Usage
ncappc(obsFile = "nca_original.npctab.dta", simFile = "nca_simulation.1.npctab.dta", str1Nm = NULL, str1 = NULL, str2Nm = NULL, str2 = NULL, str3Nm = NULL, str3 = NULL, concUnit = NULL, timeUnit = NULL, doseUnit = NULL, doseNormUnit = NULL, obsLog = FALSE, simLog = FALSE, psnOut = TRUE, idNmObs = "ID", timeNmObs = "TIME", concNmObs = "DV", idNmSim = "ID", timeNmSim = "TIME", concNmSim = "DV", AUCTimeRange = NULL, backExtrp = FALSE, LambdaTimeRange = NULL, LambdaExclude = NULL, doseAmtNm = NULL, adminType = "extravascular", doseType = "ns", doseTime = NULL, Tau = NULL, TI = NULL, method = "linear-log", blqNm = NULL, blqExcl = 1, evid = TRUE, evidIncl = 0, mdv = FALSE, filterNm = NULL, filterExcl = NULL, negConcExcl = FALSE, param = c("AUClast", "Cmax"), timeFormat = "number", dateColNm = NULL, dateFormat = NULL, spread = "npi", tabCol = c("AUClast", "Cmax", "Tmax", "AUCINF_obs", "Vz_obs", "Cl_obs", "HL_Lambda_z"), figFormat = "tiff", noPlot = FALSE, printOut = TRUE, studyName = NULL, new_data_method = TRUE, overwrite_SIMDATA = NULL, outFileNm = NULL)
Arguments
obsFile
Observed concentration-time data from an internal data frame
or an external table with comma, tab or space as separator
("nca_original.npctab.dta")
simFile
NONMEM simulation output with the simulated concentration-time
data from an internal data frame or an external table
("nca_simulation.1.npctab.dta"). NULL
produces just the
traditional NCA output, a filename or data frame prduces the NCA output as
well as the PopPK diagnosis. If new_data_method=TRUE
then this can
be a compressed file as well.
str1Nm
Column name for 1st level population stratifier
(NULL
)
str1
Stratification ID of the members within 1st level stratification
(e.g c(1,2)) (NULL
)
str2Nm
Column name for 2nd level population stratifier
(NULL
)
str2
Stratification ID of the members within 2nd level stratification
(e.g c(1,2)) (NULL
)
str3Nm
Column name for 3rd level population stratifier
(NULL
)
str3
Stratification ID of the members within 3rd level stratification
(e.g c(1,2)) (NULL
)
concUnit
Unit of concentration (e.g. "ng/mL") ("M.L^-3")
timeUnit
Unit of time (e.g. "h") ("T")
doseUnit
Unit of dose amount (e.g. "ng") ("M")
doseNormUnit
Normalization factor of dose amount if used (e.g. "kg")
(NULL
)
obsLog
Concentration in observed data in logarithmic form
(TRUE
, FALSE
) (FALSE
)
simLog
Concentration in simulated data in logarithmic form
(TRUE
, FALSE
) (FALSE
)
psnOut
observed data is an output from PsN or in NONMEM output format
(TRUE
, FALSE
) (TRUE
)
idNmObs
Column name for ID in observed data ("ID")
timeNmObs
Column name for time in observed data ("TIME")
concNmObs
Column name for concentration in observed data
("DV")
idNmSim
Column name for ID in simulated data ("ID")
timeNmSim
Column name for time in simulated data ("TIME")
concNmSim
Column name for concentration in simulated data
("DV")
AUCTimeRange
User-defined window of time used to estimate AUC
(NULL
)
backExtrp
If back-extrapolation is needed for AUC (TRUE
or
FALSE
) (FALSE
)
LambdaTimeRange
User-defined window of time to estimate elimination
rate-constant. This argument lets the user to choose a specific window of
time to be used to estimate the elimination rate constant (Lambda) in the
elimination phase. The accepted format for the input to this argument is a
numeric array of two elements; c(14,24)
will estimate the Lambda
using the data within the time units 14 to 24. If NULL
then all
times are considered.
LambdaExclude
User-defined excluded observation time points for
estimation of elimination rate-constant (NULL
)
doseAmtNm
Column name to specify dose amount (NULL
)
adminType
Route of administration
(iv-bolus,iv-infusion,extravascular) ("extravascular")
doseType
Steady-state (ss) or nonsteady-state (ns) dose
("ns")
doseTime
Dose time prior to the first observation for steady-state data (NULL
)
Tau
Dosing interval for steady-state data (NULL
)
TI
Infusion duration (NULL
)
method
linear, log or linear-log ("linear-log")
blqNm
Name of BLQ column if used (NULL
)
blqExcl
Excluded BLQ value or logical condition (e.g. 1 or ">=1" or
c(1,">3")) ("1")
evid
Use EVID (TRUE
, FALSE
) (TRUE
)
evidIncl
Included EVID ("0")
mdv
Use MDV (TRUE
(includes data for MDV==0), FALSE
)
(FALSE
)
filterNm
Column name for filter (NULL
)
filterExcl
Filter identifier or logical condition used for row
exclusion (e.g. c(1, 2, "<20", "="">=100", "!=100")) (NULL
)20",>
negConcExcl
Exclude -ve conc (FALSE
)
param
NCA parameters (AUClast, AUClower_upper, AUCINF_obs,
AUCINF_pred, AUMClast, Cmax, Tmax, HL_Lambda_z) (c("AUClast",
"Cmax"))
timeFormat
time format (number, H:M, H:M:S) ("number")
dateColNm
colunm name for date if used (Date, DATE)
(NULL
)
dateFormat
date format (D-M-Y, D/M/Y or any other combination of
D,M,Y) (NULL
)
spread
Measure of the spread of simulated data ("ppi"
(95%
parametric prediction interval) or "npi"
(95% nonparametric
prediction interval))
tabCol
Output columns to be printed in the report in addition to ID,
dose and population strata information (list of NCA metrics in a string
array) (c("AUClast", "Cmax", "Tmax", "AUCINF_obs", "Vz_obs",
"Cl_obs", "HL_Lambda_z"))
figFormat
format of the produced figures (bmp, jpeg, tiff, png)
("tiff")
noPlot
Perform only NCA calculations without any plot generation
(TRUE
or FALSE
)
printOut
Write/print output on the disk. No plot will be saved if
noPlot is set to TRUE
(TRUE
, FALSE
)
(TRUE
)
studyName
Name of the study to be added as a description in the report
(NULL
)
new_data_method
TRUE
or FALSE
. For testing a faster
method of reading data. (TRUE
)
overwrite_SIMDATA
Can be TRUE
, to create new information in the
SIMDATA directory, FALSE
, to use the information in the SIMDATA
directory or NULL
to have a dialog come up to ask the user what to
do. (NULL
)
outFileNm
Additional tag to the name of the output html and pdf output
file hyphenated to the standard ncappc report file name standard ncappc
report file name (Name of the observed data file)