Yeah, Leverage Research does tons of work on "graphically represented plans" and "preference inference based on the structure of goals", and I think they all use yEd. There's a few settings you should tweak at the beginning and then it's pretty smooth sailing.
Here are instructions for setting up the defaults the way some people have found helpful:
Then... a. Click the white background to create a box. b. Click a box and drag to create an arrow. c. Click an already existing box to select it. Once selected, click and drag to move it. d. Doubleclick an already existing box to edit its label.
Enjoy!
I use Dia. I don't entirely understand what you're trying to diagram, so I'm not sure how well it would work for you. I've used it for data flow diagrams, state transition diagrams and flow charts, and occasionally for entity relationship diagrams and UML diagrams (though it's not exactly good for those last two types). It's easy enough to use that I prefer it over paper. I don't think it has any way to automatically generate diagrams, though.
I use tikz/pgf for drawing graphs in my papers, but that is maybe not a scalable solution (unless you write some software to automatically generate tikz/pgf directives).
FWIW I've been looking into this issue for quite a while, several years actually, and never found anything worthwhile. I've taken a few stabs at writing my own code for causal tree traversal/pruning/building. All my attempts have suffered from similar failure modes, for example, the easier it is to build a complicated interlinked tree, the harder it is to edit or clean up.
The cleanest simplest tool for sequence diagrams is http://sequencediagram.org it is very easy to work with
GraphViz and freemind both are good for use but comparatively graphviz is much better than freemind. There are various other charting software available now a days with different features in them.
Let's make it! Who's in to help program? I'll start a github repo and a google group as soon as a few people are committed.
I've got a notion to develop to-do list software with an emphasis on dependencies for my own use; since I haven't written it yet I don't have any actual help for your question, but I'm curious what you mean by “preference inference based on the structure of [your] goals”, as it sounds potentially relevant.
preference inference based on the structure of [your] goals
It's nothing too formal - wisdom gleaned from an article here and a blog post there.
Most of us readily have a list of goals that come to mind, but it's likely that they are subgoals and we are unaware of why exactly we do them. So, you keep on asking "What will this goal do for me?" instead of "What will do this goal for me?", creating downwind nodes in your graph until you presumably hit your preferences. In which case you (a) could check your preferences for consistency and overlap (see Nozick), and (b) investigate if your current subgoals are the best way to maximize your preferences, or find new ones.
Apparently this can be prescribed from the Connection Theory framework, but I haven't found it necessary to study Connection Theory. They make some interesting guesses about what happens when our stated goals conflict, amongst other things.
Most of us readily have a list of goals that come to mind, but it's likely that they are subgoals and we are unaware of why exactly we do them. So, you keep on asking "What will this goal do for me?" instead of "What will do this goal for me?", creating downwind nodes your graph until you presumably hit your preferences.
That's interestingly dual to what I have in mind: the core notion is that it shows you one thing to do (as opposed to a list, to avoid excess choice or dismay). And if you want to not-do-that, you have choices such as:
That last option is what sounds similar to what you're doing, but it supposes you've already entered dependency chains all the way up to preferences. Which might be another sort of one-thing the app presents you with: “Why do you want to do this thing you entered previously?” (Which information isn't mandatory, because it should still permit quick entry of simple reminders.)
Obviously this has a whole lot of scope, the extreme case becoming a complete “outboard brain” planning system, but I'm hoping that (if I ever get around to programming it) it'll be useful even in a rudimentary form.
My notion is that managing dependencies allows avoiding the problem of having a long to-do list which you have to actually look at and consciously reject items for not being something for this exact moment, thus leading to the habit of rejecting all of the items; instead, nearly all of the “list” will be filtered out by some dependency (which ends up being another task, a topic of interest (e.g. a hobby that you only do sometimes), a time, a location, etc.) and you need not ever think about it.
That's also the reason why the user interface I imagine defaults to presenting you with exactly one item at a time: each interaction you have with it gives it more data, but there is never a long list or form inviting you to deal with many items, or many fields-to-fill-out about a single item.
But, this is all vaporware.
I've found most graphing software too clunky, or having too much mental friction, for my purpose of creating graphically represented plans, to convert written diagrams into digital form, or to do preference inference based on the structure of my goals (amongst other things).
So far the only tool that I've seen that reduces this friction is GraphViz [1], since I think I can literally just list down connection after connection in markup, with no care for structure or reasonableness, and then prune connections after I see how the entire thing looks. Point and click is for suckers.
However, I also like the approach of Freemind that quickly outputs a visual map that is easily traversable; but it doesn't do much for me when the causality is more involved.
Are there any alternatives that anyone is aware of?
[1] If you are not familiar with GraphViz, see this amusing introduction that maps the social network in R. Kelly's hit hip hopera, "Trapped in the Closet".