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projetos:reproducibleresearch [2014/03/17 17:48] joel [section 1] |
projetos:reproducibleresearch [2014/03/17 18:03] joel [Reproducible Research] |
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| ====== Reproducible Research ====== | ====== Reproducible Research ====== | ||
| + | |||
| + | In this page we show how to create a minimal report using R + Latex + Markdown Resources. Lets create a minimal report from few R commands : | ||
| + | |||
| + | <code> | ||
| + | # loaddata | ||
| + | data(iris) | ||
| + | |||
| + | # summarydata | ||
| + | summary(iris) | ||
| + | |||
| + | # boxplot | ||
| + | boxplot(iris[,1]~iris[,5]) | ||
| + | |||
| + | # table | ||
| + | table(iris[,5]) | ||
| + | |||
| + | </code> | ||
| + | |||
| + | We can embbed those commands into a simple LaTeX file according to the example below : | ||
| + | |||
| + | <code> | ||
| + | \documentclass{article} | ||
| + | |||
| + | \title{Introduction to Reproducible Research in R} | ||
| + | \author{Bioinformatics Meeting} | ||
| + | |||
| + | |||
| + | \begin{document} | ||
| + | |||
| + | \maketitle | ||
| + | |||
| + | \section{Introduction} | ||
| + | |||
| + | This document contains a minimal example of reproducible research using R. | ||
| + | |||
| + | \section{Loading Data} | ||
| + | <<loaddata>>= | ||
| + | # loading data set | ||
| + | data(iris) | ||
| + | @ | ||
| + | |||
| + | |||
| + | \section{Summary of Data} | ||
| + | <<summarydata>>= | ||
| + | # summary of the data set | ||
| + | summary(iris) | ||
| + | @ | ||
| + | |||
| + | \section{A Box Plot} | ||
| + | <<results='hide',boxplot,fig.show='hide'>>= | ||
| + | # building a box plot | ||
| + | boxplot(iris$Sepal.Length~iris$Species) | ||
| + | @ | ||
| + | \includegraphics{figure/boxplot.pdf} | ||
| + | \section{A Table} | ||
| + | |||
| + | <<table,results='asis'>>= | ||
| + | # loading xtable package | ||
| + | require(xtable) | ||
| + | |||
| + | # creating a table | ||
| + | tab<-table(iris$Species) | ||
| + | |||
| + | # buiding a table with all data | ||
| + | print(xtable(tab)) | ||
| + | @ | ||
| + | |||
| + | \section{Aditional Tips} | ||
| + | |||
| + | <<>>= | ||
| + | # let it commented | ||
| + | # purl("report.rnw") | ||
| + | # system("pandoc -s report.tex -o report.docx") | ||
| + | @ | ||
| + | |||
| + | \end{document} | ||
| + | |||
| + | </code> | ||
| + | |||
| + | Save the commands above into a file called report.rnw and compile it into a LaTeX document according to the commands below. | ||
| + | |||
| + | <code> | ||
| + | library(knitr) | ||
| + | knit("report.rnw") | ||
| + | </code> | ||
| + | |||
| + | This will generate a .tex file that can be processed by a LaTex editor! | ||
| + | |||
| + | For linux and mac users, you can run : | ||
| + | |||
| + | <code> | ||
| + | > tex2pdf report.tex | ||
| + | </code> | ||
| + | |||
| + | to convert the result into a pdf | ||
| + | |||
| + | |||
