Open MathiasRenaud opened 7 years ago
Work on this issue will also be dependent on resolving parallelization #26
@helenhe96 to try re-running with different prior specifications. For a sanity check, try priors that are tightly centered around the actual values.
The simulation took 4624 seconds (77 minutes) on one thread.
If using priors centered around the true values (with normal distribution), the posteriors are good representations of the true values:
Okay! But I'm guessing that we've "locked in" the priors tightly around the true parameter values. The next step is to relax the variance in the priors, and deflect the initial parameter values away from the true values.
When you run this analysis, can you please use multiple threads?
When I use multiple threads on this my computer crashes... I have tried 10 threads and 5 threads.
Issue #131
From dev meeting:
Next steps:
normalize
to mean
or median
). If so, try setting to none
. (Apparently it is set to none
)knitr
. Use the following sections:
Pending implementation of labelled tree kernels, see #133
Before working through the proposed experiments above, better do some checks on responsiveness of kernel distances (and perhaps other tree distances) to varying BiSSE model parameters.
All the kinks should be worked out of BiSSE model now. It run with 10,100, and 1000 particles. With all 6 priors set as a gamma distribution(rate=2, shape=1) and all proposals set to normal distribution (mean=0, sd=0.1), all parameters were overestimated (priors need tuning), but it runs:![rplot](https://user-images.githubusercontent.com/25252210/29824233-e97be604-8c9e-11e7-8fd2-6294180ffcee.png)