Problem in SVC vignette
Closed this issue · 6 comments
I was running through the examples provided in the "Fitting spatial trend models with sdmTMB" vignette and ran into an error when trying to make predictions on new data using the built-in qcs_grid dataset. The fitted model includes a spatially varying effect of scaled_year, but the qcs_grid dataset doesn't include a column for year. This may have been a recent change given that the vignette appears to have last been rendered ~1.5 years ago.
Similar to the examples in the README, would nd <- replicate_df(qcs_grid, "year", unique(pcod$year)) be a suitable workaround for this example?
Yes -- sorry about the vignette not being updated, we'll work on that. Your solution seems like a good workaround
Where are you viewing this vignette? That line should already be in there and the (web-only) vignette should get built with every push to the main branch. This is the official version:
https://pbs-assess.github.io/sdmTMB/articles/web_only/spatial-trend-models.html
Huh, you're right Sean. Maybe it's something with how the README.Rmd file was rendered?
I clicked on the link at the end of the SVC section of the README page (https://pbs-assess.github.io/sdmTMB/index.html#spatially-varying-coefficients-svc), which then brought me to the vignette dated 2023-01-03. But using the link you included or accessing from the Articles dropdown takes me to the updated version from last month.
Ah, it turns out all the links in the README file (and most links in the help files) link to versions without web_only in the URL and those linked to old cached versions. I wonder if pkgdown changed the default behaviour. What a mess. I'll figure something out. Thanks for pointing this out!
Indeed it looks like the suggested folder for web-only articles changed from web_only to articles. I've renamed the folder, removed links within the docs to the web_only URLs, and pushed the updates to GitHub. Unfortunately, now any links to the web_only versions will become out of date since GitHub pages seems to cache old versions. 🤷♂️ Eventually I'll trash the old commits on the GitHub pages branch.
Sounds good. Thanks for looking into this so quickly!