README

This dataset is from the paper titled
"Lessons from movement ecology for the return to work: modeling 
 contacts and the spread of COVID-19"

By: Allison K. Shaw, Lauren A. White, Matthew Michalska-Smith, 
    Elizabeth T. Borer, Meggan E. Craft, Eric W. Seabloom, Emilie Snell-Rood,
    Michael Travisano

Published in: PLoS One

Contact ashaw@umn.edu for assistance.

The files included here are from the 'movement model' from the paper;
  please see elsewhere for files for the 'network model' from the paper.

The following files are included:


(1) files_runcode.zip

MOVEMENT MODEL SIMULATION SCRIPTS

SEIR.m: Calculate instantaneous rate of change for susceptibles (S),
       exposed (E), infected (I), and removed (R) in a simple SEIR 
       model with frequency-dependent transmission dynamics.

run_SEIR_spatial.m: runs simulations of a semi-spatial SIR model, 
       tracking the number of susceptibles (S), exposed (E),  
       infected (I), and removed (R) individuals. All individuals
       spend a fraction of each day (T_h) at home, a fraction (T_w)
       working either from home or from work and a fraction (2*T_c)
       commuting to and from work or at home.

fig2_physicaldistancing.m: runs simulations for figure 2 (creates fig2.jpg)

fig3a_run.m, fig3b_run.m, fig3c_run.m: run simulations for a number of 
       different parameter combinations (creates fig3a_tw_theta.mat,
       fig3b_R0work_theta.mat, fig3c_R0work_tw.mat)

fig3_plot.m: plot the resuts a number of different parameter
       combinations (creates fig3.jpg)

MOVEMENT MODEL PRCC ANALYSIS SCRIPTS

set_parameters.m		sets baseline parameters

set_LHSdistributions.m		generates LHS distributions

set_parameters_monotonicity.m	sets up parameters for monotonicity check

setup_LHS.m			sets up LHS matrix

check_LHS_distributions.m	check that parameter distributions are 
				uniform

check_monotonicity_metric1.m	checks monotonicity for metric 1

check_monotonicity_metric2.m	checks monotonicity for metric 2

check_number_runs.m		determines number of runs to use

check_PRCCvals_rank.m		check rank of PRCC value for significance

run_analysis.m			MAIN script to run LHS and PRCC analysis


Downloaded from http://malthus.micro.med.umich.edu/lab/usadata/

LHS_Call.m		generates sampling of all parameters

PRCC.m			calculates PRCC values


(1) files_output.zip

fig3a_tw_theta.mat: data (.mat) file, generated by fig3a_run.m, used to make fig3

fig3b_R0work_theta.mat: data (.mat) file, generated by fig3b_run.m, used to make fig3

fig3c_R0work_tw.mat: data (.mat) file, generated by fig3c_run.m, used to make fig3

output_MonoPlots1.mat: data (.mat) file, generated by check_monotonicity_metric1.m

output_MonoPlots2.mat: data (.mat) file, generated by check_monotonicity_metric2.m

output_numruns.mat: data (.mat) file, check_number_runs.m

output_PRCC.mat: data (.mat) file, generated by run_analysis.m
