ExperimentalHuts_2017

This repository contains code used in the following paper.

Quirine A. ten Bosch,Fanny Castro-Llanos, Hortance Manda, Amy C. Morrison, John P. Grieco, Nicole L. Achee, T. Alex Perkins (2017) Model-based analysis of experimental hut data elucidates multifaceted effects of a volatile chemical on Aedes aegypti mosquitoes. BioRXivs

All code contained within this repository is released under the CRAPL v0.1 License. Data provided in this repository are sufficient to rerun all analyses. Because of the large sizes of the output files, we have deposited those on Open Science Framework https://osf.io/xtmy7/ as part of project https://osf.io/5hcpf/.

The scripts for simulations and model fitting were performed on the University of Notre Dame's Center for Research Computing cluster http://crc.nd.edu. Processing of outputs was done on desktop comuputer (Mac OSX)

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Set up of code base:

• Scripts contains code to simulate and fit the model
• ./Runfiles contains scripts to reproduce all runs described in the manuscript. Calls scripts from the Scripts folder
• ./Processingfiles contains scripts to process the results and create figures. It assumes Output is saved at same level as Scripts and saves figures in a Figures folder.

Scripts folder

The scripts in this folder are used to fit the modeling framework to simulated data as well as the experimental hut data. The outputs of these exercises are given in https://osf.io/xtmy7/ and are processed using the scripts in the Processing folder.

To run a test on simulated data and to run the algorithm on real data for baseline, high, and low dosage, run:

• Main.Manuscript.SR.R, which calls the files below

to simulate data with known parameters and fit the modeling framework to these data:

• Parameters.LTFU.SR.Exit.R
• Main.SimulateData.LTFU.SR.Exit.R
• Main.RunMCMC.LTFU.SR.Exit.R

to fit the modeling framework to the real data:

• Parameters.LTFU.SR.Exit.R
• ExitData.ltfu.RData
• Main.RunMCMConLTFUData.SR.Exit.R

Note that for a quick run, you can adjust the number of iterations in Paramers.LTFU.SR.Exit.R

Main.....: are drivers of specific procedures, SR.....: function files, ....RData: data files to reproduce results:

• ExitData.ltfu.RData contains the experimental hut data
• timespent.fixedr.RData contains the results from running the odes on the posterior outcomes to estimate the proportion of time spent in each hut. Can be reproduced with ./Processingfiles/Process_Figure6.R

Scripts/Runfiles folder

Contains the R-files to run the model framework on the experimental hut data for the three different dosages. For each dosage, the R-file is provided that runs at the default r (proportion of movement directed outside), and the low and high values used to assess sensitivity to this value.

Scripts/Runfiles/SimulationSets folder

Contains python script to automate the creation of Run-files to simulate data at different parameter values for 1000 and 25 mosquitoes and run the modeling framework on these data.

Scripts/Processingfiles folder

Contains the scripts to create all the figures in the manuscript. It uses output data deposited on https://osf.io/xtmy7/

• Process_SimulatedSet.R to recreate figures 3 and 4
• Process_Results_MCMConData.R to recreate figures 5 and S2, S3, and S4
• Process_Figure6.R to recreate figure 6
• Process_TestingConvergence.R for supplementary figures on traceplots and Gelman-Rubin statistics
• Process_Results_MCMConData.R derives outcomes and summary statistics reported in manuscript