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The RStudio "knit" button, which generated the previous README.md is closer to rmarkdown::render than knitr::knit, which appears to have been used to generate the latest README.md. Doesn't pick up on the github_document.

I added some render options to make the result a little more like just knitting. Some whitespace still changed.

Also, a parenthesis got dropped in a badge image url.

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