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README

Brief instructions for the dengue transmission model code version 1.0.
by Dennis Chao and Thomas Hladish (2012)

We have released the source code for our dengue model (described in 
the PLoS Neglected Tropical Diseases paper "Controlling dengue with 
vaccines in Thailand") under the GPLv3 (see the files LICENSE and 
gpl.txt).

This bundle includes C++ source code and data files, all placed in the
"denguemodelcode/" directory. There is no user interface, and the 
documentation is minimal and poor. There is a Makefile that works in 
Linux, and it produces an executable called "model". Run it on the 
command line with appropriate flags to specify model parameters, the 
locations of the necessary data files, and the desired output file names. 
The model sends a list of all exposed and infectious mosquitoes as well 
as all infected people to stdout.

Data files for the Bangphae model:
  locations-bangphae.txt: a list of all locations in Bangphae
  population-bangphae.txt: a list of all people in the synthetic population for Bangphae
  immunity-bangphae.txt: prior exposure to each of the four serotypes for each of the people in population-bangphae.txt
  network-bangphae.txt: a list of all "adjacent" locations corresponding to ids listed in locations-bangphae.txt. This is used for mosquito movement.

Command-line options:
  -randomseed [seed]: supply a random number seed to the GSL generator
  -runlength [days]: length of the simulation run in days. run the model for 364 days for a one-year simulation, otherwise the population will get shuffled on day 365.
  -initialinfected [num]: number of randomly selected individuals to infect before the simulation
  -initialexposed [num]: number of randomly selected individuals to expose (and possibly infect) before the simulation
  -dailyexposed [num]: number of randomly selected individuals to expose (and possibly infect) at the start of each day
  -vaccinatephased [n] [y] [a] [f] [y] [a] [f]...: used to vaccinate different age groups in different years. the first argument is the number of vaccination groups desired. this is followed by triplets specifying: the year the group should be vaccinated (occurs on January 1, and the first year is 0), the age cohort to be vaccinated (in years), and the fraction of this cohort to vaccinate (from 0.0 to 1.0).
  -primarypathogenicity [f1] [f2] [f3] [f4]: fraction of primary infections that result in illness, by serotype
  -secondaryscaling [f1] [f2] [f3] [f4]: fraction of non-primary infections (relative to the first) that result in illness, by serotype. the actual pathogenicity fraction for secondary infections is therefore the product of the primary (see the "primarypathogenicity" argument) and secondary fraction
  -betapm [x]: the probability that a mosquito is infected when biting an infectious person
  -betamp [x]: the probability that a person is infected when bitten by infectious mosquito
  -mosquitomove [p]: daily probability of mosquito movement to an adjacent location
  -mosquitomovemodel [s]: mosquitoes move to any neighbor with equal probability if "uniform" or weighted by inverse distance squared if "weighted"
  -mosquitoteleport [p]: daily probability of mosquito "teleportation" (to anywhere in the synthetic population)
  -mosquitocapacity [n]: mean number of mosquitoes per location
  -mosquitodistribution [s]: distribution of mosquitos per location. Set to "constant" for all locations to have the same number of mosquitoes or "exponential" for the number to be exponentially distributed.
  -mosquitomultipliers [n] [d] [f] [d] [f]...: relative number of mosquitoes for seasonality. the first argument is the number of pairs of numbers coming up. each pair consists of an integer that specifies a number of days followed by a floating point number that is a multiplier for the mosquito capacity to set the number of mosquitoes per location for this number of days. the number of days should sum to 365, unless you are trying to be funny and make dengue season fall out of sync with the calendar year.
  -externalincubations [n] [d1] [d2] [d3] [d4]...: external incubation periods. the first argument is the number of pairs of numbers coming up. each pair consists of an integer that specifies a number of days followed by an integer that is the external incubation period for this number of days. the number of days should sum to 365.
  -daysimmune: number of days after recovery that a person has perfect cross-protective immunity to all other serotypes
  -VES [n]: reduction in susceptibility of vaccinees, assuming all-or-none protection (0.0-1.0)
  -VESs [n1] [n2] [n3] [n4]: reduction in susceptibility (0.0-1.0) of vaccinees to each of 4 serotypes
  -VESsnaive [n1] [n2] [n3] [n4]: reduction in susceptibility (0.0-1.0) of vaccinees who had no prior exposure to any serotype. Only works for all-or-none vaccines.
  -VEI [n]: reduction in infectiousness of vaccinees (0.0-1.0)
  -VEP [n]: reduction in probability of becoming ill upon infection of vaccinees (0.0-1.0)
  -vaccineleaky: Setting this flag makes VES leaky. Default is all-or-none.
  -prevaccinate [f]: fraction of the population to pre-vaccinate
  -prevaccinateage [n] [a1] [a2] [f] [a1] [a2] [f]...: prevaccinate by age group. the first argument is the number of age groups, followed by triplets specifying the groups. fraction [f] of those who are ages [a1] to [a2] (in years) are pre-vaccinated.
  -nosecondary: no secondary transmission allowed. this is used for R0 estimation
  -maxinfectionparity [n]: specifies the maximum number of serotypes that can (serially) infect a single individual. default is 4.
  -popfile [filename]: location of the input file that contains the synthetic population
  -immfile [filename]: location of the input file that contains the prior immunity information for the synthetic population
  -locfile [filename]: location of the input file that contains the locations for the model (i.e., houses, classrooms, workplaces)
  -netfile [filename]: location of the input file that lists every pair of adjacent locations corresponding to the information in "locfile"
  -probfile [filename]: location of the (optional) input file that contains information for swapping immune statuses at the end of each year
  -peoplefile [filename]: specifies the name of the output file that will contain the information for every infection in a simulation run
  -yearlypeoplefile [filename]: specifies the filename prefix of the output file that will contain the information for every infection each year in a simulation run. the output filenames will have the year and ".csv" appended (e.g., filename5.csv)
  -dailyfile [filename]: specifies the name of the output file that will contain the number of people infected and symptomatic each day by serotype

Instructions:
A reasonable way to run the model of Bangphae from the command line is:
  ./model -locfile locations-bangphae.txt -netfile network-bangphae.txt -popfile population-bangphae.txt -immfile immunity-bangphae.txt -mosquitomove 0.15 -mosquitoteleport 0.01 -betapm 0.1 -betamp 0.25 -mosquitomultipliers 12 31 0.11 28 0.09 31 0.20 30 0.30 31 0.83 30 1.00 31 0.50 31 0.37 30 0.38 31 0.26 30 0.30 31 0.19 -primarypathogenicity 1.0 0.25 1.0 0.25 -secondaryscaling 1.0 1.0 1.0 1.0 -mosquitocapacity 42 -runlength 364 -dailyexposed 2 2 2 2 -daysimmune 365  -prevaccinate 0.30 -ves 0.7 -peoplefile people-output-bangphaeseasonal-vac30-ves70.csv -dailyfile daily-output-bangphaeseasonal-vac30-ves70.csv > output-bangphaeseasonal-vac30-ves70.csv

And an example for a 10-year simulation:
  ./model -randomseed 5489 -locfile locations-bangphae.txt -netfile network-bangphae.txt -popfile population-bangphae.txt  -immfile immunity-bangphae.txt -mosquitomove 0.15 -mosquitoteleport 0.01 -betapm 0.1 -betamp 0.25 -mosquitomultipliers 12 31 0.11 28 0.09 31 0.20 30 0.30 31 0.83 30 1.00 31 0.50 31 0.37 30 0.38 31 0.26 30 0.30 31 0.19 -primarypathogenicity 1.0 0.25 1.0 0.25 -secondaryscaling 1.0 1.0 1.0 1.0 -mosquitocapacity 42 -daysimmune 120 -runlength 3650 -dailyexposed 2 2 2 2 -ves 0.7 -yearlypeoplefile people-output-bangphae-multiseason-randomseed5489-y -dailyfile daily-output-bangphae-multiseason-randomseed5489.csv > output-bangphae-multiseason-randomseed5489.csv
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