Comments (1)
this is probably a good idea. the main reason I originally did this was so that someone could have a quick view of the tree itself by using regular class phylo operations, especially plot.phylo. But maybe it would just be best to have plot.dtrates be the default method for the data object.
I'm trying to think of anything else that might be affected by this but can't really.
~D
On Dec 10, 2013, at 7:22 PM, blueraleigh wrote:
Thoughts on changing the class of the object returned by getEventData to "bammdata" only? One advantage would be that a number of functions could dispatch methods on the bammdata object directly. So, for example,
x <- getEventData(phy, eventdata);
class(x);
[1] "bammdata" ##rather than [1] "phylo" "bamm-data"
plot(x) ##rather than calling plot.dtrates(x);
would immediately plot the dynamic rates tree if plot.dtrates is renamed to plot.bammdata. Because BAMMtools has the function as.phylo.bammdata is there a compelling reason to have two class names attached to the bammdata object?—
Reply to this email directly or view it on GitHub.
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Related Issues (20)
- node labels cause problems in plotting HOT 4
- Support non-ultrametric trees HOT 1
- Pick lambdaInit0 from prior
- New add event proposal to pick branches HOT 2
- Simplified control file HOT 5
- Time-flip proposal prior
- Write MC3 documentation
- BAMM installation documentation HOT 3
- Analyze multiple trees HOT 1
- Top information when running BAMM HOT 1
- Add version information to bamm program header HOT 2
- getBestShiftConfiguration HOT 1
- threads not working on Ubuntu 14.04 LTS HOT 20
- E0 initializations
- high resolution clock for seed HOT 2
- Feature request: the ability to turn off density dependence HOT 9
- The option validateEventConfiguration gives wrong prior distribution HOT 1
- The extinction probability, E(t), are estimated incorretly HOT 1
- ensure compatibility of lambdaIsTimeVariablePrior and updateRateLambdaShift
- plot HOT 2
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