---
title: "Concatenation"
author: "Gustavo A. Ballen and Sandra Reinales"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Concatenation}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Tools are available for concatenating matrices, although few deal with concatenating different data types. The function `concatNexus` was designed for including both DNA and morphological matrices. If the morphological matrix is in some form of table (probably a spreadsheet), we can use the function `table2nexus` to read a table file from the disk and write back the nexus-formatted.

In this example, we use these functions to concatenate the DNA alignments and morphological data for the South American Sabre-Tooth Characins of the family Cynodontidae. Data are in the `examples` directory of the package repository.

Let's set up the environment for concatenating data:

```{r eval=FALSE}
# load the package
library(tbea)

# navigate to the examples/concatenation directory in the package repository
setwd("examples/concatenation")
```

```{r eval=FALSE}
table2nexus(path="data/morpho.csv",
            datatype="standard",
            header=FALSE,
            sep=",",
            con="data/morpho.trimmed.nex")
```

The morphological matrix is now in nexus format, so we can concatenate DNA (also in nexus format) and morphology partitions as follows:

```{r eval=FALSE}
nexmatrices <- list.files(path="data", pattern=".nex", full.names=TRUE)
concatNexus(matrices=nexmatrices,
            filename="concatenatedMolmorph.nexus", 
            morpho=TRUE,
            morphoFilename="data/morpho.trimmed.nex",
            sumFilename="partitions.txt")

# also, we can provide a pattern and a path 
path <- "data"
pattern <- "trimmed.nex$"
concatNexus(pattern=pattern,
            filename="concatenatedMolmorph.nexus",
            path=path, 
            morpho=TRUE,
            morphoFilename=paste(path, grep(pattern="morpho.",
                                            x=dir(path, pattern), value=TRUE),
                                 sep="/"),
            sumFilename="partitions.txt")
```

This will generate two files, one with the concatenated nexus alignment (`concatenatedMolMorph.nexus`) and one with information on the start and end position for each partition (`partitions.txt`).