Notes on structure of examples
Externalized code so that different example scripts call identical commands for fitting and plotting to avoid duplication of code. Example scripts tend to be pretty text poor at the moment, would probably benefit by better descriptions in the markdown. May still involve redundant and potentially out of date descriptions though.
Also fixed knitcitations to at least include citations in markdown files.
Performance of GP compared to Ricker on an underlying Allee model
Using stationary data only
(see myer-example.md for code and more graphs & details)
Using more data
(from earlier myer-example.md)
Comparing GP to estimated Ricker on BH dynamics:
GP performs well, but Ricker performs adequately as well: reed-example.md (shows an example with stationary data).
Approaches shown above address a variety of issues as well:
- Compares to a Ricker estimated by MLE (#8)
- Considers fewer non-stationary observations, but include 0,0 as observation (#13)
- Includes scrap value (#10), though this does not guarentee no fishing under non-persistence estimation
A few next steps:
- measurement error should be introduced in the simulations (#11)
- Evaluate GP performance under larger noise conditions. (#14)
See issues log for further issues to explore and more details on closed issues. See commit log for full details, this entry summarizes progress over the latter half of the week.