From e464c2585255539c5731f27b55bc34c04cb55bf4 Mon Sep 17 00:00:00 2001
From: Matthew Fidler <514778+mattfidler@users.noreply.github.com>
Date: Thu, 23 Jan 2020 09:26:38 -0600
Subject: [PATCH] Update namespace/documentation

---
 NAMESPACE           | 3 +++
 R/complete.R        | 1 +
 R/foceiFit.R        | 2 +-
 R/reexports.R       | 2 --
 R/vpc.ui.R          | 2 +-
 man/foceiControl.Rd | 2 --
 man/nlmixrPrint.Rd  | 3 +--
 man/nlmixrSim.Rd    | 2 --
 man/saemControl.Rd  | 2 --
 9 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 493c08ea1..12e12eda8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -115,6 +115,7 @@ S3method(vpc,nlmixrPosthoc)
 S3method(vpc,nlmixrSaem)
 S3method(vpc,nlmixrVpc)
 S3method(vpc,saemFit)
+S3method(vpc,ui)
 export("%>%")
 export(.nmGetData)
 export(.protectSaem)
@@ -351,7 +352,9 @@ importFrom(stats,start)
 importFrom(stats,terms)
 importFrom(stats,time)
 importFrom(stats,var)
+importFrom(utils,.DollarNames)
 importFrom(utils,assignInMyNamespace)
+importFrom(utils,capture.output)
 importFrom(utils,getFromNamespace)
 importFrom(utils,head)
 importFrom(utils,sessionInfo)
diff --git a/R/complete.R b/R/complete.R
index 2e2133348..3fb442313 100644
--- a/R/complete.R
+++ b/R/complete.R
@@ -1,3 +1,4 @@
+##'@importFrom utils .DollarNames
 ##'@export
 .DollarNames.nlmixrBounds <- function(x, pattern){
   grep(pattern,
diff --git a/R/foceiFit.R b/R/foceiFit.R
index fdba17d70..74510de05 100644
--- a/R/foceiFit.R
+++ b/R/foceiFit.R
@@ -3251,7 +3251,7 @@ setOfv <- function(x, type){
     }
 }
 
-
+##' @importFrom utils capture.output
 .captureOutput <- function (expr, envir = parent.frame()) {
     eval({
         .file <- rawConnection(raw(0L), open = "w")
diff --git a/R/reexports.R b/R/reexports.R
index 34eb67d07..777b5c521 100644
--- a/R/reexports.R
+++ b/R/reexports.R
@@ -208,8 +208,6 @@ RxODE::rxParam
 ##'@export
 RxODE::et
 
-
-
 ##' @importFrom huxtable as_hux
 ##' @export
 huxtable::as_hux
diff --git a/R/vpc.ui.R b/R/vpc.ui.R
index 20993cb4b..b5582e1b7 100644
--- a/R/vpc.ui.R
+++ b/R/vpc.ui.R
@@ -256,8 +256,8 @@ vpc.nlmixrVpc <- function(sim, ...){
 }
 
 ##' @rdname vpc_ui
-##' @S3method vpc ui
 ##' @export vpc.ui
+##' @rawNamespace S3method(vpc,ui)
 vpc.ui <- function(sim, ...){
     vpc_ui(fit=sim, ...);
 }
diff --git a/man/foceiControl.Rd b/man/foceiControl.Rd
index 9c692f121..b70f288fb 100644
--- a/man/foceiControl.Rd
+++ b/man/foceiControl.Rd
@@ -155,8 +155,6 @@ optimization.}
       solving, but allows user Jacobian specification.
 \item \code{"dop853"} -- DOP853 solver.  Does not support parallel thread-based
         solving nor user Jacobain specification
-\item \code{"indLin"} -- Solving through inductive linearization.  The RxODE dll
-        must be setup specially to use this solving routine.
 }}
 
 \item{transitAbs}{boolean indicating if this is a transit
diff --git a/man/nlmixrPrint.Rd b/man/nlmixrPrint.Rd
index 166f64cd7..b5c21bb73 100644
--- a/man/nlmixrPrint.Rd
+++ b/man/nlmixrPrint.Rd
@@ -13,8 +13,7 @@ nlmixrPrint(x, ...)
 }
 \description{
 This allows the suppressMessages to work on print functions.  This
-captures the output via R.Util's captureOutput function and then
-sends it through the message routine.
+captures the output function sends it through the message routine.
 }
 \details{
 catpureOutput was used since it is much faster than the internal
diff --git a/man/nlmixrSim.Rd b/man/nlmixrSim.Rd
index d076eed51..f5b20230a 100644
--- a/man/nlmixrSim.Rd
+++ b/man/nlmixrSim.Rd
@@ -95,8 +95,6 @@ variable by 2.}
       solving, but allows user Jacobian specification.
 \item \code{"dop853"} -- DOP853 solver.  Does not support parallel thread-based
         solving nor user Jacobain specification
-\item \code{"indLin"} -- Solving through inductive linearization.  The RxODE dll
-        must be setup specially to use this solving routine.
 }}
 
 \item{transitAbs}{boolean indicating if this is a transit
diff --git a/man/saemControl.Rd b/man/saemControl.Rd
index 85e8df15f..895f2d1bb 100644
--- a/man/saemControl.Rd
+++ b/man/saemControl.Rd
@@ -75,8 +75,6 @@ achieved. This is also used in the solved linear model to check
       solving, but allows user Jacobian specification.
 \item \code{"dop853"} -- DOP853 solver.  Does not support parallel thread-based
         solving nor user Jacobain specification
-\item \code{"indLin"} -- Solving through inductive linearization.  The RxODE dll
-        must be setup specially to use this solving routine.
 }}
 
 \item{transitAbs}{boolean indicating if this is a transit