Description Usage Arguments Value Examples
Consecutively executes the following NCA steps:
correct.loq impute LOQ values
est.thalf calculate lambda_z and half-life
plot_reg plot each regression curve
calc.ctmax calculate Cmax and Tmax
correct.time correct time deviations at critical time points
correct.conc impute missing concentrations at critical time points
tab.corr tabulate data alterations
calc.par calculates parameters not dependent on lambda_z
calc.par.th calculates parameters dependent on lambda_z
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | qpNCA(
x,
by = character(0),
nomtimevar = "ntad",
timevar = "time",
depvar = "dv",
bloqvar = "bloq",
loqvar = "loq",
loqrule = 1,
includeCmax = "Y",
exclvar = NA,
plotdir = NA,
timelab = "timevar",
deplab = "depvar",
tau = NA,
tstart = NA,
tend = NA,
teval = NA,
covariates = NA,
dose = "dose",
factor = 1,
reg = "SD",
ss = "N",
route = "EV",
method = 1
)
|
x |
input dataset name |
by |
column names in x indicating grouping variables |
nomtimevar |
variable name containing the nominal sampling time after dose |
timevar |
variable name containing the actual sampling time after dose |
depvar |
variable name containing the dependent variable (e.g., concentration) |
bloqvar |
variable name containing the BLOQ flag (0: no, 1: yes) |
loqvar |
variable name containing the LOQ value |
loqrule |
rule number to be applied to the LOQ values in the curve; x$loqrule overrides if provided |
includeCmax |
include Cmax in half-life estimation? (y/n); x$includeCmax overrides if provided |
exclvar |
variable name indicating points to be excluded in half-life estimation (these should have exclvar = 1) |
plotdir |
directory where regression plots (.PNG) will be saved; NA gives default location, NULL skips regression plots |
timelab |
label for time axis in regression plots |
deplab |
label for dependent variable axis in regression plots |
tau |
dosing interval (for multiple dosing); NA (default) if single dose; x$tau overrides |
tstart |
start time of partial AUC (start>0); NA (default) if not requested; x$tstart overrides |
tend |
end time of partial AUC; NA (default) if not requested; x$tend overrides |
teval |
user selected AUC interval (starting at t=0); NA (default) if not requested; x$teval overrides |
covariates |
covariates dataset; Must contain the dose variable |
dose |
variable containing the dose amount |
factor |
conversion factor for CL and V calculation (e.g. dose in mg, conc in ng/mL, factor=1000); x$factor overrides if provided |
reg |
regimen, "SD" or "MD"; x$reg overrides if provided |
ss |
is steady state reached (y/n); x$ss overrides if provided |
route |
route of drug administration ("EV","IVB", "IVI"); x$route overrides if provided |
method |
method for trapezoidal rule; x$method overrides if provided
|
(list)
covariates covariates selected with the covariates
argument
half_life linear regression parameters
ct_corr the time and concentration corrected dataset
corrections descriptions of the corrections applied
pkpar all estimated PK parameters
plots generated plots
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | library(magrittr)
library(dplyr)
library(qpNCA)
x <- Theoph
ntad <- c(0,0.25,0.5,1,2,4,5,7,9,12,24)
for(i in 1:nrow(x)){
time <- x$Time[[i]]
delta <- abs(ntad - time)
best <- min(delta)
index <- match(best, delta)
nom <- ntad[[index]]
x$ntad[[i]] <- nom
}
rm(list = c('time','delta','best','index','nom', 'i','ntad'))
x %<>% rename(time = Time, dv = conc, subject = Subject)
x %<>% mutate(bloq = 0, loq = 0.01, tad = time,excl_th=0,
subject=as.numeric(subject),ntad=as.numeric(ntad))
x %<>% filter(dv > 0)
covs <- x %>%
select(subject, Wt, dose = Dose) %>%
distinct(subject,.keep_all=TRUE) %>%
mutate(dose = dose * Wt) # see ?Theoph
z <- qpNCA(x, by = 'subject', covariates = covs, exclvar='excl_th')
|
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