Nothing
## ---- results='hide'----------------------------------------------------------
library(dplyr)
library(qpNCA)
library(knitr)
## -----------------------------------------------------------------------------
mutate_cond <- function (.data, condition, ..., envir = parent.frame()){
condition <- eval(substitute(condition), .data, envir)
if(!any(condition))return(.data) # do nothing if nothing to do
.data[condition, ] <- .data[condition, ] %>% mutate(...)
.data
}
locf <- function(x){
good <- !is.na(x)
positions <- seq(length(x))
good.positions <- good * positions
last.good.position <- cummax(good.positions)
last.good.position[last.good.position == 0] <- NA
x[last.good.position]
}
## ---- results="markup", warnings=F--------------------------------------------
head(Theoph) %>% kable()
input.data <- Theoph
#we need nominal time variable for some tasks.
ntad <- data.frame(rn=c(1:11),ntad=c(0,0.25,0.5,1,2,4,5,7,9,12,24))
input.data %<>%
group_by(Subject) %>%
mutate(subject=as.numeric(Subject),
rn=row_number(),
dose=Dose*Wt,
bloq=ifelse(conc==0,1,0),
loq=0.1,
excl_th=0
) %>%
left_join(ntad) %>%
ungroup %>%
arrange(subject,ntad) %>%
select(subject,ntad,tad=Time,conc,dose,bloq,loq,excl_th)
input.data %<>%
mutate_cond(condition=subject==2&ntad%in%c(24),conc=NA) %>%
mutate_cond(condition=subject==4&ntad%in%c(9),conc=NA) %>%
mutate_cond(condition=subject==3&ntad==9,excl_th=1) %>%
mutate_cond(condition=subject==6&ntad==24,conc=0,bloq=1) %>%
filter(!(subject==5&ntad==12))
## ---- results="markup", warnings=F, fig.width = 7-----------------------------
# Create a covariates file, containing at least the dose given
cov = input.data %>%
distinct(subject,dose)
nca = qpNCA(
input.data,
by = "subject",
nomtimevar = "ntad",
timevar = "tad",
depvar = "conc",
bloqvar = "bloq",
loqvar = "loq",
loqrule = 1,
includeCmax = "Y",
exclvar = "excl_th",
plotdir = NA,
timelab = "Time (h)",
deplab = "Conc (ng/mL)",
tau = 24,
tstart = 4,
tend = 9,
teval = 12,
covariates = cov,
dose = "dose",
factor = 1,
reg = "sd",
ss = "n",
route = "EV",
method = 1
)
## ---- results="markup", warnings=F, fig.width = 7-----------------------------
# Covariates:
nca$covariates %>% kable()
# Corrections applied:
nca$corrections %>% kable()
# half-life estimation:
nca$half_life %>% kable()
# PK parameters:
nca$pkpar %>% kable()
# Regression plots:
nca$plots
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