diff --git a/DESCRIPTION b/DESCRIPTION index dbc7b8b..e13aeb3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,7 +23,7 @@ Description: 'Monolix' is a tool for running mixed effects model using License: MIT + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 LinkingTo: dparser, rxode2parse, diff --git a/NAMESPACE b/NAMESPACE index 72b0a87..99c7cff 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -69,6 +69,7 @@ export(logit) export(lotri) export(mlxTxt) export(mlxtran) +export(mlxtranGetMutate) export(model) export(monolix2rx) export(monolixDataImport) diff --git a/R/rxSolve.R b/R/rxSolve.R index 708d610..5d6eb09 100644 --- a/R/rxSolve.R +++ b/R/rxSolve.R @@ -5,33 +5,36 @@ rxSolve.monolix2rx <- function(object, params = NULL, events = NULL, "dop853", "indLin"), sigdig = NULL, atol = 1e-08, rtol = 1e-06, maxsteps = 70000L, hmin = 0, hmax = NA_real_, hmaxSd = 0, hini = 0, maxordn = 12L, maxords = 5L, ..., cores, covsInterpolation = c("locf", - "linear", "nocb", "midpoint"), addCov = TRUE, sigma = NULL, - sigmaDf = NULL, sigmaLower = -Inf, sigmaUpper = Inf, nCoresRV = 1L, - sigmaIsChol = FALSE, sigmaSeparation = c("auto", "lkj", "separation"), - sigmaXform = c("identity", "variance", "log", "nlmixrSqrt", - "nlmixrLog", "nlmixrIdentity"), nDisplayProgress = 10000L, - amountUnits = NA_character_, timeUnits = "hours", theta = NULL, - thetaLower = -Inf, thetaUpper = Inf, eta = NULL, addDosing = FALSE, - stateTrim = Inf, updateObject = FALSE, omega = NULL, omegaDf = NULL, - omegaIsChol = FALSE, omegaSeparation = c("auto", "lkj", "separation"), - omegaXform = c("variance", "identity", "log", "nlmixrSqrt", - "nlmixrLog", "nlmixrIdentity"), omegaLower = -Inf, omegaUpper = Inf, - nSub = 1L, thetaMat = NULL, thetaDf = NULL, thetaIsChol = FALSE, - nStud = 1L, dfSub = 0, dfObs = 0, returnType = c("rxSolve", - "matrix", "data.frame", "data.frame.TBS", "data.table", - "tbl", "tibble"), seed = NULL, nsim = NULL, minSS = 10L, - maxSS = 1000L, infSSstep = 12, strictSS = TRUE, istateReset = TRUE, - subsetNonmem = TRUE, maxAtolRtolFactor = 0.1, from = NULL, - to = NULL, by = NULL, length.out = NULL, iCov = NULL, keep = NULL, - indLinPhiTol = 1e-07, indLinPhiM = 0L, indLinMatExpType = c("expokit", - "Al-Mohy", "arma"), indLinMatExpOrder = 6L, drop = NULL, - idFactor = TRUE, mxhnil = 0, hmxi = 0, warnIdSort = TRUE, - warnDrop = TRUE, ssAtol = 1e-08, ssRtol = 1e-06, safeZero = TRUE, - sumType = c("pairwise", "fsum", "kahan", "neumaier", "c"), - prodType = c("long double", "double", "logify"), sensType = c("advan", - "autodiff", "forward", "central"), linDiff = c(tlag = 1.5e-05, - f = 1.5e-05, rate = 1.5e-05, dur = 1.5e-05, tlag2 = 1.5e-05, - f2 = 1.5e-05, rate2 = 1.5e-05, dur2 = 1.5e-05), linDiffCentral = c(tlag = TRUE, + "linear", "nocb", "midpoint"), naInterpolation = c("locf", + "nocb"), keepInterpolation = c("locf", "nocb", "na"), + addCov = TRUE, sigma = NULL, sigmaDf = NULL, sigmaLower = -Inf, + sigmaUpper = Inf, nCoresRV = 1L, sigmaIsChol = FALSE, sigmaSeparation = c("auto", + "lkj", "separation"), sigmaXform = c("identity", "variance", + "log", "nlmixrSqrt", "nlmixrLog", "nlmixrIdentity"), + nDisplayProgress = 10000L, amountUnits = NA_character_, timeUnits = "hours", + theta = NULL, thetaLower = -Inf, thetaUpper = Inf, eta = NULL, + addDosing = FALSE, stateTrim = Inf, updateObject = FALSE, + omega = NULL, omegaDf = NULL, omegaIsChol = FALSE, omegaSeparation = c("auto", + "lkj", "separation"), omegaXform = c("variance", "identity", + "log", "nlmixrSqrt", "nlmixrLog", "nlmixrIdentity"), + omegaLower = -Inf, omegaUpper = Inf, nSub = 1L, thetaMat = NULL, + thetaDf = NULL, thetaIsChol = FALSE, nStud = 1L, dfSub = 0, + dfObs = 0, returnType = c("rxSolve", "matrix", "data.frame", + "data.frame.TBS", "data.table", "tbl", "tibble"), seed = NULL, + nsim = NULL, minSS = 10L, maxSS = 1000L, infSSstep = 12, + strictSS = TRUE, istateReset = TRUE, subsetNonmem = TRUE, + maxAtolRtolFactor = 0.1, from = NULL, to = NULL, by = NULL, + length.out = NULL, iCov = NULL, keep = NULL, indLinPhiTol = 1e-07, + indLinPhiM = 0L, indLinMatExpType = c("expokit", "Al-Mohy", + "arma"), indLinMatExpOrder = 6L, drop = NULL, idFactor = TRUE, + mxhnil = 0, hmxi = 0, warnIdSort = TRUE, warnDrop = TRUE, + ssAtol = 1e-08, ssRtol = 1e-06, safeZero = TRUE, safeLog = TRUE, + safePow = TRUE, sumType = c("pairwise", "fsum", "kahan", + "neumaier", "c"), prodType = c("long double", "double", + "logify"), sensType = c("advan", "autodiff", "forward", + "central"), linDiff = c(tlag = 1.5e-05, f = 1.5e-05, + rate = 1.5e-05, dur = 1.5e-05, tlag2 = 1.5e-05, f2 = 1.5e-05, + rate2 = 1.5e-05, dur2 = 1.5e-05), linDiffCentral = c(tlag = TRUE, f = TRUE, rate = TRUE, dur = TRUE, tlag2 = TRUE, f2 = TRUE, rate2 = TRUE, dur2 = TRUE), resample = NULL, resampleID = TRUE, maxwhile = 1e+05, atolSens = 1e-08, rtolSens = 1e-06, ssAtolSens = 1e-08, @@ -118,6 +121,7 @@ rxSolve.monolix2rx <- function(object, params = NULL, events = NULL, atol = atol, rtol = rtol, maxsteps = maxsteps, hmin = hmin, hmax = hmax, hmaxSd = hmaxSd, hini = hini, maxordn = maxordn, maxords = maxords, ..., cores = cores, covsInterpolation = covsInterpolation, + naInterpolation = naInterpolation, keepInterpolation = keepInterpolation, addCov = addCov, sigma = sigma, sigmaDf = sigmaDf, sigmaLower = sigmaLower, sigmaUpper = sigmaUpper, nCoresRV = nCoresRV, sigmaIsChol = sigmaIsChol, sigmaSeparation = sigmaSeparation, sigmaXform = sigmaXform, @@ -138,13 +142,14 @@ rxSolve.monolix2rx <- function(object, params = NULL, events = NULL, indLinMatExpType = indLinMatExpType, indLinMatExpOrder = indLinMatExpOrder, drop = drop, idFactor = idFactor, mxhnil = mxhnil, hmxi = hmxi, warnIdSort = warnIdSort, warnDrop = warnDrop, ssAtol = ssAtol, - ssRtol = ssRtol, safeZero = safeZero, sumType = sumType, - prodType = prodType, sensType = sensType, linDiff = linDiff, - linDiffCentral = linDiffCentral, resample = resample, - resampleID = resampleID, maxwhile = maxwhile, atolSens = atolSens, - rtolSens = rtolSens, ssAtolSens = ssAtolSens, ssRtolSens = ssRtolSens, - simVariability = simVariability, nLlikAlloc = nLlikAlloc, - useStdPow = useStdPow, naTimeHandle = naTimeHandle, addlKeepsCov = addlKeepsCov, - addlDropSs = addlDropSs, ssAtDoseTime = ssAtDoseTime, - ss2cancelAllPending = ss2cancelAllPending, envir = envir) + ssRtol = ssRtol, safeZero = safeZero, safeLog = safeLog, + safePow = safePow, sumType = sumType, prodType = prodType, + sensType = sensType, linDiff = linDiff, linDiffCentral = linDiffCentral, + resample = resample, resampleID = resampleID, maxwhile = maxwhile, + atolSens = atolSens, rtolSens = rtolSens, ssAtolSens = ssAtolSens, + ssRtolSens = ssRtolSens, simVariability = simVariability, + nLlikAlloc = nLlikAlloc, useStdPow = useStdPow, naTimeHandle = naTimeHandle, + addlKeepsCov = addlKeepsCov, addlDropSs = addlDropSs, + ssAtDoseTime = ssAtDoseTime, ss2cancelAllPending = ss2cancelAllPending, + envir = envir) } diff --git a/man/mlxtranGetMutate.Rd b/man/mlxtranGetMutate.Rd new file mode 100644 index 0000000..feaf1c3 --- /dev/null +++ b/man/mlxtranGetMutate.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dataCov.R +\name{mlxtranGetMutate} +\alias{mlxtranGetMutate} +\title{Get the string of the mutate statement for input dataset based on +mlxtran} +\usage{ +mlxtranGetMutate(mlxtran) +} +\arguments{ +\item{mlxtran}{input mlxtran file} +} +\value{ +mlxtran string that can be applied to a model (by evaluating it) +} +\description{ +Get the string of the mutate statement for input dataset based on +mlxtran +} +\examples{ + +covD <- system.file("cov", package="monolix2rx") +m <- mlxtran(file.path(covD, "phenobarbital_project.mlxtran")) +message(mlxtranGetMutate(m)) +} +\author{ +Matthew L. Fidler +} diff --git a/man/monolix2rx.Rd b/man/monolix2rx.Rd index 43502c2..5117585 100644 --- a/man/monolix2rx.Rd +++ b/man/monolix2rx.Rd @@ -60,6 +60,8 @@ pkgTheo <- system.file("theo", package="monolix2rx") rx <- monolix2rx(file.path(pkgTheo, "theophylline_project.mlxtran")) +rx <- monolix2rx(file.path(system.file("cov", package="monolix2rx"), "warfarin_covariate3_project.mlxtran")) + rx } \author{