Code for running the model presented in: "[Placeholder Title -- Landscape Disease Model]" submitted to XXXX on XXXX, XX, 2021.
All code and data needed to run the model is included in this repo. Model output for the figures presented in the manuscript are not included here because of their size. For these saved model results contact me.


---------------
Sub directories
---------------

/disease_parameters -- data from the lit needed for the model
/figure_code        -- R scripts for plotting of saved output (code for manuscript plots primarily)
/saved_input        -- derived and saved inputs for the model (e.g., simulated landscapes)
/saved_output       -- location for completed simulations

---------
R scripts
---------

top_level_script.R      -- The first/main script to load to run the model. All other needed scripts are sourced from within this script in the order in which they are needed. Open this, and follow the commenting to set up and run the model

**In alphabetical order, not in the order of use / sourcing**

adj_models.R               -- Predictions from fitted models to physiological responses of hosts and mosquitoes
convert_landscapes_sim.R   -- Simulate reforestation on the empirical landscape
convert_landscapes.R       -- Convert a geotiff raster into an ''empirical'' landscape
fit_models.R               -- Fit models to physiological responses of hosts and mosquitoes
functions.R                -- Functions for landscape-disease simulations
ggplot_theme.R             -- Custom theme for beautified ggplots
host_movement_setup.R      -- For R0 calculation need to figure out where the infected host spends its time and 
landscape_containers.R     -- Set up containers for model output
mosq_dispersal.R           -- Determine the expected number of host-seeking mosquitoes in a given landscape cell
needed_packages.R          -- Required packages to run this code
parameters_dynamic.R       -- For every given cell that the infected host enters determine which mosquitoes are there and where they come from
parameters_top.R           -- Set up the key parameters for the simulation
parameters.R               -- Key transmission parameters
pop_dens.R                 -- Obtain mosquito and other-host densities on the landscape
R0_calc.R                  -- Calculate host-to-mosquito transmission and mosquito-to-host transmission
results_containers.R       -- Set up containers for results
run_sim.R                  -- Run the WAIFW model across the landscape
sim_landscapes.R           -- Obtain simulated landscapes across a gradient of heterogeneity
summarize_results.R        -- Take calculated R0 and summarize for overall R0, direction of infection flow etc

----
Data
----

biting_rate.csv                 -- Some biting rate parameters from the lit for all relevant mosquito genera 
feeding_preference              -- Blood meal data extracted from the lit for all relevant mosquito genera 
flight_distance                 -- Some mark recapture and other data to help parameterize mosquito flight distance
gonotrophic_cycle_length        -- For Haemagogus spp. to help figure out biting rate
haem_trans                      -- Transmission for Haemagogus spp. (separate file than mosquito_to_host_transmission because of a different style of experiment (generally))
host_titer.csv                  -- Host physiological response to infection
host_to_mosquito_transmission   -- Infection probability of mosquitoes given a bite on an infected host 
mosquito_to_host_transmission   -- Transmission probability of mosquitoes to hosts given a bite on a susceptible host
survival                        -- Mosquito survival 

-----------
Other files
-----------

bogota_samps.csv                                      -- CSV of NDVI for landscape near Bogota 
cali_samps.csv                                        -- CSV of NDVI for landscape near Cali
cor_-0.55_-0.45_mean_0.48_0.52_dim_60_sim_land.Rds    -- Saved simulated landscapes
empirical_land_sim_land.Rds                           -- Saved simulated reforestation scenarios for "empirical" landscapes