If the table has significant irregularities then almost any re-usable function won't be much use. There is always the option of composing it manually, using backticks to plug in numbers where you want.
The "tables" package is good for Rnw (LateX), but not so good with irregular layout. The "xtables" package is good for either html (Rmd) or LateX (Rnw), but again not for irregular layout.
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Some versions of markdown (e.g. pandoc) include a simple table translation syntax, but most require you to use html table syntax, which is rather more verbose than typical markdown [1]. You will probably need to study HTML and CSS syntax to get the results you want, and it may still not satisfy you due to the independent decisions that browsers can make in displaying the table. That is one reason I do more work in Rnw files than in Rmd files.
[1] http://daringfireball.net/projects/markdown/syntax
[2] Google to learn, for example see http://www.w3schools.com/css/css_table.asp
Hi Jeff,Thank you for your response! Would you direct me to the references of how to make the irregular tables manually in markdown?Thanks,Qike