Quadrat.Rmd

---
title: "DB_QuadratSummary"
author: "Douglas Bates"
date: "09/26/2014"
output:
  pdf_document:
    fig_caption: yes
---

# Reading the data

An initial examination of the data file
```{r input}
str(summ <- read.delim("/afs/cs.wisc.edu/p/stat/Data/MS.exam/s11/DB_QuadratSummary_MSTest.txt"))
```
shows that `Plot`, `Transect` and `Quadrat` should probably be converted to factors and that the last four variables are likely indicators.
```{r}
for (i in 8:11) {print(unique(summ[[i]]))}
```

At this point I would go back and regenerate the dataset
```{r input2}
str(summ <- within(read.delim("/afs/cs.wisc.edu/p/stat/Data/MS.exam/s11/DB_QuadratSummary_MSTest.txt"), {
    Plot <- factor(Plot)
    Transect <- factor(Transect)
    Quadrat <- factor(Quadrat)
    X2m_SppPresent <- factor(X2m_SppPresent,labels=c("N","Y"))
    X2m_SppBrowsed <- factor(X2m_SppBrowsed,labels=c("N","Y"))
    X4m_SppPresent <- factor(X4m_SppPresent,labels=c("N","Y"))
    X4m_SppBrowsed <- factor(X4m_SppBrowsed,labels=c("N","Y"))
}))
```
then examine a summary
```{r summary}
summary(summ)
```