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ctmm-initiative / ctmm

Continuous-Time Movement Modeling. Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
http://biology.umd.edu/movement.html
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package website automated workflow #3

Closed xhdong-umd closed 7 years ago

xhdong-umd commented 7 years ago

@chfleming

Source this should generate website automatically.

If the html preview method is preferred, the lines after 16 can be ignored.

chfleming commented 7 years ago

I figured out that this bug was the issue:

https://github.com/hadley/pkgdown/issues/207

If I start in a fresh R session and build the vignettes first:

pkgdown::build_articles() pkgdown::build_news() pkgdown::build_reference() pkgdown::build_home()

then everything seems to work (I had to clear my browser cache to see the updates).

dracodoc commented 7 years ago

That's good news! So we don't need any hack anymore. And every reference to vignettes will have right link (I noticed akde mentioned variogram and that was correctly linked.) Opening vignette will also not leave the website, keeping the top navigation bar.

Though will the build_article take another hour to finish?

It's interesting that the bug is known for long time but not mentioned in package readme, and the build_site didn't change the order of calling functions.

chfleming commented 7 years ago

It takes a little while, but the plots are rendered at a higher resolution and the navigation menu is built in.

I'm working on a parallelized quasi-Newton optimization routine right now and after that parallelized differentiation (that can handle boundaries), so the fitting will be much faster and that will cut down the vignette compilation time.

dracodoc commented 7 years ago

Great. The website is looking pretty good now.