AGmccoy/Phytopthora-sojae-Pathotype-analysis: Beta-release of Phytophthora sojae pathotype analysis code

Phytophthora sojae has been managed primarily via deployment of resistance genes (Rps genes, resistance to Phytophthora sojae) in commercial soybean cultivars and by the application of fungicide seed treatments. However, repeated use of resistance genes can cause populations to adapt over time rendering these resistance genes ineffective. To determine current effectiveness of resistance genes for managing Phytophthora sojae, state-wide surveys must be conducted to determine the pathotype (previously referred to as "race") structure within sampled population of P. sojae.

The goal of these scripts was to provide all the necessary analyses needed when conducting a Phytophthora sojae pathotype survey, including: Distribution of susceptibilities (effective and non-effective Rps genes), Distribution of pathotype complexities with statistics, Pathotype frequency distribution, as well as diversity indices for pathotypes.

These scripts should allow for all users to simply change the file pathway to that of their own data as well as changing column titles within each sections associated function (annotations are provided and will walk user throught it). Little to no editing should be necessary (other than column headings in the functions) for data outputs to be generated. Annotations for all code are provided, as well as a sample data sheet that will allow you to test the code on something other than your data.