%\VignetteIndexEntry{Categorical FDA Tutorial}
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\title{Guide to Turning an RDP File into a Data Set}
\author{Berkley Shands, Patricio S. La Rosa, Elena Deych, William Shannon}

\begin{document}

\maketitle
	
Below we will define the basic steps required to generate a data set from an RDP file \\*

1. Take an RDP file such as this example: \\*
;Root:1.0;Bacteria:1.0;Firmicutes:1.0;Bacilli:1.0;Bacillales:1.0;Staphylococcaceae:1.0; \\*
;Root:1.0;Bacteria:1.0;Firmicutes:1.0;Bacilli:1.0;Lactobacillales:1.0;Carnobacteriaceae:0.8; \\*
;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Bacteroidales:1.0;Prevotellaceae:1.0; \\*
;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Bacteroidales:1.0;Prevotellaceae:1.0;\\*
;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Unclassified:0.5;Unclassified:0.5; \\*


2. Take the first entry and seperate each level into its own row, while seperating levels by a period: \\*
Root, 1\\*
Root.Bacteria, 1\\*
Root.Bacteria.Firmicutes, 1\\*
Root.Bacteria.Firmicutes.Bacilli, 1\\*
Root.Bacteria.Firmicutes.Bacilli.Bacillales, 1\\*
Root.Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1\\*


3. Do the same with each following row, adding to the number at the end if it is the same:\\*
Root, 5\\*
Root.Bacteria, 5\\*
Root.Bacteria.Firmicutes, 2\\*
Root.Bacteria.Firmicutes.Bacilli, 2\\*
Root.Bacteria.Firmicutes.Bacilli.Bacillales, 1\\*
Root.Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1\\*
Root.Bacteria.Firmicutes.Bacilli.Lactobacillales, 1\\*
Root.Bacteria.Firmicutes.Bacilli.Lactobacillales.Carnobacteriaceae, .8\\*
Root.Bacteria.Bacteroidetes, 3\\*
Root.Bacteria.Bacteroidetes.Bacteroidia, 3\\*
Root.Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales, 2\\*
Root.Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae, 2\\*
Root.Bacteria.Bacteroidetes.Bacteroidia.Unclassified, .5\\*
Root.Bacteria.Bacteroidetes.Bacteroidia.Unclassified.Unclassified, .5\\*


4. Change any unclassifieds or anything else that could appear under multiple different parents (we prefer adding a 'U' to the parents name):\\*
Root.Bacteria.Bacteroidetes.Bacteroidia.BacteroidiaU, .5\\*
Root.Bacteria.Bacteroidetes.Bacteroidia.BacteroidiaU.BacteroidiaUU, .5\\*


5. Remove the 'Root' level since we are only looking at Bacteria in this example:\\*
Bacteria, 5\\*
Bacteria.Firmicutes, 2\\*
Bacteria.Firmicutes.Bacilli, 2\\*
Bacteria.Firmicutes.Bacilli.Bacillales, 1\\*
Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1\\*
Bacteria.Firmicutes.Bacilli.Lactobacillales, 1\\*
Bacteria.Firmicutes.Bacilli.Lactobacillales.Carnobacteriaceae, 1\\*
Bacteria.Bacteroidetes, 3\\*
Bacteria.Bacteroidetes.Bacteroidia, 3\\*
Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales, 2\\*
Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae, 2\\*
Bacteria.Bacteroidetes.Bacteroidia.BacteroidiaU, .5\\*
Bacteria.Bacteroidetes.Bacteroidia.BacteroidiaU.BacteroidiaUU, .5\\*


6. Repeat for any additonal RDP files and add them as new columns (and rows as needed) in our data set:\\*
Taxa, Sample 1, Sample 2\\*
Bacteria, 5, 5\\*
Bacteria.Firmicutes, 2, 5\\*
Bacteria.Firmicutes.Bacilli, 2, 5\\*
Bacteria.Firmicutes.Bacilli.Bacillales, 1, 5\\*
Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1, 5\\*
Bacteria.Firmicutes.Bacilli.Lactobacillales, 1, 0\\*
Bacteria.Firmicutes.Bacilli.Lactobacillales.Carnobacteriaceae, 1, 0\\*
Bacteria.Bacteroidetes, 3, 0\\*
Bacteria.Bacteroidetes.Bacteroidia, 3, 0\\*
Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales, 2, 0\\*
Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae, 2, 0\\*
Bacteria.Bacteroidetes.Bacteroidia.BacteroidiaU, .5, 0\\*
Bacteria.Bacteroidetes.Bacteroidia.BacteroidiaU.BacteroidiaUU, .5, 0\\*
Bacteria.Firmicutes.Bacilli.Lactobacillales.Streptococcaceae, 0, 5\\*


7. Save the file as a .csv (or anything other file readable by R) and load it in R:\\*

\textbf{Notes:}
\begin{itemize}
  \item Any symbol can be used as a taxa level seperator except colons.
  \item There can only be one top level node, if we were looking at Archaea too we would need to keep the Root level in.
\end{itemize}

\end{document}