plot.HydeNetwork() defaults for decision nets

[jarrod-dalton]

Here is some code that uses separate node shapes/colors depending on the type (random vs. determ vs. decision vs. utility). I didn't do anything with the edges yet. Any ideas on edge coloring? May be good to somehow gray out edges associated with deterministic nodes.

By the way, ignore the actual formulas in the setNode commands - I just did those commands so I could color the deterministic nodes.

net <- HydeNetwork(~ card1.ace | card1
                   + card2.ace | card2
                   + initialPoints | card1*card2*card1.ace*card2.ace
                   + hit1 | initialPoints*dealerUpcard
                   + card3 | hit1
                   + card3.ace | card3
                   + pointsAfterCard3 | initialPoints*card3*card3.ace
                   + hit2 | pointsAfterCard3*dealerUpcard
                   + card4 | hit2
                   + card4.ace | card4
                   + pointsAfterCard4 | pointsAfterCard3*card4*card4.ace
                   + hit3 | pointsAfterCard4*dealerUpcard
                   + card5 | hit3
                   + card5.ace | card5
                   + pointsAfterCard5 | pointsAfterCard4*card5*card5.ace
                   + playerFinalPoints | initialPoints*hit1*pointsAfterCard3
                                         *hit2*pointsAfterCard4*hit3*pointsAfterCard5
                   + dealerFinalPoints | dealerUpcard
                   + payoff | playerFinalPoints*dealerFinalPoints)

net <- setNode(net, card1.ace, "determ", define=fromFormula(), nodeFormula=card1.ace ~ ifelse(card1==1,1,0))
net <- setNode(net, card2.ace, "determ", define=fromFormula(), nodeFormula=card2.ace ~ ifelse(card2==1,1,0))
net <- setNode(net, card3.ace, "determ", define=fromFormula(), nodeFormula=card3.ace ~ ifelse(card3==1,1,0))
net <- setNode(net, card4.ace, "determ", define=fromFormula(), nodeFormula=card4.ace ~ ifelse(card4==1,1,0))
net <- setNode(net, card5.ace, "determ", define=fromFormula(), nodeFormula=card5.ace ~ ifelse(card5==1,1,0))
net <- setNode(net, initialPoints, "determ", define=fromFormula(), nodeFormula=initialPoints~card1+card2)
net <- setNode(net, pointsAfterCard3, "determ", define=fromFormula(),
               nodeFormula=pointsAfterCard3 ~ initialPoints+card3)
net <- setNode(net, pointsAfterCard4, "determ", define=fromFormula(),
               nodeFormula=pointsAfterCard4 ~ pointsAfterCard3+card4)
net <- setNode(net, pointsAfterCard5, "determ", define=fromFormula(),
               nodeFormula=pointsAfterCard5 ~ pointsAfterCard4+card5)
net <- setNode(net, playerFinalPoints, "determ", define=fromFormula(),
               nodeFormula=playerFinalPoints ~ playerFinalPoints+3)


net <- setDecisionNodes(net, hit1, hit2, hit3)
net <- setUtilityNodes(net, payoff)

decisionNodes <- names(which(unlist(net$nodeDecision)))
utilityNodes <- "payoff"  #names(which(unlist(net$nodeDecision)))
determNodes <- names(which(unlist(net$nodeType)=="determ"))

shapes <- rep("box",length(decisionNodes)+length(utilityNodes));
names(shapes) <- c(decisionNodes, utilityNodes)

fills <- c(rep("cyan",length(decisionNodes)), rep("yellow",length(utilityNodes)))
names(fills) <- c(decisionNodes, utilityNodes)

fontcols <- rep("gray70", length(determNodes))
names(fontcols) <- c(determNodes)

cols <- rep("gray70",length(determNodes));
names(cols) <- determNodes

nodeAttribs <- list(shape=shapes, fillcolor=fills, fontcolor=fontcols, color=cols)

attribs <- list(node=list(shape="ellipse", fixedsize=FALSE, fillcolor="white", style="solid"))

plot(net, attrs=attribs, nodeAttrs=nodeAttribs)

[nutterb]

I added default plot settings in the options(Hyde_plotOptions), but I still need to do a little tweaking. I'll need to add a new function to modify the options that isn't as tedious as setting all the node attributes.

[nutterb]

Given the new functionality for customizing plots with plot.HydeNetwork, do we still need to keep the plot.compiledHydeNetwork method? On the one hand, we could apply the default plotting mechanism and just alter the observed variables. On the other, it isn't hard to do that from plot.HydeNetwork anymore.

Thoughts?

[jarrod-dalton]

Good point. I guess I hadn't thought about the issue with observed vs. unobserved nodes. It's hard to think about formatting all these different node classes with only 2 shapes supported by the Rgraphviz API (I know the Graphviz software has several more shapes):

Random observed/unobserved
Decision observed/unobserved
Deterministic evaluated or not evaluated (could combine those two, i.e., keep with the gray presentation - I like it)
Utility (could keep with the present visualization)

If we were to consider observed nodes as separate formats, couldn't that be incorporated into the new functionality instead of via plot.compiledHydeNetwork? In this case, it would be nice, but probably I'd recommend we create a separate issue for this and do this on a later release.

One thing that should probably be a default is the global attribute fixedsize=FALSE.

[nutterb]

So, I think I'm going to go ahead and delete plot.compiledHydeNetwork for now. My reasoning is this:

I think I can build a better functionality using the DiagrammeR package. I've played with it some, and it looks an awful lot better and should be quite a bit easier to manipulate than the Rgraphviz stuff. For the moment, everything is working as expected, and even if it takes me a little while to get the DiagrammeR plotting to work, I can work all of the new stuff into the existing framework.

So, the take home message is that I will reconstruct this function when I finish plot.HydeNetwork. It will be easier to modify the plot for the compiled network using the HydeNetwork method.

[jarrod-dalton]

DiagrammeR looks awesome!

Let's leave this issue open and revisit default node styles. Let's wait on this until after the v1.0 release.

Open to suggestions re: the default formats, but here's a possibility (based on http://www.graphviz.org/doc/info/shapes.html):

nodeType	shape	border	text	textWhenObserved	font style (if it exists?)
random variable	rounded	black	black	red	regular
deterministic	plaintext	transparent (ignored for plaintext?)	gray	light red	italics
decision	hexagon or doubleoctagon	blue	blue	red	bold
utility	invhouse	green (something darker than rgb(0,1,0))	green	red	bold