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ncappc_func.r
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library(ncappc)
Loading required package: ggplot2
Loading required package: gridExtra
> ncappc
function (obsFile = NULL, simFile = NULL, grNm = NULL, grp = NULL,
flNm = NULL, flag = NULL, doseNm = NULL, dose = NULL, concUnit = NULL,
timeUnit = NULL, doseUnit = NULL, doseNormUnit = NULL, obsLog = "FALSE",
simLog = "FALSE", psnOut = "FALSE", 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", Tau = NULL, TI = NULL, method = "mixed",
blqNm = NULL, blqExcl = 1, evid = "FALSE", 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)
{
"..density.." <- "meanObs" <- "sprlow" <- "sprhgh" <- "AUClast" <- "AUCINF_obs" <- "Cmax" <- "Tmax" <- "FCT" <- "ID" <- "GROUP" <- "FLAG" <- "NPDE" <- "mcil" <- "mciu" <- "sdu" <- "sducil" <- "sduciu" <- "scale_linetype_manual" <- "scale_color_manual" <- "xlab" <- "ylab" <- "guides" <- "guide_legend" <- "theme" <- "element_text" <- "unit" <- "element_rect" <- "geom_histogram" <- "aes" <- "geom_vline" <- "grid.arrange" <- "unit.c" <- "grid.grab" <- "ggsave" <- "facet_wrap" <- "ggplot" <- "labs" <- "geom_point" <- "geom_errorbarh" <- "knit2html" <- "knit2pdf" <- "knit" <- "file_test" <- "tail" <- "read.csv" <- "read.table" <- "dev.off" <- "write.table" <- "head" <- "write.csv" <- "coef" <- "dist" <- "lm" <- "median" <- "na.omit" <- "percent" <- "qchisq" <- "qnorm" <- "qt" <- "quantile" <- "scale_y_continuous" <- "sd" <- NULL
rm(list = c("..density..", "meanObs", "sprlow", "sprhgh",
"AUClast", "AUCINF_obs", "Cmax", "Tmax", "FCT", "ID",
"GROUP", "FLAG", "NPDE", "mcil", "mciu", "sdu", "sducil",
"sduciu", "scale_linetype_manual", "scale_color_manual",
"xlab", "ylab", "guides", "guide_legend", "theme", "element_text",
"unit", "element_rect", "geom_histogram", "aes", "geom_vline",
"grid.arrange", "unit.c", "grid.grab", "ggsave", "facet_wrap",
"ggplot", "labs", "geom_point", "geom_errorbarh", "knit2html",
"knit2pdf", "knit", "file_test", "tail", "read.csv",
"read.table", "dev.off", "write.table", "head", "write.csv",
"coef", "dist", "lm", "median", "na.omit", "percent",
"qchisq", "qnorm", "qt", "quantile", "scale_y_continuous",
"sd"))
options(warning.length = 5000)
options(scipen = 999)
usrdir <- getwd()
if (is.null(obsFile)) {
stop("Name of the file with observed data is required\n")
}
if (!is.data.frame(obsFile)) {
if (!file_test("-f", obsFile)) {
stop("File for the observed data does not exist\n")
}
if (psnOut == "FALSE") {
extn <- tail(unlist(strsplit(obsFile, ".", fixed = T)),
n = 1)
if (extn == "csv") {
indf <- read.csv(obsFile)
}
else {
indf <- read.table(obsFile, header = T)
}
}
else if (psnOut == "TRUE") {
indf <- read.table(obsFile, header = T, skip = 1)
}
}
else {
indf <- obsFile
}
refdf <- indf
if ((!is.null(simFile)) && (!is.data.frame(simFile)) && (!file_test("-f",
simFile))) {
stop("File for the simulated data does not exist\n")
}
if (doseType == "ss" && (is.null(Tau))) {
setwd(usrdir)
stop("Dosing interval is required for steady-state data\n")
}
if (idNmObs %in% colnames(indf) == F | timeNmObs %in% colnames(indf) ==
F | concNmObs %in% colnames(indf) == F) {
setwd(usrdir)
stop("Incorrect column names of ID, TIME and/or DV\n")
}
else {
idCol <- which(colnames(indf) == idNmObs)
id <- unique(indf[, idCol])
timeCol <- which(colnames(indf) == timeNmObs)
concCol <- which(colnames(indf) == concNmObs)
}
if (!is.null(filterNm)) {
if (filterNm %in% colnames(indf) == T & !is.null(filterExcl)) {
filterCol <- which(colnames(indf) == filterNm)
for (i in 1:length(filterExcl)) {
if (grepl("^[-]?[0-9]*[.]?[0-9]*[eE]?[-]?[0-9]*[.]?[0-9]*$",
filterExcl[i])) {
indf <- indf[indf[, filterCol] != filterExcl[i],
]
}
else {
indf <- eval(parse(text = paste("subset(indf, !",
filterNm, "%in% indf[indf[,", filterCol,
"]", filterExcl[i], ",filterCol])", sep = "")))
}
}
}
else {
setwd(usrdir)
stop("Incorrect filterNm or filterExcl specification\n")
}
}
if (!is.null(grNm)) {
if (grNm %in% colnames(indf) == F) {
setwd(usrdir)
stop("Incorrect name for the group column\n")
}
else {
grCol <- which(colnames(indf) == grNm)
}
if (is.null(grp)) {
grp <- unique(sort(indf[, grCol]))
}
ngrp <- length(grp)
for (i in 1:ngrp) {
if (nrow(indf[indf[, grCol] == grp[i], ]) == 0) {
setwd(usrdir)
stop("Group identifier does not match the group column\n")
}
}
}
if (!is.null(flNm)) {
if (flNm %in% colnames(indf) == F) {
setwd(usrdir)
stop("Incorrect name for the flag column\n")
}
else {
flCol <- which(colnames(indf) == flNm)
}
if (is.null(flag)) {
flag <- unique(indf[, flCol])
}
nflag <- length(flag)
for (i in 1:nflag) {
if (nrow(indf[indf[, flCol] == flag[i], ]) == 0) {
setwd(usrdir)
stop("Flag identifier does not match the flag column\n")
}
}
}
if ((!is.null(AUCTimeRange)) && (length(AUCTimeRange) !=
2 | class(AUCTimeRange) != "numeric")) {
setwd(usrdir)
stop("Incorrect time range for AUC calculation\n")
}
if ((!is.null(LambdaTimeRange)) && (length(LambdaTimeRange) !=
2 | class(LambdaTimeRange) != "numeric")) {
setwd(usrdir)
stop("Incorrect time range for Lambda calculation\n")
}
if (adminType == "iv-infusion" & is.null(TI) & ("AMT" %in%
colnames(indf) == F | "RATE" %in% colnames(indf) == F)) {
setwd(usrdir)
stop("Duration of the infusion time is needed if AMT and RATE are absent in the input data\n")
}
if (!is.null(simFile)) {
backExtrp <- "FALSE"
}
if (!is.null(doseNm)) {
if (doseNm %in% colnames(indf) == F) {
setwd(usrdir)
stop("Incorrect name for the dose column\n")
}
else {
doseCol <- which(colnames(indf) == doseNm)
}
oidNm <- doseNm
if (is.null(dose)) {
dose <- unique(sort(indf[, doseCol]))
}
ndose <- length(dose)
for (i in 1:ndose) {
if (nrow(indf[indf[, doseCol] == dose[i], ]) == 0) {
setwd(usrdir)
stop("Dose identifier does not match the dose column\n")
}
}
}
else {
oidNm <- "OID"
dose <- 1
ndose <- 1
}
if (is.null(doseAmtNm)) {
if ("AMT" %in% colnames(indf) == F) {
setwd(usrdir)
stop("Dose amount column is required as AMT column is absent\n")
}
doseAmtNm <- "AMT"
}
if (is.null(doseUnit))
doseUnit <- "[M]"
dunit <- ifelse(is.null(doseNormUnit), doseUnit, paste(doseUnit,
"/", doseNormUnit))
tunit <- ifelse(is.null(timeUnit), "T", timeUnit)
cunit <- ifelse(is.null(concUnit), "M.L^-3", concUnit)
if (!is.null(blqNm)) {
if (blqNm %in% colnames(indf) == T) {
blqCol <- which(colnames(indf) == blqNm)
for (i in 1:length(blqExcl)) {
if (grepl("^[-]?[0-9]*[.]?[0-9]*[eE]?[-]?[0-9]*[.]?[0-9]*$",
blqExcl[i]) == T) {
indf <- indf[indf[, blqNm] != blqExcl[i], ]
}
if (grepl("^[-]?[0-9]*[.]?[0-9]*[eE]?[-]?[0-9]*[.]?[0-9]*$",
blqExcl[i]) == F) {
indf <- eval(parse(text = paste("subset(indf, !",
blqNm, "%in% indf[as.numeric(as.character(indf[,",
blqCol, "]))", blqExcl[i], ",blqCol])", sep = "")))
}
}
}
else {
setwd(usrdir)
stop("Incorrect BLQ column name\n")
}
}
if ((evid == "TRUE") & ("EVID" %in% colnames(indf) == T)) {
uevid <- unique(as.numeric(as.character(indf$EVID)))
ievid <- setdiff(uevid, as.numeric(evidIncl))
if (length(ievid) != 0) {
for (i in 1:length(ievid)) {
indf <- indf[indf$EVID != ievid[i], ]
}
}
}
if (mdv == "TRUE") {
if ("MDV" %in% colnames(indf) == T) {
indf <- indf[indf$MDV == 0, ]
}
}
if (!is.null(dateColNm)) {
if (dateColNm %in% colnames(indf) == F) {
setwd(usrdir)
stop("Incorrect name for the date column\n")
}
if (dateFormat == "D-M-Y") {
dateFormat <- "%d-%m-%Y"
}
else if (dateFormat == "D-Y-M") {
dateFormat <- "%d-%Y-%m"
}
else if (dateFormat == "M-D-Y") {
dateFormat <- "%m-%d-%Y"
}
else if (dateFormat == "M-Y-D") {
dateFormat <- "%m-%Y-%d"
}
else if (dateFormat == "Y-M-D") {
dateFormat <- "%Y-%m-%d"
}
else if (dateFormat == "Y-D-M") {
dateFormat <- "%Y-%d-%m"
}
else if (dateFormat == "D/M/Y") {
dateFormat <- "%d/%m/%Y"
}
else if (dateFormat == "D/Y/M") {
dateFormat <- "%d/%Y/%m"
}
else if (dateFormat == "M/D/Y") {
dateFormat <- "%m/%d/%Y"
}
else if (dateFormat == "M/Y/D") {
dateFormat <- "%m/%Y/%d"
}
else if (dateFormat == "Y/M/D") {
dateFormat <- "%Y/%m/%d"
}
else if (dateFormat == "Y/D/M") {
dateFormat <- "%Y/%d/%m"
}
else {
setwd(usrdir)
stop("Incorrect date format. Currently allowed date formats are \"D-M-Y\", \"D/M/Y\", or any combination of D, M and Y separated by either - or /\n")
}
}
if (timeFormat != "number") {
if (timeFormat == "H:M") {
timeFormat <- "%H:%M"
}
else if (timeFormat == "H:M:S") {
timeFormat <- "%H:%M:%S"
}
else {
setwd(usrdir)
stop("Incorrect time format. Currently allowed date formats are \"number\", \"H:M\", \"H:M:S\"\n")
}
}
outData <- data.frame()
if (is.null(grNm) & is.null(flNm))
case <- 1
if (!is.null(grNm) & is.null(flNm))
case <- 2
if (is.null(grNm) & !is.null(flNm))
case <- 3
if (!is.null(grNm) & !is.null(flNm))
case <- 4
alwprm <- c("AUClast", "AUClower_upper", "AUCINF_obs", "AUCINF_pred",
"AUMClast", "Cmax", "Tmax", "HL_Lambda_z")
npr <- length(param)
fctNm <- data.frame()
for (p in 1:npr) {
if (param[p] %in% alwprm == F) {
setwd(usrdir)
stop("Incorrect NCA parameters. Please select NCA parameters from \"AUClast\", \"AUClower_upper\", \"AUCINF_obs\", \"AUCINF_pred\", \"AUMClast\", \"Cmax\", \"Tmax\", \"HL_Lambda_z\"\n")
}
if (param[p] == "AUClast" | param[p] == "AUClower_upper" |
param[p] == "AUCINF_obs" | param[p] == "AUCINF_pred") {
fctNm <- rbind(fctNm, data.frame(prmNm = param[p],
prmUnit = paste(param[p], " (", cunit, "*", tunit,
")", sep = "")))
}
else if (param[p] == "AUMClast") {
fctNm <- rbind(fctNm, data.frame(prmNm = param[p],
prmUnit = paste(param[p], " (", cunit, "*", tunit,
"^2)", sep = "")))
}
else if (param[p] == "Cmax") {
fctNm <- rbind(fctNm, data.frame(prmNm = param[p],
prmUnit = paste(param[p], " (", cunit, ")", sep = "")))
}
else if (param[p] == "Tmax") {
fctNm <- rbind(fctNm, data.frame(prmNm = param[p],
prmUnit = paste(param[p], " (", tunit, ")", sep = "")))
}
else if (param[p] == "HL_Lambda_z") {
fctNm <- rbind(fctNm, data.frame(prmNm = param[p],
prmUnit = paste(param[p], " (", tunit, ")", sep = "")))
}
}
obsFileNm <- ifelse(is.data.frame(obsFile), deparse(substitute(obsFile)),
obsFile)
if (!is.null(studyName)) {
txt <- paste0("Name of the study: \"", studyName, "\"")
txt <- paste(txt, paste0("Name of the file with the observed data: \"",
obsFileNm, "\""), sep = "\n")
}
else {
txt <- paste0("Name of the file with the observed data: \"",
obsFileNm, "\"")
}
txt <- paste(txt, paste0("Route of administration: ", adminType),
sep = "\n")
if (doseType == "ss") {
txt <- paste(txt, paste0("Dose type: steady-state with dosing interval (Tau) of",
Tau), sep = "\n")
}
else {
txt <- paste(txt, "Dose type: non-steady-state", sep = "\n")
}
txt <- paste(txt, paste0("No. of dosing occasions: ", ndose),
sep = "\n")
if (ndose == 1) {
txt <- paste(txt, "Occasion flag or OID: OID", sep = "\n")
txt <- paste(txt, "Occasion ID: 1", sep = "\n")
}
else if (ndose > 1) {
txt <- paste(txt, paste0("Occasion flag: ", oidNm), sep = "\n")
txt <- paste(txt, paste0("Occasion ID (OID): ", paste(dose,
collapse = ", ")), sep = "\n")
}
txt <- paste(txt, paste0("Total number of subjects in the input file = ",
length(unique(indf[, idNmObs]))), sep = "\n")
if (case == 2) {
txt <- paste(txt, paste0("Population group flag or GID: ",
grNm), sep = "\n")
txt <- paste(txt, paste0("Population group ID: ", paste(grp,
collapse = ", ")), sep = "\n")
}
if (case == 3) {
txt <- paste(txt, paste0("Population group flag or GID: ",
flNm), sep = "\n")
txt <- paste(txt, paste0("Population group ID: ", paste(flag,
collapse = ", ")), sep = "\n")
}
if (case == 4) {
txt <- paste(txt, paste0("Population group flag or GID: ",
grNm), sep = "\n")
txt <- paste(txt, paste0("Population group ID: ", paste(grp,
collapse = ", ")), sep = "\n")
txt <- paste(txt, paste0("Population sub-group flag or SGID: ",
flNm), sep = "\n")
txt <- paste(txt, paste0("Population sub-group ID: ",
paste(flag, collapse = ", ")), sep = "\n")
}
if (npr <= 2) {
ncol <- 2
hth <- 12
wth <- 16
phth <- 6
pwth <- 7
}
else if (npr > 2 & npr <= 4) {
ncol <- 2
hth <- 18
wth <- 18
phth <- 9
pwth <- 7
}
else if (npr > 4 & npr <= 6) {
ncol <- 3
hth <- 18
wth <- 25
phth <- 9
pwth <- 9
}
else if (npr > 6) {
ncol <- 3
hth <- 26
wth <- 25
phth <- 10
pwth <- 9
}
concplot <- list()
histobsplot = list()
popplot <- list()
devplot <- list()
outlierplot <- list()
forestplot <- list()
npdeplot <- list()
histnpdeplot <- list()
dset = "obs"
ncaId <- function(ifdf, ID) {
if (adminType == "iv-infusion" & is.null(TI)) {
amt <- ifdf[ifdf[, idCol] == ID & ifdf$AMT > 0, "AMT"][1]
rate <- ifdf[ifdf[, idCol] == ID & ifdf$RATE > 0,
"RATE"][1]
if (is.na(amt) | is.na(rate) | rate == 0) {
setwd(usrdir)
stop(paste("Incorrect AMT and/or RATE value for ",
ID, sep = ""))
}
else {
TI <- amt/rate
}
}
else {
TI <- "NaN"
}
if (timeFormat != "number") {
time <- numeric(0)
if (!is.null(dateColNm)) {
tm <- as.POSIXct(paste(ifdf[ifdf[, idCol] ==
ID, dateColNm], ifdf[ifdf[, idCol] == ID, timeCol]),
format = paste(dateFormat, timeFormat, sep = " "))
}
else {
tm <- ifdf[ifdf[, idCol] == ID, timeCol]
}
for (j in 1:length(tm)) {
time[j] <- ifelse((is.null(dateColNm)), as.numeric(difftime(strptime(tm[j],
format = timeFormat), strptime(tm[1], format = timeFormat),
units = "hours")), as.numeric(difftime(strptime(tm[j],
format = "%Y-%m-%d %H:%M:%S"), strptime(tm[1],
format = "%Y-%m-%d %H:%M:%S"), units = "hours")))
}
}
else {
time <- suppressWarnings(as.numeric(as.character(ifdf[ifdf[,
idCol] == ID, timeCol])))
}
tconc <- ifdf[ifdf[, idCol] == ID, concCol]
conc <- numeric(0)
for (c in 1:length(tconc)) {
conc <- c(conc, ifelse((tconc[c] == "."), 0, as.numeric(as.character(tconc[c]))))
}
rm(tconc)
if (length(which(is.na(time))) != 0) {
zidx <- which(is.na(time))
time <- time[-zidx]
conc <- conc[-zidx]
}
if (length(which(is.na(conc))) != 0) {
zidx <- which(is.na(conc))
time <- time[-zidx]
conc <- conc[-zidx]
}
if (obsLog == "TRUE") {
for (c in 1:length(conc)) {
conc[c] <- ifelse((conc[c] != 0), exp(conc[c]),
0)
}
}
tc <- data.frame(time, conc)
if (nrow(tc) > 0) {
tc <- tc[order(tc$time), ]
tc$time <- tc$time + abs(min(tc$time))
}
return(tc)
}
cdata <- data.frame(Time = numeric(0), Conc = numeric(0),
ID = character(0), FCT = character(0))
pddf <- data.frame(a = character(0), b = character(0), c = character(0))
if (case == 1) {
for (d in 1:ndose) {
if (!is.null(doseNm)) {
ifdf <- indf[indf[, doseNm] == dose[d], ]
}
else {
ifdf <- indf
}
if (length(which(is.na(ifdf[, concCol]) | ifdf[,
concCol] == "")) != 0) {
ifdf <- ifdf[-which(is.na(ifdf[, concCol]) |
ifdf[, concCol] == ""), ]
}
if (nrow(ifdf) == 0) {
next
}
idd <- unique(ifdf[, idCol])
DoseNumber <- dose[d]
if (is.null(doseNm)) {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
doseAmtNm] > 0, doseAmtNm])), collapse = ", ")
}
else {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
doseNm] == dose[d] & refdf[, doseAmtNm] > 0,
doseAmtNm])), collapse = ", ")
}
pddf <- rbind(pddf, data.frame(a = DoseNumber, b = doseAmount,
c = length(idd)))
for (i in 1:length(idd)) {
if (is.null(doseNm)) {
idzAmt <- as.numeric(refdf[refdf[, idNmObs] ==
idd[i] & refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
else {
idzAmt <- as.numeric(refdf[refdf[, doseNm] ==
dose[d] & refdf[, idNmObs] == idd[i] & refdf[,
doseAmtNm] > 0, doseAmtNm][1])
}
tc <- ncaId(ifdf, idd[i])
if (nrow(tc) == 0)
next
time <- as.numeric(tc$time)
conc <- as.numeric(tc$conc)
cdata <- rbind(cdata, cbind(Time = time, Conc = conc,
ID = as.character(idd[i]), FCT = paste(oidNm,
"-", dose[d], sep = "")))
NCAprm <- est.nca(time = time, conc = conc, backExtrp = backExtrp,
negConcExcl = negConcExcl, doseType = doseType,
adminType = adminType, doseNm = doseNm, dose = dose,
doseNumber = DoseNumber, doseAmt = idzAmt,
method = method, AUCTimeRange = AUCTimeRange,
LambdaTimeRange = LambdaTimeRange, LambdaExclude = LambdaExclude,
Tau = Tau, TI = TI, simFile = simFile, dset = dset)
outData <- rbind(outData, data.frame(ID = idd[i],
DoseNumber = DoseNumber, DoseAmount = idzAmt,
t(NCAprm)))
}
if (noPlot == "FALSE") {
plotData <- subset(outData, DoseNumber = dose[d],
select = c(AUClast, AUCINF_obs, Cmax, Tmax))
if (nrow(plotData) <= 5)
next
pltPrm <- c("AUClast", "AUCINF_obs", "Cmax",
"Tmax")
for (p in 1:length(pltPrm)) {
if (nrow(plotData[plotData[, p] != "NaN", ]) <
5)
pltPrm <- pltPrm[-p]
}
if (length(pltPrm) == 0)
next
figlbl <- paste(oidNm, "-", dose[d], sep = "")
histobsgrob <- histobs.plot(plotData = plotData,
figlbl = figlbl, param = pltPrm, cunit = cunit,
tunit = tunit, spread = spread)
gdr <- histobsgrob$gdr
mylegend <- histobsgrob$legend
lheight <- histobsgrob$lheight
if (printOut == "TRUE") {
fl <- paste(usrdir, "/HistObs_", figlbl, sep = "")
eval(parse(text = paste(figFormat, "(file=\"",
fl, ".", figFormat, "\",height=15,width=14,units=\"cm\",res=200)",
sep = "")))
suppressMessages(suppressWarnings(grid.arrange(gdr,
mylegend, heights = unit.c(unit(1, "npc") -
lheight, lheight))))
dev.off()
}
suppressMessages(suppressWarnings(grid.arrange(gdr,
mylegend, heights = unit.c(unit(1, "npc") -
lheight, lheight))))
ggr <- grid.grab()
histobsplot[[length(histobsplot) + 1]] <- ggr
}
}
cnm <- c(paste("OID (", oidNm, ")", sep = ""), paste("Dose (",
dunit, ")", sep = ""), "No. of individuals")
names(pddf) <- cnm
if (noPlot == "FALSE") {
fct <- unique(cdata$FCT)
nfct <- length(fct)
for (p in seq(1, nfct, 3)) {
str <- ""
if ((nfct - p) >= 2) {
dht <- 16
dwd <- 15
str <- gsub("^_", "", paste(str, fct[p:(p +
2)], sep = "_", collapse = ""))
pdata <- subset(cdata, FCT == fct[p] | FCT ==
fct[p + 1] | FCT == fct[p + 2])
}
else if ((nfct - p) == 1) {
dht <- 11
dwd <- 13
str <- gsub("^_", "", paste(str, fct[p:(p +
1)], sep = "_", collapse = ""))
pdata <- subset(cdata, FCT == fct[p] | FCT ==
fct[p + 1])
}
else if ((nfct - p) == 0) {
dht <- 7
dwd <- 11
str <- gsub("^_", "", paste(str, fct[p], sep = "_",
collapse = ""))
pdata <- subset(cdata, FCT == fct[p])
}
gdr <- dv.plot(pdata = pdata, cunit = cunit,
tunit = tunit)
suppressMessages(suppressWarnings(grid.arrange(gdr)))
ggr <- grid.grab()
concplot[[length(concplot) + 1]] <- ggr
if (printOut == "TRUE")
ggsave(filename = paste(usrdir, "/TimeConc_",
str, ".", figFormat, sep = ""), plot = gdr,
height = dht, width = dwd, units = "cm",
dpi = 200)
}
}
}
if (case == 2) {
for (g in 1:ngrp) {
for (d in 1:ndose) {
if (!is.null(doseNm)) {
ifdf <- indf[indf[, grCol] == as.character(grp[g]) &
indf[, doseNm] == dose[d], ]
}
else {
ifdf <- indf[indf[, grCol] == as.character(grp[g]),
]
}
if (length(which(is.na(ifdf[, concCol]) | ifdf[,
concCol] == "")) != 0) {
ifdf <- ifdf[-which(is.na(ifdf[, concCol]) |
ifdf[, concCol] == ""), ]
}
if (nrow(ifdf) == 0) {
next
}
idd <- unique(ifdf[, idCol])
DoseNumber <- dose[d]
igr <- as.character(grp[g])
if (is.null(doseNm)) {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
grCol] == as.character(grp[g]) & refdf[,
doseAmtNm] > 0, doseAmtNm])), collapse = ", ")
}
else {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
grCol] == as.character(grp[g]) & refdf[,
doseNm] == dose[d] & refdf[, doseAmtNm] >
0, doseAmtNm])), collapse = ", ")
}
pddf <- rbind(pddf, data.frame(a = as.character(grp[g]),
b = DoseNumber, c = doseAmount, d = length(idd)))
for (i in 1:length(idd)) {
if (is.null(doseNm)) {
idzAmt <- as.numeric(refdf[refdf[, grCol] ==
as.character(grp[g]) & refdf[, idNmObs] ==
idd[i] & refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
else {
idzAmt <- as.numeric(refdf[refdf[, grCol] ==
as.character(grp[g]) & refdf[, doseNm] ==
dose[d] & refdf[, idNmObs] == idd[i] &
refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
tc <- ncaId(ifdf, idd[i])
if (nrow(tc) == 0)
next
time <- as.numeric(tc$time)
conc <- as.numeric(tc$conc)
cdata <- rbind(cdata, cbind(Time = time, Conc = conc,
ID = as.character(idd[i]), FCT = paste(grNm,
"-", as.character(grp[g]), "_", oidNm,
"-", dose[d], sep = "")))
NCAprm <- est.nca(time = time, conc = conc,
backExtrp = backExtrp, negConcExcl = negConcExcl,
doseType = doseType, adminType = adminType,
doseNm = doseNm, dose = dose, doseNumber = DoseNumber,
doseAmt = idzAmt, method = method, AUCTimeRange = AUCTimeRange,
LambdaTimeRange = LambdaTimeRange, LambdaExclude = LambdaExclude,
Tau = Tau, TI = TI, simFile = simFile, dset = dset)
outData <- rbind(outData, cbind(data.frame(GROUP = igr),
data.frame(ID = idd[i], DoseNumber = DoseNumber,
DoseAmount = idzAmt, t(NCAprm))))
}
if (noPlot == "FALSE") {
plotData <- subset(outData, DoseNumber == dose[d],
select = c(AUClast, AUCINF_obs, Cmax, Tmax))
if (nrow(plotData) <= 5)
next
pltPrm <- c("AUClast", "AUCINF_obs", "Cmax",
"Tmax")
for (p in 1:length(pltPrm)) {
if (nrow(plotData[plotData[, p] != "NaN",
]) < 5)
pltPrm <- pltPrm[-p]
}
if (length(pltPrm) == 0)
next
figlbl <- paste(grNm, "-", as.character(grp[g]),
"_", oidNm, "-", dose[d], sep = "")
histobsgrob <- histobs.plot(plotData = plotData,
figlbl = figlbl, param = c("AUClast", "AUCINF_obs",
"Cmax", "Tmax"), cunit = cunit, tunit = tunit,
spread = spread)
gdr <- histobsgrob$gdr
mylegend <- histobsgrob$legend
lheight <- histobsgrob$lheight
if (printOut == "TRUE") {
fl <- paste(usrdir, "/HistObs_", figlbl,
sep = "")
eval(parse(text = paste(figFormat, "(file=\"",
fl, ".", figFormat, "\",height=15,width=14,units=\"cm\",res=200)",
sep = "")))
suppressMessages(suppressWarnings(grid.arrange(gdr,
mylegend, heights = unit.c(unit(1, "npc") -
lheight, lheight))))
dev.off()
}
suppressMessages(suppressWarnings(grid.arrange(gdr,
mylegend, heights = unit.c(unit(1, "npc") -
lheight, lheight))))
ggr <- grid.grab()
histobsplot[[length(histobsplot) + 1]] <- ggr
}
}
}
cnm <- c(paste("GID (", grNm, ")", sep = ""), paste("OID (",
oidNm, ")", sep = ""), paste("Dose (", dunit, ")",
sep = ""), "No. of individuals")
names(pddf) <- cnm
if (noPlot == "FALSE") {
fct <- unique(cdata$FCT)
nfct <- length(fct)
for (p in seq(1, nfct, 3)) {
str <- ""
if ((nfct - p) >= 2) {
dht <- 16
dwd <- 15
str <- gsub("^_", "", paste(str, fct[p:(p +
2)], sep = "_", collapse = ""))
pdata <- subset(cdata, FCT == fct[p] | FCT ==
fct[p + 1] | FCT == fct[p + 2])
}
else if ((nfct - p) == 1) {
dht <- 11
dwd <- 13
str <- gsub("^_", "", paste(str, fct[p:(p +
1)], sep = "_", collapse = ""))
pdata <- subset(cdata, FCT == fct[p] | FCT ==
fct[p + 1])
}
else if ((nfct - p) == 0) {
dht <- 7
dwd <- 11
str <- gsub("^_", "", paste(str, fct[p], sep = "_",
collapse = ""))
pdata <- subset(cdata, FCT == fct[p])
}
gdr <- dv.plot(pdata = pdata, cunit = cunit,
tunit = tunit)
suppressMessages(suppressWarnings(grid.arrange(gdr)))
ggr <- grid.grab()
concplot[[length(concplot) + 1]] <- ggr
if (printOut == "TRUE")
ggsave(filename = paste(usrdir, "/TimeConc_",
str, ".", figFormat, sep = ""), plot = gdr,
height = dht, width = dwd, units = "cm",
dpi = 200)
}
}
}
if (case == 3) {
for (f in 1:nflag) {
for (d in 1:ndose) {
if (!is.null(doseNm)) {
ifdf <- indf[indf[, flCol] == as.character(flag[f]) &
indf[, doseNm] == dose[d], ]
}
else {
ifdf <- indf[indf[, flCol] == as.character(flag[f]),
]
}
if (length(which(is.na(ifdf[, concCol]) | ifdf[,
concCol] == "")) != 0) {
ifdf <- ifdf[-which(is.na(ifdf[, concCol]) |
ifdf[, concCol] == ""), ]
}
if (nrow(ifdf) == 0) {
next
}
idd <- unique(ifdf[, idCol])
DoseNumber <- dose[d]
iflag <- as.character(flag[f])
if (is.null(doseNm)) {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
flCol] == as.character(flag[f]) & refdf[,
doseAmtNm] > 0, doseAmtNm])), collapse = ", ")
}
else {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
flCol] == as.character(flag[f]) & refdf[,
doseNm] == dose[d] & refdf[, doseAmtNm] >
0, doseAmtNm])), collapse = ", ")
}
pddf <- rbind(pddf, data.frame(a = as.character(flag[f]),
b = DoseNumber, c = doseAmount, d = length(idd)))
for (i in 1:length(idd)) {
if (is.null(doseNm)) {
idzAmt <- as.numeric(refdf[refdf[, flCol] ==
as.character(flag[f]) & refdf[, idNmObs] ==
idd[i] & refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
else {
idzAmt <- as.numeric(refdf[refdf[, flCol] ==
as.character(flag[f]) & refdf[, doseNm] ==
dose[d] & refdf[, idNmObs] == idd[i] &
refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
tc <- ncaId(ifdf, idd[i])
if (nrow(tc) == 0)
next
time <- as.numeric(tc$time)
conc <- as.numeric(tc$conc)
cdata <- rbind(cdata, cbind(Time = time, Conc = conc,
ID = as.character(idd[i]), FCT = paste(flNm,
"-", as.character(flag[f]), "_", oidNm,
"-", dose[d], sep = "")))
NCAprm <- est.nca(time = time, conc = conc,
backExtrp = backExtrp, negConcExcl = negConcExcl,
doseType = doseType, adminType = adminType,
doseNm = doseNm, dose = dose, doseNumber = DoseNumber,
doseAmt = idzAmt, method = method, AUCTimeRange = AUCTimeRange,
LambdaTimeRange = LambdaTimeRange, LambdaExclude = LambdaExclude,
Tau = Tau, TI = TI, simFile = simFile, dset = dset)
outData <- rbind(outData, cbind(data.frame(FLAG = iflag),
data.frame(ID = idd[i], DoseNumber = DoseNumber,
DoseAmount = idzAmt, t(NCAprm))))
}
if (noPlot == "FALSE") {
plotData <- subset(outData, DoseNumber == dose[d],
select = c(AUClast, AUCINF_obs, Cmax, Tmax))
if (nrow(plotData) <= 5)
next
pltPrm <- c("AUClast", "AUCINF_obs", "Cmax",
"Tmax")
for (p in 1:length(pltPrm)) {
if (nrow(plotData[plotData[, p] != "NaN",
]) < 5)
pltPrm <- pltPrm[-p]
}
if (length(pltPrm) == 0)
next
figlbl <- paste(flNm, "-", as.character(flag[f]),
"_", oidNm, "-", dose[d], sep = "")
histobsgrob <- histobs.plot(plotData = plotData,
figlbl = figlbl, param = c("AUClast", "AUCINF_obs",
"Cmax", "Tmax"), cunit = cunit, tunit = tunit,
spread = spread)
gdr <- histobsgrob$gdr
mylegend <- histobsgrob$legend
lheight <- histobsgrob$lheight
if (printOut == "TRUE") {
fl <- paste(usrdir, "/HistObs_", figlbl,
sep = "")
eval(parse(text = paste(figFormat, "(file=\"",
fl, ".", figFormat, "\",height=15,width=14,units=\"cm\",res=200)",
sep = "")))
suppressMessages(suppressWarnings(grid.arrange(gdr,
mylegend, heights = unit.c(unit(1, "npc") -
lheight, lheight))))
dev.off()
}
suppressMessages(suppressWarnings(grid.arrange(gdr,
mylegend, heights = unit.c(unit(1, "npc") -
lheight, lheight))))
ggr <- grid.grab()
histobsplot[[length(histobsplot) + 1]] <- ggr
}
}
}
cnm <- c(paste("GID (", flNm, ")", sep = ""), paste("OID (",
oidNm, ")", sep = ""), paste("Dose (", dunit, ")",
sep = ""), "No. of individuals")
names(pddf) <- cnm
if (noPlot == "FALSE") {
fct <- unique(cdata$FCT)
nfct <- length(fct)
for (p in seq(1, nfct, 3)) {
str <- ""
if ((nfct - p) >= 2) {
dht <- 16
dwd <- 15
str <- gsub("^_", "", paste(str, fct[p:(p +
2)], sep = "_", collapse = ""))
pdata <- subset(cdata, FCT == fct[p] | FCT ==
fct[p + 1] | FCT == fct[p + 2])
}
else if ((nfct - p) == 1) {
dht <- 11
dwd <- 13
str <- gsub("^_", "", paste(str, fct[p:(p +
1)], sep = "_", collapse = ""))
pdata <- subset(cdata, FCT == fct[p] | FCT ==
fct[p + 1])
}
else if ((nfct - p) == 0) {
dht <- 7
dwd <- 11
str <- gsub("^_", "", paste(str, fct[p], sep = "_",
collapse = ""))
pdata <- subset(cdata, FCT == fct[p])
}
gdr <- dv.plot(pdata = pdata, cunit = cunit,
tunit = tunit)
suppressMessages(suppressWarnings(grid.arrange(gdr)))
ggr <- grid.grab()
concplot[[length(concplot) + 1]] <- ggr
if (printOut == "TRUE")
ggsave(filename = paste(usrdir, "/TimeConc_",
str, ".", figFormat, sep = ""), plot = gdr,
height = dht, width = dwd, units = "cm",
dpi = 200)
}
}
}
if (case == 4) {
for (g in 1:ngrp) {
for (f in 1:nflag) {
for (d in 1:ndose) {
if (!is.null(doseNm)) {
ifdf <- indf[(indf[, flCol] == as.character(flag[f]) &
indf[, grCol] == as.character(grp[g]) &
indf[, doseNm] == dose[d]), ]
}
else {
ifdf <- indf[(indf[, flCol] == as.character(flag[f]) &
indf[, grCol] == as.character(grp[g])),
]
}
if (length(which(is.na(ifdf[, concCol]) | ifdf[,
concCol] == "")) != 0) {
ifdf <- ifdf[-which(is.na(ifdf[, concCol]) |
ifdf[, concCol] == ""), ]
}
if (nrow(ifdf) == 0) {
next
}
idd <- unique(ifdf[, idCol])
DoseNumber <- dose[d]
igr <- as.character(grp[g])
iflag <- as.character(flag[f])
if (is.null(doseNm)) {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
grCol] == as.character(grp[g]) & refdf[,
flCol] == as.character(flag[f]) & refdf[,
doseAmtNm] > 0, doseAmtNm])), collapse = ", ")
}
else {
doseAmount <- paste(as.numeric(unique(refdf[refdf[,
grCol] == as.character(grp[g]) & refdf[,
flCol] == as.character(flag[f]) & refdf[,
doseNm] == dose[d] & refdf[, doseAmtNm] >
0, doseAmtNm])), collapse = ", ")
}
pddf <- rbind(pddf, data.frame(a = as.character(grp[g]),
b = as.character(flag[f]), c = DoseNumber,
d = doseAmount, e = length(idd)))
for (i in 1:length(idd)) {
if (is.null(doseNm)) {
idzAmt <- as.numeric(refdf[refdf[, grCol] ==
as.character(grp[g]) & refdf[, flCol] ==
as.character(flag[f]) & refdf[, idNmObs] ==
idd[i] & refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
else {
idzAmt <- as.numeric(refdf[refdf[, grCol] ==
as.character(grp[g]) & refdf[, flCol] ==
as.character(flag[f]) & refdf[, doseNm] ==
dose[d] & refdf[, idNmObs] == idd[i] &
refdf[, doseAmtNm] > 0, doseAmtNm][1])
}
tc <- ncaId(ifdf, idd[i])
if (nrow(tc) == 0)