Parameters

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PARAM NAME: 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.)

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PARAM NAME: start_date

DEFAULT VALUE: 2012-01-02
TYPE: string

DEFINITION: The calendar date used as the start date for each simularion
run. The format is YYYY-MM-DD.

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PARAM NAME: 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.

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PARAM NAME: 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.

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PARAM NAME: debug

DEFAULT VALUE: 0
TYPE: int

DEFINITION: If set, print verbose debugging output to stdout. Higher
values produce more output.

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PARAM NAME: 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.

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PARAM NAME: 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.

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PARAM NAME: report_age_of_infection

DEFAULT VALUE: 0
TYPE: int

DEFINITION: If set, the output file 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.

---

PARAM NAME: 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.

---

PARAM NAME: report_distance_of_infection

DEFAULT VALUE: 0
TYPE: int
DEFINITION:

---

PARAM NAME: report_presenteeism

DEFAULT VALUE: 0
TYPE: int
DEFINITION:

---

PARAM NAME: 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".

---

PARAM NAME: 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".

---

PARAM NAME: report_incidence_by_county

DEFAULT VALUE: 0
TYPE: int

DEFINITION: If set, the putput file contains a daily report of incidence
based on the household of each infected person.  The ourpur 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.

---

PARAM NAME: report_incidence_by_census_tract

DEFAULT VALUE: 0
TYPE: int
DEFINITION:

---

PARAM NAME: 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.

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PARAM NAME: track_age_distribution

DEFAULT VALUE: 0
TYPE: int

DEFINITION: 

---

PARAM NAME: track_household_distribution

DEFAULT VALUE: 0
TYPE: int
DEFINITION:

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PARAM NAME: track_network_stats

DEFAULT VALUE: 0
TYPE: int
DEFINITION:

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