- conc
concentration data, the output of run_DrugLevel,
a filename (CSV, RData, RDS), or a correctly formatted data.frame
- conc.columns
a named list that should specify columns in concentration
data; ‘id’, ‘datetime’, ‘druglevel’ are required.
‘idvisit’ may also be specified; ‘idvisit’ can be used when there are multiple visits
(i.e., several occasions) for the same subject. ‘datetime’ is date and time for
concentration measurement, which can refer to a single date-time variable
(datetime = ‘date_time’) or two variables holding date and time
separately (e.g., datetime = c(‘Date’, ‘Time’)).
- dose
dose data, the output of run_MedStrI, a filename
(CSV, RData, RDS), or a correctly formatted data.frame
- dose.columns
a named list that should specify columns in dose data;
‘id’ is required. ‘infuseDatetime’ and ‘infuseDose’
should be set if infusion dose data is present. ‘infuseTimeExact’
may also be specified for infusion data -- this variable represents an
precise time, if for example the ‘infuseDatetime’ variable is rounded.
‘bolusDatetime’ and ‘bolusDose’ should be set if bolus dose
data is present. A generic ‘date’ variable may be provided, agnostic
to either infusion or bolus dosing. ‘gap’ and ‘weight’ column
names may also be set. Any of the date-time variables can be specified as a
single date-time variable (infuseDatetime = ‘date_time’) or two variables
holding date and time separately (e.g., infuseDatetime = c(‘Date’, ‘Time’)).
- censor
censoring information, if available; this will censor concentration
and dose data for dates occuring after the censor datetime variable.
- censor.columns
a named list that should specify columns in censoring data; ‘id’,
and ‘datetime’ are required. ‘datetime’ is the date and time when
data should be censored. This can refer to a single date-time variable
(datetime = ‘date_time’) or two variables holding date and time separately
(e.g., datetime = c(‘Date’, ‘Time’)).
- demo.list
demographic information, if available; the output from
run_Demo or a correctly formatted data.frame
- demo.columns
a named list that should specify columns in demographic data;
‘id’ is required. ‘weight’ and ‘idvisit’
may also be used to specify columns for weight or the unique idvisit. Any other columns
present in the demographic data are treated as covariates.
- lab.list
lab data, if available; the output from run_Labs or
a correctly formatted list
- lab.columns
a named list that should specify columns in lab data; ‘id’,
and ‘datetime’ are required. ‘datetime’ is the date and time when
the lab data was obtained, which can refer to a single date-time variable
(datetime = ‘date_time’) or two variables holding date and time separately
(e.g., datetime = c(‘Date’, ‘Time’)). Any other columns present in lab
data are treated as lab values.
- dosePriorWindow
Dose data is merged with drug level data. This value sets the
time frame window with the number of days prior to the first drug level data; defaults to 7.
- labPriorWindow
Lab data is merged with drug level data. This value sets the
time frame window with the number of days prior to the first drug level data; defaults to 7.
- postWindow
Data is merged with drug level data. This postWindow can set the end time
for the drug level data, being the number of days after the first drug level data. The
default (NA) will use the date of the last drug level data.
- pk.vars
variables to include in the returned PK data. The variable ‘date’
is a special case; when included, it maps the ‘time’ offset to its original date-time.
Other named variables will be merged from the concentration data set. For example,
rather than being separate data sets, labs or demographics may already be present in
the concentration data. These columns should be named here.
- drugname
drug of interest, included in filename of check files. The default (NULL)
will produce filenames without drugname included.
- check.path
path to ‘check’ directory, where check files are
created. The default (NULL) will not produce any check files.
- missdemo_fn
filename for checking NA frequency among demographic data
- faildupbol_fn
filename for duplicate bolus data
- date.format
output format for ‘date’ variable
- date.tz
output time zone for ‘date’ variable
- isStrict
logical; when TRUE dose amount totals are strictly summed rather than repeated
hourly until stopped