ReadMe for 'TRAIT-SPECIFIC TRADE-OFFS PREVENT NICHE EXPANSION IN TWO PARASITES' by Lievens et al.

2019-09-17

This readme file describes the data files and analysis file accompanying the above manuscript, which can be found at https://doi.org/10.1101/621581 
For any further questions please contact eva.j.lievens@gmail.com

The following files are included:

1) "analysis.rmd"
This script reproduces the analysis of the experiment, as described in the paper. The comments should make it self explanatory.
This file is an R Markdown script (.rmd, http://rmarkdown.rstudio.com/). R Markdown is a free extension to R that allows easy commenting of code. If the user does not wish to use this program, the code can be opened as a text file and chunks (sections between ``` marks) analysed as regular R code.

2) "data.zip"
This folder contains the 8 data files (.cvs) needed to analyse the experiment:

	a) "DATA final assays - infectivity.csv"
	This is the main dataset tracking infection in the 1st final assay. Its variables are described in the relevant section of the analysis file.

	b) "DATA final assays - PCRs plates 1-29.csv"
	Each host individual in the 2nd final assay was tested for the presence of microsporidian DNA after it died; this dataset contains those results. Its variables are described in the relevant section of the analysis file.

	c) "DATA final assays - virtrans.csv"
	This is the main dataset tracking host individuals in the 2nd final assay. Its variables are described in the relevant section of the analysis file.

	d) "DATA final assays - virtrans - checks of infection in spore samples.csv"
	This dataset records whether hosts that died during the 2nd final assay and tested negative for infection had or didn't have spores in their fecal samples. It is used to build the dataframe in the 'Data' section of the analysis of the 2nd final assay.

	e) "DATA final assays - virtrans - spore collection.csv"
	This dataset records the plate and well in which individual fecal samples from the 2nd final assay were kept. It is used to link dataframes in the 'Data' section of the analysis of the 2nd final assay.

	f) "DATA final assays - virtrans - transmission week 3.csv"
	This dataset contains the spore production data (raw counts) from the 2nd final assay. Its variables are described in the relevant section of the analysis file.

	g) "DATA msp population size checks.csv"
	This dataset lists the number of spores present (calculated from the raw counts, which are not included) in the samples used to measure the microsporidian population size during the serial passaging. Its variables are described in the relevant section of the analysis file.

	h) "DATA survival during passages.csv"
	This dataset contains the results results for host survival during the serial passaging. Its variables are described in the relevant section of the analysis file.