Comments (9)
I concur. In addition to simply testing for signal of density dependence, it would be beneficial to be able to determine if the difference in results using different methods are the result of different models or methods. As @josephwb mentions, if MEDUSA finds different shifts, is it the result of the MEDUSA employing stepwise, or is it because MEDUSA doesn't include density dependence.
from bamm.
It is trivial to turn off the temporal variation in rates. Just set:
updateRateLambdaShift = 0
in the control file, and make sure
lambdaShiftInit = 0
and you run a MEDUSA like analysis. However, the likelihoods for MEDUSA and BAMM are not the same, and the way they deal with incomplete sampling is not the same. Different likelihood for this part. Hence, if you specify incomplete sampling fractions in BAMM, I would be surprised if you get the same results, at least if your tree is fairly incomplete (< 50% taxa sampled)
from bamm.
more formally, for some terminal branch or clade in the tree:
BAMM likelihood = likelihood of the tree, e.g., distribution of times and speciation events, given the sampling level
MEDUSA likelihood = likelihood obtaining N species after some amount of time T.
My intuition is that if you integrate the BAMM likelihood over all possible topologies and branch lengths that are consistent with a tree of age T and N species, you will get the same thing. But I haven't proved it. (FYI, the likelihood used in BAMM with incomplete sampling is the same as for BiSSE etc and follows from Nee et al 1994 and earlier work)
from bamm.
Final comment here would be the ability to use Bayes factors to compare the model with time variation turned off to the MEDUSA like model
In some ways, this will be superseded, because the "time-flip" model does exactly what you want to do in some ways - rate shifts can be either time-dependent versus constant-rate processes and these 2 alternatives are sampled in proportion to their posterior probability. See documentation on this option on website - we've implemented and tested it extensively but haven't published it yet.
from bamm.
OK, will check this out.
from bamm.
Oh, that is easy! Maybe not obvious? (No one here knew that).
BTW, the MEDUSA likelihood uses your 2007 equation (i.e. distribution of times and speciation events); e.g. altering internal node ages while keeping the root age constant will give you different likelihoods, so it is not just the likelihood obtaining N species after some amount of time T. The incomplete sampling is clearly way different though.
from bamm.
Yeah, MEDUSA uses the "topology" birth-death process but only for the backbone. And it's an updated equation because there's an error in the equation for the backbone in my paper (you guys corrected this earlier). The tip likelihood (with incomplete sampling) is what I describe above. The MEDUSA model is a hybrid of the two models applied to different parts of the tree. Honestly, it would be better to go back to this approach for BAMM for the modeling of highly incomplete data, until a better solution is found (e.g. using PASTIS to add missing species within the incompletely sampled clades)
from bamm.
I guess I will close this, although it would be nice to explicitly state this stuff somewhere. The updateRateLambdaShift parameter is described here, but it is not obvious that setting it to 0 (or that the concommital setting lambdaShiftInit also to 0) will bring about the desired configuration.
I think actually having something like:
timeVariableRates = false
in the control file would be nicer.
from bamm.
Just to be clear, the MEDUSA like model) and constraining models from BAMM to less-complex submodels are all described here on the advanced options page:
http://bamm-project.org/advanced.html#modeling-less-complex-evolutionary-scenarios
but we could make this more prominent somehow I guess
from bamm.
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
- 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
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bamm.