FOCE

DESCRIPTION

@@ -45,6 +45,6 @@ LinkingTo: dparser(>= 0.1.8), Rcpp (>= 0.12.3),
 URL: https://github.com/nlmixrdevelopment/nlmixr
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
 Packaged: 2018-04-30 01:43:13 UTC; annie
 Maintainer: Wenping Wang <wwang8198@gmail.com>

R/foceiFit.R

@@ -168,6 +168,9 @@ is.latex <- function() {
 ##' @param noAbort Boolean to indicate if you should abort the FOCEi
 ##'     evaluation if it runs into troubles.  (default TRUE)
 ##'
+##' @param interaction Boolean indicate FOCEi should be used (TRUE)
+##'     instead of FOCE (FALSE)
+##'
 ##' @inheritParams RxODE::rxSolve
 ##'
 ##' @details
@@ -228,6 +231,7 @@ foceiControl <- function(sigdig=4,
                          boundTol=NULL,
                          calcTables=TRUE,
                          noAbort=TRUE,
+                         interaction=TRUE,
                          ..., stiff){
     if (is.null(boundTol)){
         boundTol <- 5 * 10 ^ (-sigdig + 1)
@@ -336,7 +340,8 @@ foceiControl <- function(sigdig=4,
                  boundTol=as.double(boundTol),
                  calcTables=calcTables,
                  printNcol=as.integer(printNcol),
-                 noAbort=as.integer(noAbort));
+                 noAbort=as.integer(noAbort),
+                 interaction=as.integer(interaction));
     class(.ret) <- "foceiControl"
     return(.ret);
 }
@@ -448,15 +453,20 @@ constructLinCmt <- function(fun){
 ##' w7$EVID <- 0
 ##' w7$AMT <- 0
 ##'
-##' ## Wang2007 prop error 39.458 for NONMEM, nlmixr matches.
-##' fitP <- foceiFit(w7, inits, mypar2,mod,pred,errProp,
+##' ## Wang2007 prop error 39.458 for NONMEM FOCEi, nlmixr matches.
+##' fitPi <- foceiFit(w7, inits, mypar2,mod,pred,errProp,
 ##'      control=foceiControl(maxOuterIterations=0,covMethod=""))
 ##'
+##' ## Wang2007 prop error 39.207 for NONMEM FOCE; nlmixr matches.
+##' fitP <- foceiFit(w7, inits, mypar2,mod,pred,errProp,
+##'      control=foceiControl(maxOuterIterations=0,covMethod="",
+##'      interaction=FALSE))
+##'
 ##' ## Note if you have the etas you can evaluate the likelihood
 ##' ## of an arbitrary model.  It doesn't have to be solved by
 ##' ## FOCEi
 ##'
-##' etaMat <- matrix(fitP$eta[,-1])
+##' etaMat <- matrix(fitPi$eta[,-1])
 ##'
 ##' fitP2 <- foceiFit(w7, inits, mypar2,mod,pred,errProp, etaMat=etaMat,
 ##'       control=foceiControl(maxOuterIterations=0,maxInnerIterations=0,
@@ -786,7 +796,9 @@ foceiFit.data.frame0 <- function(data,
     if (!exists("noLik", envir=.ret)){
         .ret$model <- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad=(control$derivMethod == 2L),
                                               pred.minus.dv=TRUE, sum.prod=control$sumProd,
-                                              theta.derivs=FALSE, optExpression=control$optExpression, run.internal=TRUE);
+                                              theta.derivs=FALSE, optExpression=control$optExpression,
+                                              interaction=(control$interaction == 1L),
+                                              run.internal=TRUE);
 
         .covNames <- .parNames <- RxODE::rxParams(.ret$model$pred.only);
         .covNames <- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1];
@@ -1264,8 +1276,8 @@ print.nlmixrFitCore <- function(x, ...){
     }
     .posthoc <- (x$control$maxOuterIterations == 0L & x$control$maxInnerIterations > 0L)
     .posthoc <- ifelse(.posthoc, paste0(crayon::bold(" posthoc"), " estimation"), " fit");
-    message(cli::rule(paste0(crayon::bold$blue("nlmix"), crayon::bold$red("r"), " ", crayon::bold$yellow(x$method),.posthoc,
-                             x$extra)))
+    message(cli::rule(paste0(crayon::bold$blue("nlmix"), crayon::bold$red("r"), " ", crayon::bold$yellow(x$method),
+                             x$extra, .posthoc)))
     print(x$objDf)
     message(paste0("\n", cli::rule(paste0(crayon::bold("Time"), " (sec; ", crayon::yellow(.bound), crayon::bold$blue("$time"), "):"))));
     print(x$time)

R/simulate.R

@@ -90,7 +90,8 @@
 ##' simulated from the uncertainty in the Omega/Sigma matrices based
 ##' on the number of subjects and observations the model was based on.
 ##'
-##' @inheritParams RxODE::rxSolve
+##' @param object nlmixr object
+##' @param ... Other arguments sent to \code{rxSolve}
 ##'
 ##' @export
 nlmixrSim <- function(object, ...){
@@ -208,26 +209,13 @@ plot.nlmixrSim <- function(x, y, ...){
 ##' @param ipred Flag to calculate individual predictions. When
 ##'     \code{ipred} is \code{TRUE}, calculate individual predictions.
 ##'     When \code{ipred} is \code{FALSE}, set calculate typical population predations.
-##'     When \code{ipred} is \code{NA}, calculateboth individual and
+##'     When \code{ipred} is \code{NA}, calculate both individual and
 ##'     population predictions.
 ##'
 ##' @inheritParams RxODE::rxSolve
 ##'
 ##' @export
-nlmixrPred <- function(object, params=NULL, events=NULL, inits = NULL, scale = NULL,
-                       covs = NULL, method = c("liblsoda", "lsoda", "dop853"),
-                       transitAbs = NULL, atol = 1.0e-6, rtol = 1.0e-4,
-                       maxsteps = 5000L, hmin = 0L, hmax = NULL, hini = 0L, maxordn = 12L, maxords = 5L, ...,
-                       cores, covsInterpolation = c("linear", "locf", "nocb", "midpoint"),
-                       addCov = FALSE, matrix = FALSE, sigma = NULL, sigmaDf = NULL,
-                       nCoresRV = 1L, sigmaIsChol = FALSE, nDisplayProgress=10000L,
-                       amountUnits = NA_character_, timeUnits = "hours", stiff,
-                       theta = NULL, eta = NULL, addDosing=FALSE, updateObject=FALSE,doSolve=TRUE,
-                       omega = NULL, omegaDf = NULL, omegaIsChol = FALSE,
-                       nSub = 1L, thetaMat = NULL, thetaDf = NULL, thetaIsChol = FALSE,
-                       nStud = 1L, dfSub=0.0, dfObs=0.0, returnType=c("data.frame", "rxSolve", "matrix"),
-                       seed=NULL, nsim=NULL,
-                       ipred=FALSE){
+nlmixrPred <- function(object, ..., ipred=FALSE){
     lst <- as.list(match.call()[-1]);
     if (RxODE::rxIs(lst$params, "rx.event")){
         if (!is.null(lst$events)){