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The file `_site.yml` specifies the look and nav bar structure. A footer can be added to that file in which case the same footer is added to each page. If you don't want that, then you can delete the `footer.html` bit in `_site.yml` and instead add this code at the end of each Rmd file.
```{r child="footerrmd.Rmd"}
```
## Level 2
Some information and a link. <http://rmarkdown.rstudio.com>.