrete Node: Item_4 > 

$Item_5
<Discrete Node: Item_5 > 

> irt5.x$Item_3
<Discrete Node: Item_3 > 
> unclass(irt5)
[1] "IRT5"
attr(,"Netica_bn")
<pointer: 0x000000000eadb360>
attr(,"Filename")
[1] "T:/Documents/R/win-library/2.13/RNetica/sampleNets/IRT5.dne"
> irt5 <- ReadNetworks(irt5)
> irt5.theta
<Discrete Node: Theta > 
> help("RNetica-package")
> NodeNet(irt5.theta)
<Netica BN: IRT5 > 
> NodeNet(irt5.theta) == irt5
[1] FALSE
> DeleteNetwork(irt5)
> irt5
<Deleted Netica BN: IRT5 > 
> is.active(irt5)
[1] FALSE
> irt5 <- NodeNet(irt5.theta)
> irt5
<Netica BN: IRT5 > 
> ## Homework problem 6.17
> 
> irt3 <- CreateNetwork("IRT3")
> irt3
<Netica BN: IRT3 > 
> ?NetworkTitle
> NetworkTitle(irt3) <- "3-item IRT network, four levels for theta"
> NetworkComment(irt3) <- "Almond et al (2015) problem 6.17"
> NetworkTitle(irt3)
[1] "3-item IRT network, four levels for theta"
> theta <- NewDiscreteNode(irt3,"theta",c("VeryLow","Low","High","VeryHigh"))
> NodeStates(theta)
   VeryLow        Low       High   VeryHigh 
 "VeryLow"      "Low"     "High" "VeryHigh" 
> ?NodeStates
> NodeStateTitles(theta) <- paste(c(-1.5,-0.5,0.5,1.5))
> NodeStateTitles(theta)
 VeryLow      Low     High VeryHigh 
  "-1.5"   "-0.5"    "0.5"    "1.5" 
> NodeLevels(theta) <- c(-1.5,-0.5,0.5,1.5)
> paste("Item",1:3,sep="_")
[1] "Item_1" "Item_2" "Item_3"
> items <- NewDiscreteNode(irt3,paste("Item",1:3,sep="_"),c("Right","Wrong"))
> items
[[1]]
<Discrete Node: Item_1 > 

[[2]]
<Discrete Node: Item_2 > 

[[3]]
<Discrete Node: Item_3 > 

> items[[2]]
<Discrete Node: Item_2 > 
> items[2]
[[1]]
<Discrete Node: Item_2 > 

> AddLink(theta,items[[1]])
> NodeParents(theta)
named list()
> NodeParents(items[[1]])
[[1]]
<Discrete Node: theta > 

> NodeParents(items[[2]]) <- theta
Error in `NodeParents<-`(`*tmp*`, value = "theta") : 
  Value must be list of Netica nodes, or NULLs
> NodeParents(items[[2]]) <- list(theta)
> for(i in 3:3) {
+   AddLink(theta,items[[i]])
+ }
> ?Extract.NeticaNode
> theta[]
 theta.VeryLow      theta.Low     theta.High theta.VeryHigh 
            NA             NA             NA             NA 
> theta[] <- c(1,3,3,1)/8
> NodeProbs(theta)
theta
 VeryLow      Low     High VeryHigh 
   0.125    0.375    0.375    0.125 
attr(,"class")
[1] "CPA"   "array"
> items[[1]][]
     theta Item_1.Right Item_1.Wrong
1  VeryLow           NA           NA
2      Low           NA           NA
3     High           NA           NA
4 VeryHigh           NA           NA
> items[[1]]["VeryLow"]
    theta Item_1.Right Item_1.Wrong
1 VeryLow           NA           NA
> items[[1]][2]
  theta Item_1.Right Item_1.Wrong
1   Low           NA           NA
> items[[1]]["VeryLow"]<-.378
> items[[1]][]
     theta  Item_1.Right  Item_1.Wrong
1  VeryLow  3.780000e-01  6.220000e-01
2      Low -3.396031e+38 -3.396031e+38
3     High -3.396031e+38 -3.396031e+38
4 VeryHigh -3.396031e+38 -3.396031e+38
> items[[1]][2:4]<- c(0.622,0.818,0.924)
> items[[1]][]
     theta Item_1.Right Item_1.Wrong
1  VeryLow        0.378        0.622
2      Low        0.622        0.378
3     High        0.818        0.182
4 VeryHigh        0.924        0.076
> library(CPTtools)
Loading required package: stats4

> invlogit <- function (x) exp(x)/(1+exp(x))
> invlogit(NodeLevels(theta)-0)
  VeryLow       Low      High  VeryHigh 
0.1824255 0.3775407 0.6224593 0.8175745 
> items[[2]][] <- invlogit(NodeLevels(theta)-0)
Error in `[<-.NeticaNode`(`*tmp*`, , value = c(0.182425523806356, 0.377540668798145,  : 
  Number of rows selected and rows in value do not match; nodeItem_2
> items[[2]]
<Discrete Node: Item_2 > 
> items[[2]][]
     theta Item_2.Right Item_2.Wrong
1  VeryLow           NA           NA
2      Low           NA           NA
3     High           NA           NA
4 VeryHigh           NA           NA
> items[[2]][] <- matrix(invlogit(NodeLevels(theta)-0),4,1)
Error in `[<-.NeticaNode`(`*tmp*`, , value = c(0.182425523806356, 0.377540668798145,  : 
  Number of rows selected and rows in value do not match; nodeItem_2
> items[[2]][1:4] <- matrix(invlogit(NodeLevels(theta)-0),4,1)
> items[[2]][1:4] <- invlogit(NodeLevels(theta)-0)
> items[[2]][]
     theta Item_2.Right Item_2.Wrong
1  VeryLow    0.1824255    0.8175745
2      Low    0.3775407    0.6224594
3     High    0.6224594    0.3775407
4 VeryHigh    0.8175745    0.1824255
> invlogit(NodeLevels(theta)-1)
   VeryLow        Low       High   VeryHigh 
0.07585818 0.18242552 0.37754067 0.62245933 
> items[[3]][1:4] <- invlogit(NodeLevels(theta)-1)
> CompileNetwork(irt3)
> NodeBeliefs(theta)
 VeryLow      Low     High VeryHigh 
   0.125    0.375    0.375    0.125 
> NodeExpectedValue(theta)
[1] 0
attr(,"std_dev")
[1] 0.8660254
> attr(NodeExpectedValue(theta),"std_dev")
[1] 0.8660254
> for( i in 1:3) {
+   NodeFinding(items[[1]])<-"Wrong"
+ }
> NodeBeliefs(theta)
   VeryLow        Low       High   VeryHigh 
0.26156431 0.47687134 0.22960471 0.03195963 
> NodeExpectedValue(theta)
[1] -0.4680403
attr(,"std_dev")
[1] 0.7861209
> for( i in 1:3) {
+   NodeFinding(items[[i]])<-"Wrong"
+ }
> NodeBeliefs(theta)
   VeryLow        Low       High   VeryHigh 
0.39806399 0.48881882 0.10868357 0.00443363 
> NodeExpectedValue(theta)
[1] -0.7805132
attr(,"std_dev")
[1] 0.6676784
> for (i in 1:3) {
+   NodeFinding(items[[i]])<-"Right"
+   NodeExpectedValue(theta)
+ }
> for( i in 1:3) {
+   NodeFinding(items[[i]])<-"Wrong"
+ }
> NodeBeliefs(theta)
   VeryLow        Low       High   VeryHigh 
0.39806399 0.48881882 0.10868357 0.00443363 
> NodeExpectedValue(theta)
[1] -0.7805132
attr(,"std_dev")
[1] 0.6676784
> for (i in 1:3) {
+   NodeFinding(items[[i]])<-"Right"
+   print(NodeExpectedValue(theta))
+ }
[1] -0.276932
attr(,"std_dev")
[1] 0.7387278
[1] 0.2770373
attr(,"std_dev")
[1] 0.7384468
[1] 0.7805601
attr(,"std_dev")
[1] 0.6679294
> RetractNetFindings(irt3)
> NodeBeliefs(theta)
 VeryLow      Low     High VeryHigh 
   0.125    0.375    0.375    0.125 
> WriteNetworks(irt3,"T:/My Documents/BayesNets/irt3.dne")