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dismodat.py database csv2db configure_csv measure_csv
dismod_at.csv2db_command(database, configure_csv, measure_csv)
mtall
in the
measure_csv
file has special meaning.
We assume it has been converted to constraints on other cause
mortality; see mtother
below.
For this reason, it should not be included when fitting,
and is only in
measure_csv
as a check that the desired values
are satisfied (by checking residuals in a data fit).
For this reason, hold_out
must be
one for all the mtall data; i.e., it is not included during a fit.
mtother
in the
measure_csv
file has special meaning.
It is intended to represent the all cause mortality data
as constraints on other cause mortality in the model.
To be specific, the meas_value
is a constraint on @(@
\omega
@)@ at the corresponding age-time pairs.
integrand = mtother
must have
age_lower == age_upper
and
time_lower == time_upper
.
mtother data must be specified on a rectangular grid; i.e.,
each age that appears, appears in one and only one row for every time
that appears.
This property can also be stated as
each time that appears, appears in one and only one row for every age
that appears.
mtother data because
it is a constraint, not data, during a fit.
mtother data.
In other words, they are modeled as piecewise bilinear between the
age-time points at which mtother is specified.
str containing the name of the dismod_at database
file that is written by this command.
str containing the configuration file name and must
end with the .csv extension.
The first row contains the following column names
name, value.
Column names that begin with c_ are comments
and will not be used by future versions of csv2db.
The configuration options are documented by the corresponding
name below.
value
in this row is a list rates that are non-zero
in the model.
The possible rates are
pini, iota, rho, chi, omega.
The rates in the list are separated by a single space
and omega must appear in the list.
There is no default value for this value; i.e., it must appear.
str containing the data file name
and must end with the .csv extension.
Each row of the data file corresponds to one data point.
The first row of the file contains the column names.
The other rows correspond to data points.
Each column of the necessary columns in the data file is documented
under its column name below.
Column names that begin with c_ are comments
and will not be used by future versions of csv2db.
measure_csv
contains
one of the valid integrands:
measure_csv
contains
The initial age for averaging the integrand for this row; @(@
b
@)@.
measure_csv
contains
the final age for averaging the integrand for this row; @(@
c
@)@.
measure_csv
contains
the initial time for averaging the integrand for this row; @(@
r
@)@.
measure_csv
contains
the final time for averaging the integrand for this row; @(@
s
@)@.
measure_csv
contains
the value of the average integrand plus measurement noise
@[@
e + \frac{1}{c-b} \frac{1}{s-r} \int_b^c \int_r^s I(a , t) \; da \; dt
@]@
where @(@
e
@)@ is the measurement noise,
@(@
a
@)@ and @(@
t
@)@ are the age and time integration variables,
and @(@
I(a, t)
@)@ is the value of the integrand for this row.
measure_csv
contains
the standard deviation of the measurement noise @(@
e
@)@.
measure_csv
contains
either zero or one. If it is one, this row is included
dismod_at fits. Otherwise it is excluded.
In either case, the residuals are computed for this row.