Analysis of P. ramorum epidemic isolates

Citation

Please use the following DOI to cite this data and associated functions/analyses.

R markdown files

These files contain the steps used to perform the analyses with comments. Reports are written in \*.Rmd files and rendered as HTML documents. Folders contain cached figures and data from respective analyses. Below is a table describing each analysis.

File	Description
DAPC	Discriminant analysis of principal components over forest data.
Diversity_stats	file with genotypic, genotype, and allelic diversity. This includes AMOVA analysis
ForestNursery	Analyzing the combined forest and nursery data.
Gst	Calculating $G_{st}$ values for the data set
Gst_clonecorrect	Calculating $G_{st}$ values for clone corrected data.
Mantel	Analyzing correlations between space and genotype with mantel tests and linear models.
maps	plotting multilocus genotypes onto maps. Note: the output is not kept in the online repository as the file size with all the images becomes too large to host freely on github.
mlg_distribution	Displaying the distribution of multilocus genotypes in the data.
msn	Displays minimum spanning networks based off of Bruvo's distance.
Pop_structure	dendrograms of populations based on Nei's distance.

R package

PramCurry

This package contains data and functions utilized in this analysis.

installation can be done from within the main directory using devtools:

devtools::install("./PramCurry")

Data Sets

• ramdat - a data set of all the unique forest isolates genotyped over five loci from Curry County, OR from 2001 to 2014. The csv file containing this data is in the main directory under Pramorum_Curry_County_2001_2014.csv in GenAlEx format with xy coordinates. This can be accessed from within the PramCurry package with the command data(ramdat)
• for2nur - combination of forest and nursery isolates genotyped over five loci. The csv file containing this data is in the main directory under Pramorum_Forest_Nursery.csv in GenAlEx format. This can be accessed from within the PramCurry package with the command data(for2nur)

Misc

Shapefiles

A folder called shapefiles/ contains all of the shapefiles necessary to produce figure 1.

Packrat

This project is managed via packrat. There is a folder called packrat/ that contains all the information about the R packages utilized to perform this analysis. It also contains a folder called src/, which holds all of the tarballs for each package.

Exceptions

The R package rgdal is a library that will read and translate shapefiles into a format that R can understand. It requires that you download and install GDAL onto your system. I have left it out because OSX >10.9 does not have a readily available binary for it. For users on any other system, you should install GDAL and then install rgdal normally: install.packages("rgdal"). For users of OSX >10.9, please use install.packages("rgdal_0.8-16.tgz", repos = NULL) with the file in this repository.

Various Files

Many of the analyses will produce either image files (*.gif, *.pdf, *.png, *.svg), data files (*.nex), or tables (*.csv). These were saved in the main folder of the repository.