Tuesday: manuscript and appendix edits

Today’s log

  • Edited cover letter summary for public.

  • Soliciting feedback on examples in manuscript vs appendix, see Monday’s entry.  (Entry posted, images added to flickr database)

  • Jeff fixed the double-post bug in twitteR, tested update.

  • Improved initialization estimates for LSN model in fit_models (code), as identified & discussed in Sunday’s entry. Needs testing on a unit case, trying on ibm_analysis.R now… seems to work fine.

  • Running this ibm_analysison a small dataset at 2000 replicates (zero, nice 19).

  • Model choice sets (i.e. see in stream) finally finished – but some trouble in corresponding data records to the figures??

  • Reworking model section of appendix, consider Levins-style model in place of traditional logistic as the transcritical bifurcation.

  • Flushed out appendix discussion of Cox’s delta.

  • Adding data descriptions to appendix.

  • Updates to appendix examples: Skew (pull out kurtosis, never really proposed/applied).

  • Model generality comments

To Do

  • Text: adjust to reflect a single Figure.  Adjust captions.  adjust to reflect Algae example.

  • Specify which Glaciation example, specify data treatments Specify which Algae example

  • Examples: Remove kurtosis examples.  Add IBM examples with sufficient and insufficient power.

  • R package and examples cleanup

  • Update parameter estimates without convergence failure runs.

  • Review remaining comments