Drought, infection complexity (COI), and prevalence of Plasmodium mexicanum

This data and R code were used for the research reported in the manuscript listed below, which was being reviewed by a journal at the time this data set was published.

• Title: Drought correlates with reduced infection complexity and possibly prevalence in a decades-long study of the lizard malaria parasite Plasmodium mexicanum
• Authors: Allison Neal, Joshua Sassi, Anne Vardo-Zalik

There are 6 files:

1. HOPDroughtAnalysis20201221.R- an R script; the main data analysis file
2. DroughtAnalysisDataFull.csv- a data file containing data on all of the lizards collected at the University of California's Hopland Research and Extension Center from 1978 to 2016. This file does NOT contain any information on drought, but HOPDroughtAnalysis20201221.R will import data from both this file and the droughtMonitorDataUkiah.csv and align them. Alternatively, use DroughtData_AsAnalyzed.csv (see below).  Metadata are provided in a separate file (see below).
3. DroughtData_AsAnalyzed.csv- this data set combines data from DroughtAnalysisDataFull.csv and droughtMonitorDataUkiah.csv. It contains only the lizards that were analyzed for this paper. This file may be useful for repeating the data analysis outside of R, but does not allow for easy adjustment of what data were excluded or how drought measures were aligned with prevalence and COI measures.
4. DroughtAnalysisMetadata.csv- a description of the data in DroughtAnalysisDataFull.csv and DroughtData_AsAnalyzed.csv.
5. droughtMonitorDataUkiah.csv- a data file containing a summary of data from the US Drought Monitor. The original data were downloaded here: https://droughtmonitor.unl.edu/DmData/DataDownload.aspx. Week is reported as YYYYMMDD. The original data, as downloaded, were recorded as the percentage of Ukiah (Mendocino County, California) that was in each of six categories: no drought or drought of severity D0 (abnormally dry) to D4 (exceptional drought). We converted this data to a single number by converting the categories into a numerical scale (0 = no drought, 1 = D0, etc.) and calculating a weighted average of the drought severity for the county for each week. These averages are recorded in this file.
6. HRECRainfall.csv- a data file containing rainfall data from the Hopland Research and Extension Center (https://hrec.ucanr.edu/), posted with permission from John Bailey (HREC director, 2022). It reports the monthly rainfall at HREC from 1952 to 2017.