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In fact, as long as you specifies format in kable() (which can be set globally through option ), functions in this package will pick the right way to manipulate the table be themselves. Most functionalities in kableExtra can work in both HTML and PDF. There is no reason why we cannot use it with tables. We see similar approaches to deal with plots in packages like ggvis and plotly. It is a package that can "add features" to a kable() output using a syntax that every useR loves - the pipes %>%.
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KableExtra is NOT a table generating package. For customized rmarkdown templates, it is recommended to load related LaTeX packages manually. This package can load required LaTeX package automatically in vanilla rmarkdown.
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Only have to mess with raw HTML/LaTeX in the last 10% cases where kableExtra cannot solve the problem.Use kable() with kableExtra to generate 90 % of complex/advanced/self-customized/beautiful tables in either HTML or LaTeX.Use default base kable() (Or a good alternative for markdown tables is pander::pander()) for all simple tables.That's why this package kableExtra was created. For LaTeX, it's even worse since I'm almost Stack Overflow dependent for LaTeX. Also, for me personally, I found myself repeatedly parsing CSS into kable() for some very simple features like striped lines. It is not rare to see people including experienced users asking questions like how to center/left-align a table on Stack Overflow. However, the ultimate simplicity of kable() also brought troubles to some of us, especially for new R users, who may not have a lot of experience on generating tables in R. It is not intended to replace any other R packages for making tables. Just as it claimed in its function description, Unlike those powerful table rendering engines such as xtable, the philosophy behind knitr::kable() is to make it easy for programmers to use. When we are talking about table generators in R, knitr's kable() function is usually a popular choice because of its ultimate simplicity.