[Pomp-commits] r570 - in pkg: . R man tests

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2011-12-24 17:31:01 +0100 (Sat, 24 Dec 2011)
New Revision: 570

Modified:
   pkg/NAMESPACE
   pkg/R/profile-design.R
   pkg/R/slice-design.R
   pkg/R/sobol.R
   pkg/man/profile-design.Rd
   pkg/man/slice-design.Rd
   pkg/man/sobol.Rd
   pkg/tests/fhn.R
Log:
- remove deprecated codes 'slice.design', 'sobol.design', and 'profile.design'


Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/NAMESPACE	2011-12-24 16:31:01 UTC (rev 570)
@@ -67,11 +67,8 @@
        gillespie.sim,
        sobol,
        sobolDesign,
-       sobol.design,
        sliceDesign,
-       slice.design,
        profileDesign,
-       profile.design,
        bspline.basis,
        periodic.bspline.basis,
        compare.mif,

Modified: pkg/R/profile-design.R
===================================================================
--- pkg/R/profile-design.R	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/R/profile-design.R	2011-12-24 16:31:01 UTC (rev 570)
@@ -1,8 +1,3 @@
-profile.design <- function (..., lower, upper, nprof) {
-  .Deprecated(new="profileDesign",package="pomp")
-  profileDesign(...,lower,upper,nprof)
-}
-
 profileDesign <- function (..., lower, upper, nprof) {
   prof <- list(...)
   pvars <- names(prof)

Modified: pkg/R/slice-design.R
===================================================================
--- pkg/R/slice-design.R	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/R/slice-design.R	2011-12-24 16:31:01 UTC (rev 570)
@@ -1,8 +1,3 @@
-slice.design <- function (center, ...) {
-  .Deprecated(new="sliceDesign",package="pomp")
-  sliceDesign(center,...)
-}
-
 sliceDesign <- function (center, ...) {
   slices <- list(...)
   if ((!is.numeric(center))||is.null(names(center)))

Modified: pkg/R/sobol.R
===================================================================
--- pkg/R/sobol.R	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/R/sobol.R	2011-12-24 16:31:01 UTC (rev 570)
@@ -16,11 +16,6 @@
   as.data.frame(y)
 }
 
-sobol.design <- function (lower = numeric(0), upper = numeric(0), nseq) {
-  .Deprecated(new="sobolDesign",package="pomp")
-  sobolDesign(lower,upper,nseq)
-}
-
 sobolDesign <- function (lower = numeric(0), upper = numeric(0), nseq) {
   if (length(lower)!=length(upper))
     stop(sQuote("lower")," and ",sQuote("upper")," must have same length")

Modified: pkg/man/profile-design.Rd
===================================================================
--- pkg/man/profile-design.Rd	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/man/profile-design.Rd	2011-12-24 16:31:01 UTC (rev 570)
@@ -1,13 +1,11 @@
 \name{profileDesign}
 \alias{profileDesign}
-\alias{profile.design}
 \title{Design matrices for likelihood profile calculations.}
 \description{
   \code{profileDesign} generates a data-frame where each row can be used as the starting point for a profile likelihood calculation.
 }
 \usage{
 profileDesign(\dots, lower, upper, nprof)
-profile.design(\dots, lower, upper, nprof)
 }
 \arguments{
   \item{\dots}{
@@ -23,7 +21,6 @@
 \value{
   \code{profileDesign} returns a data frame with \code{nprof} points per profile point.
   The other parameters in \code{vars} are sampled using \code{sobol}.
-  The equivalent form (\code{profile.design}) is now deprecated.
 }
 \seealso{\code{\link{sobol}}}
 \author{Aaron A. King \email{kingaa at umich dot edu}}

Modified: pkg/man/slice-design.Rd
===================================================================
--- pkg/man/slice-design.Rd	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/man/slice-design.Rd	2011-12-24 16:31:01 UTC (rev 570)
@@ -1,13 +1,11 @@
 \name{sliceDesign}
 \alias{sliceDesign}
-\alias{slice.design}
 \title{Design matrices for likelihood slices.}
 \description{
   \code{sliceDesign} generates a data-frame representing points taken along one or more slices through a point in a multidimensional space.
 }
 \usage{
 sliceDesign(center, ...)
-slice.design(center, ...)
 }
 \arguments{
   \item{center}{
@@ -20,9 +18,8 @@
 \value{
   \code{sliceDesign} returns a data frame with one row per point along a slice.
   The column \code{slice} is a factor that tells which slice each point belongs to. 
-  The equivalent form (\code{slice.design}) is now deprecated.
 }
-\seealso{\code{\link{profile.design}}}
+\seealso{\code{\link{profileDesign}}}
 \author{Aaron A. King \email{kingaa at umich dot edu}}
 \examples{
 ## A single 11-point slice through the point c(A=3,B=8,C=0) along the B direction.

Modified: pkg/man/sobol.Rd
===================================================================
--- pkg/man/sobol.Rd	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/man/sobol.Rd	2011-12-24 16:31:01 UTC (rev 570)
@@ -1,7 +1,6 @@
 \name{sobol}
 \alias{sobol}
 \alias{sobolDesign}
-\alias{sobol.design}
 \title{Sobol' low-discrepancy sequence}
 \description{
   Generate a data-frame containing a Sobol' low-discrepancy sequence.
@@ -9,7 +8,6 @@
 \usage{
 sobol(vars, n)
 sobolDesign(lower, upper, nseq)
-sobol.design(lower, upper, nseq)
 }
 \arguments{
   \item{vars}{Named list of ranges of variables.}
@@ -22,7 +20,6 @@
   }
   \item{sobolDesign}{
     Returns a data frame with \code{nseq} \sQuote{observations} of the variables over the range specified.
-    The equivalent form \code{sobol.design} is now deprecated and will be removed in a future release.
   }
 }
 \references{

Modified: pkg/tests/fhn.R
===================================================================
--- pkg/tests/fhn.R	2011-12-14 12:14:52 UTC (rev 569)
+++ pkg/tests/fhn.R	2011-12-24 16:31:01 UTC (rev 570)
@@ -37,7 +37,8 @@
             t0=0,
             tcovar=seq(0,21,by=0.1),
             covar=cbind(i=sin(2*pi*seq(0,21,by=0.1))),
-            skeleton.vectorfield=function(x,t,params,covars,...) {
+            skeleton.type="vectorfield",
+            skeleton=function(x,t,params,covars,...) {
               c(
                 V=unname(params['c']*(x['V']-(x['V']^3)/3-x['R']+covars['i'])),
                 R=unname((x['V']+params['a']-params['b']*x['R'])/params['c'])