Major reorganization to get rid of redundant files and clean up the directory structure. I deleted the "new" RMarkdown (Auke_Coho_InitSRFits.Rmd) and associated output to focus on one script (auke_coho_ipm.R) and one RMarkdown document (auke_coho_ipm.Rmd).
I used knitr chunk syntax to allow the RMarkdown to ingest chunks from the script, reflecting my preference for doing code development in an R script rather than an .Rmd.
While re-fitting the models, I encountered pathologies associated with extreme changes in curvature as tau_M and tau_S approach zero. I more or less resolved the issue by fiddling with the priors in salmonIPM: IPM_SMaS_np.
I updated the plots and added them to the RMarkdown. I did not spend a lot of time revising the RMarkdown overall -- in particular, the author list and data description need to be updated.
Major reorganization to get rid of redundant files and clean up the directory structure. I deleted the "new" RMarkdown (Auke_Coho_InitSRFits.Rmd) and associated output to focus on one script (auke_coho_ipm.R) and one RMarkdown document (auke_coho_ipm.Rmd).
I used knitr chunk syntax to allow the RMarkdown to ingest chunks from the script, reflecting my preference for doing code development in an R script rather than an .Rmd.
While re-fitting the models, I encountered pathologies associated with extreme changes in curvature as
tau_Mandtau_Sapproach zero. I more or less resolved the issue by fiddling with the priors in salmonIPM:IPM_SMaS_np.I updated the plots and added them to the RMarkdown. I did not spend a lot of time revising the RMarkdown overall -- in particular, the author list and data description need to be updated.