The input data set (data_set) is a data frame that specifies
observations, model events, and / or parameter values for a population
of individuals.
data_set(x, data, ...)# S4 method for mrgmod,data.frame
data_set(
x,
data,
.subset = TRUE,
.select = TRUE,
object = NULL,
need = NULL,
...
)
# S4 method for mrgmod,ANY
data_set(x, data, ...)
# S4 method for mrgmod,ev
data_set(x, data, ...)
# S4 method for mrgmod,missing
data_set(x, object, ...)
a model object.
input data set as a data frame.
other arguments passed along when object is a function.
an unquoted expression passed to
dplyr::filter(); retain only certain rows in the data set
passed to dplyr::select(); retain only certain
columns in the data set; this should be the result of a call to
dplyr::vars().
character name of an object existing in $ENV
to use for the data set.
passed to inventory().
Input data sets are R data frames that can include columns
with any valid name, however columns with selected names are
treated specially by mrgsolve and incorporated into the
simulation.
ID specifies the subject ID and is required for every
input data set.
When columns have the same name as parameters ($PARAM or $INPUT in
the model specification file), the values in those columns will
be used to update the corresponding parameter as the simulation
progresses.
Input data set may include the following columns related to
PK dosing events: TIME, CMT, AMT, RATE, II, ADDL, SS.
Both ID and TIME are required columns in the input data set unless
$PRED is in use. Lower case PK dosing column names including
time, cmt, amt, rate, ii, addl, ss are also recognized.
However, an error will be generated if a mix of both upper case and lower
case columns in this family are found. Use the functions lctran() and
uctran() to convert between upper and lower case naming for these
data items.
TIME is the observation or event time, CMT is the compartment number
(see init()), AMT is the dosing amount, RATE is the infusion rate,
II is the dosing interval, ADDL specifies additional doses to
administer, and ss is a flag indicating that the system should be advanced
to a pharmacokinetic steady state prior to administering the dose. These
column names operate similarly to other non-linear mixed effects modeling
software.
EVID is an integer value specifying the ID of an event record. Values
include:
0: observation
1: dose event, either bolus or infusion
2: other-type event; in mrgsolve, this functions like an observation record, but a discontinuity is created in the simulation at the time of the event (i.e., the ODE solver will stop and restart at the time of the event)
3: reset the system
4: reset the system and dose
8: replace the amount in a compartment
For all EVID greater than 0, a discontinuity is created in the
simulation, as described for EVID 2.
An error will be generated when mrgsolve detects that the data set
is not sorted by time within an individual. mrgsolve does not allow time
to be reset to zero on records where EVID is set to 4 (reset and dose).
Only numeric data can be brought in to the problem. Any non-numeric data
columns will be dropped with warning. See numerics_only(), which is used
to prepare the data set.
An error will be generated if any parameter columns in the
input data set contain missing values (NA). Likewise, and error will
be generated if missing values are found in the following
columns: ID, time/TIME, rate/RATE.
See exdatasets for several example data sets that are provided by mrgsolve.
idata_set(), ev(), valid_data_set(), valid_idata_set(),
lctran(), uctran().
mod <- mrgsolve::house()
data <- expand.ev(ID = seq(3), amt = c(10, 20))
mod %>% data_set(data, ID > 1) %>% mrgsim()
data(extran1)
head(extran1)
mod %>% data_set(extran1) %>% mrgsim()
mod %>% mrgsim(data = extran1)
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