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Parameters
John Grefenstette edited this page Sep 12, 2015
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parameter: days
default value: 240
type: INT
definition:
The number of days in a single simulation run. FRED runs for the given
number of days regardless of the epidemic state (that is, FRED does not
stop early if no one is currently infected.)
parameter: start_date
default value: 2012-01-02
type: STRING
definition:
The value used as the start date for each simulation run. The format is
YYYY-MM-DD.
parameter: seed
default value: 123456
type: INT
definition:
The seed for the random number generator. The seed values for all runs
of the simulation are based on the initial seed and the run number, and
are independent of the number of random numbers generated in other runs.
The user should not normally have to change the seed value.
parameter: verbose
default value: 1
type: INT
definition:
If set, print information for monitoring system progress to the LOG
file. Higher values produce more (probably too much) output.
parameter: debug
default value: 0
type: INT
definition:
If set, print verbose debugging output to stdout. Higher values produce
more output.
parameter: outdir
default value: OUT
type: STRING
definition:
The directory containing the output files. If the string beings with "/"
it is interpreted as an absolute path. If it begins with "$FRED_HOME/",
it is relative the ${FRED_HOME} directory. Otherwise, it is relative to
the current working directory.
parameter: quality_control
default value: 1
type: INT
definition:
If set, information about the size and age distribution for the various
types of places is printed out in the Log file.
parameter: report_age_of_infection
default value: 0
type: INT
definition:
If set, the output file includes info on daily incidence by age groups. You get
different info depending on the value of the parameter.
report_age_of_infection = 1
The output includes variables giving the daily incidence counts for the
following age groups (not including the upper bounds):
Infants: 0.0 - 0.5 yrs
Toddlers: 0.5 - 2.0
Pre_School: 2 - 6
Elementary 6 - 12
High_School: 12 - 18
Young_Adults: 18 - 21
Adults: 21 - 65
Elderly: 65 - 120
report_age_of_infection = 2
A slightly different set of age groups:
Infants: 0.0 - 1.5 yrs
Toddlers: 1.5 - 2.0
Pre_School: 2 - 5
Elementary 5 - 12
High_School: 12 - 18
Young_Adults: 18 - 21
Adults: 21 - 65
Elderly: 65 - 120
report_age_of_infection = 3
The output will include variables
A0, A1, ..., A120
which give the daily counts for new infections in people in each yearly
age group, and also variables
Age0, Age1, ... Age120
which give the daily counts per 100,000 people in each yearly age group.
parameter: report_place_of_infection
default value: 0
type: INT
definition:
If set to 1, the output file contains the daily incidence count by place
of infection, including the following:
X: number of people externally infected (seeds).
H: number of people infected in households.
Nbr: number of people infected in neighborhoods.
Sch: number of people infected in schools.
Cls: number of people infected in classrooms.
Wrk: number of people infected in workplaces.
Off: number of people infected in offices.
Hosp: number of people infected in hospitals.
parameter: report_generation time
default value: 0
type: INT
definition:
If set to 1, the output file contains the mean generation time for all
infections occurring on the given day. The generation time (or serial
interval) is defined as the number of days between the infection of the
infector and the current infectee.
The output variable for gneration time is "Tg".
parameter: report_serial_interval
default value: 0
type: INT
definition:
If set to 1, the output file contains the mean generation time for all
infections occurring on the given day. The generation time (or serial
interval) is defined as the number of days between the infection of the
infector and the current infectee.
The output variable for gneration time is "Tg".
parameter: report_incidence_by_county
default value: 0
type: INT
definition:
If set, the output file contains a daily report of incidence based on
the household of each infected person. The output variable is
"County_NNNNN", where NNNNN is the five digit FIPS code for the county.
For example, County_42003 for the incidence of Allegheny County, PA.
parameter: track_infection_events
default value: 0
type: INT
definition:
If set, then a file called infections<n>.txt is created for run <n>.
This file contains one line per disease transmission event, showing the
id of the infector, the infectee, and various other information. The
format for the infections file is:
DAY DISEASE_ID HOST_ID HOST_AGE INFECTOR_ID INFECTOR_AGE PLACE_ID
If track_infection_events > 1, additional data is written on each line.
For further details, see: Infection.cc.
© 2012-2015 [Public Health Dynamics Laboratory] (http://www.phdl.pitt.edu "PHDL website"), University of Pittsburgh