This repository contains code to replicate results and figures in

Latitude, seasonality, and urbanness interact to predict raccoon rabies case reports

Meggan E Craft, Matthew Michalska-Smith, Amy J Davis, Amy T Gilbert, Richard Chipman, Jordona Kirby, Kathleen Nelson, Xiaoyue Ma, Ryan Wallace, Grace Miller, & Kim M Pepin

N.b. the example models and figures provided in this repository use the hypothetical data and therefore should not be interpreted as meaningful biological relationships

Repository Structure

code

This directory contains scripts necessary to replicate the results and figures in the aforementioned manuscript

data

This directory contains ___

figures

This directory contains output figures corresponding to figures presented in the aforementioned manuscript

Analysis pipeline

loading data

A hypothetical dataset is provided to demonstrate structure and code functionality. The proposed models require the following data inputs:

county fips identifiers (used as a random effect)
month of sampling
latitude (centroid of sampling county)
density (population density of sampling county)
habitat quality (the fraction of land area in the county with raccoon suitable habitat)
the number of positive tests in that county-month
the number of tests conducted in that county-month

fitting models

run_models.R

base_formula:

~ bs(month, df={df_month}, degree={degree_month}) +
  bs(latitude, df={df_latitude}, degree={degree_latitude}) +
  bs(density, df={df_density}, degree={degree_density}) +
  bs(density, df={df_density}, degree={degree_density}) : bs(latitude, df={df_latitude}, degree={degree_latitude}) +
  bs(month, df={df_month}, degree={degree_month}) : bs(latitude, df={df_latitude}, degree={degree_latitude}) +
  habitat + temporal_lag + spatial_lag"))

response variables

presence: the existence of at least one positive test in that county-month
positivity: the proportion of all tests that were positive in that county-month
persistence: a binary measure of whether a certain number n of the past m months have had at least one positive test per month for a given county

plotting model output

plot_figures_and_tables.R

N.b. map figures are not replicated here, as the hypothetical data is scrambled in such a way as to make it no longer spatially explicit

mjsmith037/Raccoon_Rabies_Across_Urbanness_And_Latitude