Comments (1)
SpaceMix uses an "auto-tuning" approach to adaptively update the scale of the various tuning parameters to aim for an optimal acceptance ratio (that's why the acceptance rate plot for the nugget parameters looks kind of like a dampened sine wave converging on 45%). So, if you're not seeing good mixing behavior, there's not much you can tweak to change the acceptance rate. You could try one of a few alternative approaches:
- increase the number of iterations. maybe the chain just needs more time?
- increase the number of "fast" initial runs, which may help the longer chain find a reasonable area of parameter space to explore.
- If you go with route 1, you could start from the last location in parameter space from another long run
- From the plot of the nugget parameters, it looks like you have a lot of samples. You could try dropping some, or collapsing some into a multi-individual sample (e.g., by location), which will certainly make things go faster, and may help improve mixing as well.
Sorry I don't see an easy fix here!
from spacemix.
Related Issues (14)
- compute goodness of fit along the genome
- bypass SNP calling
- Should we move from SNPs to averages over regions?
- Please move the ".tar.gz" distribution file to a release.
- make.spacemix.map requires X11
- Negative infinity HOT 1
- Parallel runs HOT 6
- Plotting admixture when there is no admixture HOT 3
- "system computationally singular" crash HOT 3
- Possible numeric instability? HOT 1
- Error in solve.default(par.cov)? HOT 1
- Burnin valid values? HOT 1
- Error in make.spacemix.map.list HOT 5
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 spacemix.