1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
|
################################################################
#
# 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 describe the network
# "shapefile" is the map layer that will be used as a background for
# the simulation display. It is defined as a list with three elements:
# the .shp filename, the variable containing the site's names,
# and the variable containing unique integers to be used as geocodes.
# ex: shapefile = ['shape.shp','sitename','sitecode']
# "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.
shapefile = []
sites = sitios3.csv
edges = edgesout.csv
encoding = utf8
#==============================================================#
[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 = Custom
#==============================================================#
[MODEL PARAMETERS]
#==============================================================#
# They can be specified as constants or as functions of global or
# site-specific variables. Site-specific variables are provided
# in the sites .csv file. In this file, all columns after the 4th
# are collected into a values tuple, which can be referenced here
# as values[0], values[1], values[2], etc.
# Examples:
# beta = 0.001
# beta=values[0] #assigns the first element of values to beta
# beta=0.001*values[1]
# beta=0.001*N # N is a global name for total site population
# Currently, Epigrass requires that parameters beta, alpha, e, r, delta, B, w, p
# be present in the .epg even if they will not be used. Do not erase these lines.
# Just disregard them if they are not useful to you.
# Required parameters
beta = 0.6 #transmission coefficient Lipsitch 2003 for R0 = 3
alpha = 1 # clumping parameter
e = 1 # inverse of incubation period
r = 0.1 # inverse of infectious period
delta = 1 # 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), at time 0, 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
# Note. Epigrass expects to find S,E,I here. If not, an error will occur
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', variable, n),('locality2's geocode',variable, 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 variable:
# all: Apply the same values to all sites
seed = [(355030800,'I',1)] #Sao Paulo
Vaccinate = []
Quarantine = []
# The following events have not yet been implemented
# Quarantine
# 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 simulated; doTransp=0, otherwise
doTransp = 1
# Transportation Simulation can be stochatic (1) or deterministic(0).
stochastic = 1
#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 = 100
# 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
# MySQLout can be 0 (no database output) or 1
MySQLout = 1
# 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 consolidated before storing.
# RandSeed = 1: the seed will be randomized on each replicate
# RandSeed = 2: seeds are taken sequentially from the site's file
# Note: 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 = []
################################################################
################################################################
|
