Updating Sparta Documentation

[AugustT]

This is an issue to track documentation work on Sparta. This is focusing on the vignette and the help docs for occupancy model functions:

• [ ] Add occupancy models background information to vignette @bjornbeckmann from thesis
• [ ] Add reporting rate model background information to vignette @bjornbeckmann from thesis
• [ ] Add comparison table of RR Occ and Telfer from @bjornbeckmann thesis (add after section on occupancy models)
• [ ] Add elements of Bayesian guide to the occupancy model section as apporiate @bjornbeckmann @GPowney
• [x] Review issue with 'closure_period' in occDetFunc help file (see #82, and here) @galinajonsson
• [ ] Add description of JAGS model output (i.e. psi.fs, alpha etc.) to vignette. This should be detailed and you might want to print some tables to show what you are talking about @GPowney
• [x] Add description of JAGS model output (i.e. psi.fs, alpha etc.) to help files for occupancy modelling, might need to be brief, with link to vignette longer form description @GPowney
• [ ] Add examples of regional analyses to the vignette @AugustT
• [ ] Add links to further reading on Bayesian models (Garys guide and Mark Kery book) @GPowney
• [ ] Add details of the model types to the vignette. What do they do, why would you use them and what is the recommendation. Reference Charlie's paper @GPowney
• [ ] Update the help doc around modelType, link to the section in the vignette @AugustT
• [ ] Document HTML summary function in the vignette @AugustT
• [ ] Add more examples to occDetFunc @AugustT
• [ ] Change refs to time_period to survey in vignette @drnickisaac
• [ ] Vignette - add detail as to why you look for changes in list length and records over time. Page 4 of vignette @jksheard

Please check off joblets as you complete them and add new ones that i might have missed off @drnickisaac

[AugustT]

@JackHHatfield91 is the new @BjornBeckmann

[sjcowtan]

Please can we have a version of the vignette available for new users? The link from the main page is broken. Thanks :)

[JHHatfield]

Thanks for letting us know about the link. The PDF version was lost from my last commits due to a software issue. The vignettes folder still has R markdown and html versions available though.

[AugustT]

For now visit: http://biologicalrecordscentre.github.io/sparta/articles/sparta_vignette.html

[AugustT]

Link on main page is now fixed

[drnickisaac]

Would be good to revisit and pick up on this list. I just checked the modeltype options as a user and found it quite confusing. For example, there are three list length options but it doesn't state that only one can be chosen.