SupportingInformation

Directory Information

• Supporting Information : This folder contains all the analyses used in the supporting information.

  • Model Simulation

      This folder contains the code to simulate the disease-structured generalized N-mixture model
    

  • NaivePrevalence

      This folder contains data, code, and output to calculate the naive prevalence (i.e., the proportion of individuals infected)
    
      	- ALL_Cope2008_2014.txt
    
      			Contains data in long format from El Copé, Panama from 2008 to 2014
    
      	- Prevalence code.R
    
      			Code used to calculate prevalence each season
    
      	- prev.csv
    
      			Results from model (R output)
    
      	- prev.xlxs
    
      			Formatted R output
    

  • Ordination

      This code performs the non-metric multidimensional scaling analysis used to determine if community composition varied by season, habitat, and transect.
    
      	- Cope2010_2014.txt
    
      			Contains data in long format from El Copé, Panama from 2010 to 2014
    
      	- Ordination 20 July 2017.pdf
    
      			Ordination output
    
      	- Ordination.R
    
      			R code for Ordination
    

  • Testing_closure_assumption

      This folder contains code, data, and final figures testing the closure assumption.
    
      	- Code
    
      		- To create figures
    
      			- Closure Assumption.R
    
      			Contains code to determine the difference in the number of individuals found within a season from the first to the last survey each season
    
      		- To format data 
      			
      			Contains code to format data from long to wide format
    
      	- Data Survey dates
    
      			Contains raw data of the Julian days the survey was performed
    
      	- Figures
    
      			- Infected_seasonal.pdf
    
      				Histogram of infected individuals each season
    
      			- Not_infected_seasonal.pdf
    
      				Histogram of uninfected individuals each season	
    

  • Testing_Poisson_assumption

      	- Poisson assumption.R
    
      	Code used to calculate the mean and the variance of the number of individuals captured at each 20 m section
    
      	- Poisson_assumption.pdf
    
      	Figure used in the Supporting information
    

  • Testing_distribution_of_snout_to_vent_length

      	- SVL distribution.R
    
      	Code to create histograms describing the snout-to-vent length of each species. Examined for sexual dimorphism and age structure in the data. 
    

  • Testing_for_prior_sensitivity

      	- Prior sensitivity.R
    
      	Code to create the figure examining the parameter estimates when priors are changed in the model
    

  • Testing_for_spatial_autocorrelation

      	- Testing4SpatialAutocorrelation.R
    
      	Contains code to test for spatial autocorrelation among the 20-m sections