Files for "Validation of a mechanistic Ixodes scapularis (Ixodida: Ixodidae) population dynamics model across multi-site, long-term tick sampling datasets"

Files for "Validation of a mechanistic Ixodes scapularis (Ixodida: Ixodidae) population dynamics model across multi-site, long-term tick sampling datasets" This repository contains data and code in support of a manuscript under review, which presents a new blacklegged tick (Ixodes scapularis) population dynamics model. The model was validated against three tick sampling datasets: Eight years of tick sampling data in Vermont Tick, small mammal, and deer data from a two-decade study in the Hudson Valley, NY Tick sampling data collected by the National Ecological Observatory Network (NEON) This repository provides all processed data and R code required to reproduce the results presented in the manuscript. Replication of all figures and analyses can be performed using the main_script.R file. Reconstruction of model predictors from raw external data sources (e.g., NEON and PRISM) is also documented, but requires downloading licensed or externally hosted datasets and is optional. How to reproduce manuscript results: Download the full repository. Set the working directory to the repository root. Run desired sections of main_script.R This will reproduce figures and analyses presented in the manuscript using the included processed predictors. Repository Contents: inputs/:Raw input files and metadata used to create the environmental and host predictors for the model. Some raw data must be downloaded from external sources (see main_script.R for comments and downloading instructions). main_script.R: The file to replicate the results from the manuscript. It calls scripts from scripts/ to do each part of the analysis. predictors/: Processed predictors (temperature, VPD, day length, and host community) for the three validation datasets, formatted as required for an `IxPopDyMod` model. Predictor units are: temperature (C), vapor pressure deficit (kPa), and host density (per ha). README.md: This file. results/: Model output results. This is empty but will be filled when main_script.R is run. scripts/: R scripts to conduct all analyses in the manuscript, including: downloading NEON data, processing raw inputs into model predictors, running the model, and comparing model output to observed tick density data.