Drawing path diagrams - options part 2

Having said in my last post that I wan't going to use R/Graphviz, the last couple of days I've investigating using Graphviz! I like to change my mind sometimes.

After some thought, I decided that the way that Graphviz will automatically lay out and create the path diagram based on the specified links has to be worth looking into. The tikz/Latex method is more labour intensive in some ways because it doesn't automatically decide things like arrow head placement.

I couldn't instantly figure out how to make the Graphviz GUI work! I think I was quite tired. But it's simple (on Windows at any rate): install it from this website, open it up, and then paste some dot code into the GUI. Then press the 'running man' icon. It should tell you if and where there are syntax errors.

You can get dot code from R using the sem package and the function pathDiagram(). However, I have found that the messing around involved in getting to that stage with sem in R is not worth my time (as I don't want to use sem for the analysis). I kept getting an error message at earlier stages in the process (as pathDiagram needs a fitted sem model object, so you need to get that done first). So I just looked at some example dot codes for structural equation models (SEM) and worked out by trial-and-error how to modify the dot code.

For my needs the Graphviz syntax is quite simple. Here is a quickly made-up example of what I managed to achieve.

digraph "sem.wh.1" {
rankdir=LL;
size="24,24";
node [fontname="Helvetica" fontsize=10 shape=box];
edge [fontname="Helvetica" fontsize=10];
center=1;

"mrt" -> "states.pres" [label=""];
"us.cult" -> "states.pres" [label=""];
"flor.zone" -> "states.pres" [label=""];
"squares.cz" -> "states.pres" [label=""];
"flower.period" -> "states.pres" [label=""];
"dispersal.vectors2" -> "states.pres" [label=""];
"pollination.vectors2" -> "states.pres" [label=""];
"propagule length" -> "states.pres" [label=""];
"grime" -> "states.pres" [label=""];
"life.span.ingolf" -> "states.pres" [label=""];

"cz.cult" -> "mrt" [label=""];
"habitats" -> "mrt" [label=""];
"flor.zone" -> "mrt" [label=""];
"alt.range.cz" -> "mrt" [label=""];
"life.span.ingolf" -> "mrt" [label=""];
"growth.form" -> "mrt" [label=""];
"grime" -> "mrt" [label=""];
"flower.period" -> "mrt" [label=""];
"flower.period" -> "mrt" [label=""];


"habitats" -> "cz.cult" [label=""];
"flor.zone" -> "cz.cult" [label=""];
"alt.range.cz" -> "cz.cult" [label=""];
"squares.cz" -> "cz.cult" [label=""];
"sla" -> "cz.cult" [label=""];
"life.span.ingolf" -> "cz.cult" [label=""];
"growth.form" -> "cz.cult" [label=""];

"cz.cult" -> "us.cult" [label=""];
"habitats" -> "us.cult" [label=""];
"flor.zone" -> "us.cult" [label=""];
"alt.range.cz" -> "us.cult" [label=""];
"squares.cz" -> "us.cult" [label=""];

"flor.zone" -> "habitats" [label=""];
"alt.range.cz" -> "habitats" [label=""];
"squares.cz" -> "habitats" [label=""];
"ssb.range" -> "habitats" [label=""];
"life.span.ingolf" -> "habitats" [label=""];
"growth.form" -> "habitats" [label=""];
"grime" -> "habitats" [label=""];
"height" -> "habitats" [label=""];
"flower.period" -> "habitats" [label=""];
"dispersal.vectors2" -> "habitats" [label=""];



}

It's ok. It's getting quite complicated already though. Doing all this has forced me to really think about what I'm trying to model here. There are so many hypothesised links that it might be better to use some kind of machine-learning network analysis to look at the strong links instead. Something to look into.