Examples landing page populated

[erex]

The 7 vignettes associated with Distance are on the site and described on the landing page, along with a link not only to the html, but also the Rmd files. I'm not inclined to create purl versions of the Rmd files as I think the narrative is the reason the vignettes were created, stripping out the narrative to create the purl versions defeats the purpose of explanation.

I've not produce a tabular form for the landing page; if there are strong feelings against the page in current form, I can mock up a tabular version.

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Unaddressed at this point is what to do about previous vignettes we have on distancesampling.org. Seems as if they should no longer be at their old location, but brought over here (main argument for creating the subdomain). However in my opinion, the newest vignettes superceed the need for the old vignettes with the exception of

• MRDS of crabbies
• dsm for spotted dolphins
• Gui's dsm with point counts

If we substituted golf tees for crabbies, then we wouldn't need an additional .csv file of data. In that case, the only vignette that needs data beyond what is in the package is Gui's dsm.

Comments? @dill @lenthomas

[erex]

In housecleaning mode on distancesampling.org:

• I think we should remove the Getting Started section from the R page, as the vignettes are migrating (comment above)
• should the wikis for mrds, Distance and dsm be maintained, (last updated 3, 4, 5 years ago respectively) or removed?
• I suspect there are now orphaned pages that are no longer linked
  • For example, DistWin project to accompany Burt et al. (2017) MEE paper on MRDS
  • I'll hunt around for such things.

[erex]

Thinking about bringing dsm spotted dolphin vignette to the new examples subdomain, I looked to see if the .Rmd code would still work (vignette dated August 2015 with dsm 2.2.11--current version is 2.2.17)

Of course, the code fell over, when trying to use varprop in this chunk, after I removed the attach(mexdolphins) command in line 50

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The dsm.var.prop function will estimate the variance of the abundance for each element in the list provided in pred.data. In our case we wish to obtain an abundance for each of the prediction cells, so we use split to chop our data set into list elements to give to dsm.var.prop.

preddata.varprop <- split(preddata, 1:nrow(preddata))
dsm.xy.varprop <- dsm.var.prop(dsm.xy, pred.data=preddata.varprop,
                               off.set=preddata$area)
Quitting from lines 630-635 (mexico-analysis.Rmd) 
Error in dsm_varprop(dsm.obj, pred.data[[1]]) : 
  varprop doesn't work when there are no covariates in the detection function
Calls: <Anonymous> ... withVisible -> eval -> eval -> dsm.var.prop -> dsm_varprop
Execution halted

[dill]

can this issue be closed now?

[erex]

only outstanding issue is whether to remove the links to the stale wiki pages

[dill]

Ah sorry, missed that one.

I've updated the wikis for dsm and Distance, leaving in useful information. I've removed the mrds wiki as there is no useful information there and removed the link on distancesampling.org/R.

In a future phase of the website we might want to think about moving that wiki information over to the main site. Don't have time to think about that this week though.

[erex]

mmmm, there's still dross (excuse the expression) in the Distance wiki: need for obs, sample, region tables; reference to minke vignette (broken link)

Understand you are pressed for time. Would you prefer that I open a new issue about the Distance wiki so this one can be closed? Would really like the website to contain current info.

[dill]

Sounds good. Please feel free to edit the Distance wiki if you have immediate things that stick out (like broken links).

…

On 04/02/2020 09:02, erex wrote: mmmm, there's still dross (excuse the expression) in the Distance wiki: need for obs, sample, region tables; reference to minke vignette (broken link) Understand you are pressed for time. Would you prefer that I open a new issue about the Distance wiki so this one can be closed? Would really like the website to contain current info. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AAAAPIJ7JIKSYZM6RL7KBWDRBEVKFA5CNFSM4KKYI4QKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKW26YI#issuecomment-581807969>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAAPIKII3MIOZIMJLIOT6DRBEVKFANCNFSM4KKYI4QA>.

[erex]

will poke at wiki as time permits