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rio.epg
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rio.epg
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################################################################
#
# EPIGRASS -Model Definition
# This script describes model and parameters specified
# by the user.
# It can be edited by the user directly, by means of a text editor.
# WARNING: No variables may be removed, even if not used by the chosen model .
# Any comments added by the user must be preceeded by the symbol #
#
################################################################
################################################################
#==============================================================#
[THE WORLD]
#==============================================================#
# Here you add information about the files that described the world the model is enclosed
# "shapefile" is the map layer that will be used as a background for
# the network display. It is defined as a list with file name and the
# name of two variables: the first containing locality names,
# and the other containing unique integers to be used as geocodes.
# "sites" and "edges" are the files that describe the topology of the network (see Documentation)
# The encoding variable can be set to a string stating the encoding of your
# sites and edges files. If left empty iso-8859-1 (latin-1) is assumed.
# See Usermanual for acceptable encoding strings.
#['riozonas_LatLong.shp','nome_zonas','zona_trafe']
shapefile =['riozonas_LatLong.shp','NOME_ZONAS','ZONA_TRAFE']
sites = sites.csv
edges = edges.csv
encoding =
#==============================================================#
[EPIDEMIOLOGICAL MODEL]
#==============================================================#
#model types available: SIS, SIS_s ,SIR, SIR_s, SEIS, SEIS_s, SEIR, SEIR_s,
# SIpRpS, SIpRpS_s,SIpR,SIpR_s,Influenza or Custom (see documentation for description).
modtype = SIR
#==============================================================#
[MODEL PARAMETERS]
#==============================================================#
# They can be specified as constants or as functions of global or
# site-specific variables. these site-specific variables, are provided
# in the sites file. All the numbers given after the geocode (4th column)
# are collected into the values tuple.
# If a multiple model is chosen, parameters must be specified as a tuple of size
# equal to the number of models per site.
# Examples:
# beta = 0.001
# beta=values[0] #assigns the first element of values to beta
# beta=0.001*values[1]
beta = 10 #transmission coefficient (contact rate * transmissibility)
alpha = 1 # clumping parameter
e = 0.1 # inverse of incubation period
r = 0.1 # inverse of infectious period
delta = 0 # probability of acquiring full immunity [0,1]
B = 0 # Birth rate
w = 0 # probability of immunity waning [0,1]
p = 0 # Probability of a recovered become infected per time step [0,1]
#==============================================================#
[INITIAL CONDITIONS]
#==============================================================#
# Here, the number of individuals in each epidemiological
# state (SEI) is specified. They can be specified in absolute
# or relative numbers.
# N is the population size of each site.
# The rule defined here will be applied equally to all sites.
# For site-specific definitions, use EVENTS (below)
# Examples:
# S,E,I = 0.8*N, 10, 0.5*E
# S,E,I = 0.5*N, 0.01*N, 0.05*N
# S,E,I = N-1, 1, 0
S = N
E = 0
I = 0
#=============================================================#
[EPIDEMIC EVENTS]
#=============================================================#
# Specify isolated events.
# Localities where the events are to take place should be Identified by the geocode, which
# comes after population size on the sites data file.
# All coverages must be a number between 0 and 1.
# Seed : [('locality1's geocode', n),('locality2's geocode', n)].
# N infected cases will be added to locality at time 0.
# Vaccinate: [('locality1's geocode', [t1,t2], [cov1,cov2]),('locality2's geocode', [t1,t2], [cov1,cov2])]
# Multiple vaccination campaigns with specific coverages can be specified as lists (see manual)
# Quarantine: [(locality1's geocode,time,coverage), (locality2's geocode,time,coverage)]
# Keywords may be used instead of the geocode in the vacinate and quarantine variables:
# all: Apply the same values to all sites
seed = [(4550603,'I',100)] #Rodoviaria 4550603
Vaccinate = []
Quarantine = []
# The following events have not yet been implemented
#Screening = (locality, time, coverage) #screening for sick people on aiports bus stations
#Vector_control = (locality, time, coverage)
#Prophylaxis = (locality, time, target, coverage, eficacy)
# Intervention acts reducing progression between epidemiological states
# target is the name of the modified parameter
# One may specify as many treatments as necessary
#
#Intervention = (locality, time, target, coverage, eficacy)
#Intervention = [('all', 0, 'pp1', 0.3, 0.5),('all', 0, 'pp2', 0.3, 0.5)]
#==============================================================#
[TRANSPORTATION MODEL]
#==============================================================#
# If doTransp = 1 the transportation dynamics will be included. Use 0 here only for debugging purposes.
doTransp = 1
# Mechanism can be stochatic (1) or deterministic(0).
stochastic = 0
#Average speed of transportation system in km per time step. Enter 0 for instantaneous travel.
#Distance unit must be the same specified in edges files
speed = 0 #1440 # km/day -- equivalent to 60 km/h
#==============================================================#
[SIMULATION AND OUTPUT]
#==============================================================#
# Number of steps
steps = 150
# Output dir. Must be a full path. If empty the output will be generated on the
# outdata-<date> sub-directory of same path as the model script.
outdir =
# Database Output
# SQLout can be 0 (no database output) or 1
SQLout = 1
# Report Generation
# The variable report can take the following values:
# 0 - No report is generated.
# 1 - A network analysis report is generated in PDF Format.
# 2 - An epidemiological report is generated in PDF Format.
# 3 - A full report is generated in PDF Format.
# siteRep is a list with site geocodes. For each site in this list, a detailed report is apended to the main report.
report = 0
siteRep = [4550603]
#Replicate runs
#If replicas is set to an integer(n) larger than zero, the model will be run n times and the results will be con-
#solidated before storing.
# if RandSeed is set to 1 the seed will be randomized on each replicate
#Replicate mode automatically turn off report and batch options.
Replicas = 0
RandSeed = 0
#Batch Run
# list other scripts to be run in after this one. don't forget the extension .epg
# model scripts must be in the same directory as this file or provide full path.
# Example: Batch = ['model2.epg','model3.epg','/home/jose/model4.epg']
Batch = []
################################################################
################################################################