deprecate corIdent(); new Version: 3.1-162

git-svn-id: https://svn.r-project.org/R-packages/trunk@8184 694ef91d-65df-0310-b7bb-92e67a308ead

Author: maechler

nlme/ChangeLog

@@ -1,3 +1,11 @@
+2023-01-28  Martin Maechler  <[email protected]>
+
+	* DESCRIPTION (Version): 3.1-162 (to be released)
+
+	* R/corStruct.R (corIdent, *.corIdent): deprecated corIdent() and
+	some of the "corIdent" methods.
+	* man/nlme-deprecated.Rd: deprecation
+
 2023-01-26  Sebastian Meyer  <[email protected]>
 
 	* src/matrix.h: fix return value in C declaration of Fortran

nlme/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: nlme
-Version: 3.1-161
-Date: 2022-11-18
+Version: 3.1-162
+Date: 2023-01-28
 Priority: recommended
 Title: Linear and Nonlinear Mixed Effects Models
 Authors@R: c(person("José", "Pinheiro", role = "aut", comment = "S version"),

nlme/NAMESPACE

@@ -28,7 +28,9 @@ importFrom("lattice",
 export(ACF, allCoef, asOneFormula, asTable, augPred, balancedGrouped,
        "coef<-", "coefficients<-", collapse, compareFits,
        comparePred, corAR1, corARMA, corCAR1, corCompSymm,
-       corExp, corFactor, corGaus, corIdent, corLin, corMatrix,
+       corExp, corFactor, corGaus
+     , corIdent # deprecated
+     , corLin, corMatrix,
        corNatural, corRatio, corSpatial, corSpher, corSymm,
        "covariate<-", Dim, fdHess, fixed.effects, fixef, gapply,
        getCovariate, getCovariateFormula, getData, getGroups,
@@ -78,7 +80,6 @@ S3method(coef, corAR1)
 S3method(coef, corARMA)
 S3method(coef, corCAR1)
 S3method(coef, corCompSymm)
-S3method(coef, corIdent)
 S3method(coef, corLin)
 S3method(coef, corNatural)
 S3method(coef, corSpatial)
@@ -113,7 +114,6 @@ S3method("coef<-", corAR1)
 S3method("coef<-", corARMA)
 S3method("coef<-", corCAR1)
 S3method("coef<-", corCompSymm)
-S3method("coef<-", corIdent)
 S3method("coef<-", corNatural)
 S3method("coef<-", corSpatial)
 S3method("coef<-", corStruct)
@@ -148,7 +148,6 @@ S3method(corMatrix, corAR1)
 S3method(corMatrix, corARMA)
 S3method(corMatrix, corCAR1)
 S3method(corMatrix, corCompSymm)
-S3method(corMatrix, corIdent)
 S3method(corMatrix, corNatural)
 S3method(corMatrix, corSpatial)
 S3method(corMatrix, corStruct)
@@ -228,7 +227,6 @@ S3method(Initialize, corAR1)
 S3method(Initialize, corARMA)
 S3method(Initialize, corCAR1)
 S3method(Initialize, corCompSymm)
-S3method(Initialize, corIdent)
 S3method(Initialize, corLin)
 S3method(Initialize, corNatural)
 S3method(Initialize, corSpatial)
@@ -259,7 +257,6 @@ S3method(lme, groupedData)
 S3method(lme, lmList)
 S3method(lmList, formula)
 S3method(lmList, groupedData)
-S3method(logDet, corIdent)
 S3method(logDet, corStruct)
 S3method(logDet, pdBlocked)
 S3method(logDet, pdCompSymm)
@@ -401,7 +398,6 @@ S3method(recalc, corAR1)
 S3method(recalc, corARMA)
 S3method(recalc, corCAR1)
 S3method(recalc, corCompSymm)
-S3method(recalc, corIdent)
 S3method(recalc, corNatural)
 S3method(recalc, corSpatial)
 S3method(recalc, corStruct)
@@ -436,7 +432,6 @@ S3method(summary, corCAR1)
 S3method(summary, corCompSymm)
 S3method(summary, corExp)
 S3method(summary, corGaus)
-S3method(summary, corIdent)
 S3method(summary, corLin)
 S3method(summary, corNatural)
 S3method(summary, corRatio)
@@ -500,3 +495,11 @@ S3method(varWeights, varComb)
 S3method(varWeights, varFunc)
 S3method(vcov, gls)
 S3method(vcov, lme)
+
+## deprecated:
+S3method("coef<-", corIdent)
+S3method(summary, corIdent)
+S3method(recalc, corIdent)
+S3method(logDet, corIdent)
+S3method(Initialize, corIdent)
+S3method(corMatrix, corIdent)

nlme/R/corStruct.R

@@ -771,14 +771,15 @@ summary.corNatural <-
   object
 }
 
-###*# corIdent - independent structure
+###*# corIdent - independent structure === DEPRECATED
 
 ####* Constructor
 
 corIdent <-
   ## Constructor for the corIdent class
   function(form = NULL)
 {
+  .Deprecated("corAR1(0, *)", "nlme")
   value <- numeric(0)
   attr(value, "formula") <- form
   attr(value, "fixed") <- TRUE
@@ -791,6 +792,7 @@ corIdent <-
 corMatrix.corIdent <-
   function(object, covariate = getCovariate(object), corr, ...)
 {
+  .Deprecated(package="nlme", old = "corMatrix.corIdent(): \"corIdent\" class")
   if(is.list(covariate)) {# by group
     as.list(lapply(covariate, function(el, object) corMatrix(object, el)))
   } else {
@@ -808,6 +810,7 @@ coef.corIdent <-
 Initialize.corIdent <-
   function(object, data, ...)
 {
+  .Deprecated(package="nlme", old = "Initialize.corIdent(): \"corIdent\" class")
   attr(object, "logDet") <- 0
   object
 }
@@ -819,6 +822,7 @@ recalc.corIdent <- function(object, conLin, ...) conLin
 summary.corIdent <-
   function(object, structName = "Independent", ...)
 {
+  .Deprecated(package="nlme", old = "summary.corIdent(): \"corIdent\" class")
   summary.corStruct(object, structName)
 }
 

nlme/man/Initialize.corStruct.Rd

@@ -13,7 +13,6 @@
 \alias{Initialize.corCAR1}
 \alias{Initialize.corCompSymm}
 \alias{Initialize.corHF}
-\alias{Initialize.corIdent}
 \alias{Initialize.corLin}
 \alias{Initialize.corNatural}
 \alias{Initialize.corSpatial}

nlme/man/coef.corStruct.Rd

@@ -14,7 +14,6 @@
 \alias{coef.corCAR1}   
 \alias{coef.corCompSymm}
 \alias{coef.corHF}
-\alias{coef.corIdent}  
 \alias{coef.corLin}
 \alias{coef.corNatural}
 \alias{coef.corSpatial}
@@ -27,7 +26,6 @@
 \alias{coef<-.corCompSymm}
 \alias{coef<-.corNatural}
 \alias{coef<-.corHF}
-\alias{coef<-.corIdent}  
 \alias{coef<-.corLin}
 \alias{coef<-.corSpatial}
 \alias{coef<-.corSpher}

nlme/man/corClasses.Rd

@@ -5,11 +5,10 @@
 \name{corClasses}
 \title{Correlation Structure Classes}
 \alias{corClasses}
-\alias{corIdent}
 \alias{corStruct}
 \description{
   Standard classes of correlation structures (\code{corStruct})
-  available in the \code{nlme} package. 
+  available in the \code{nlme} package.
 }
 \value{
   Available standard classes:
@@ -22,16 +21,17 @@
     constant correlation.}
   \item{corExp}{exponential spatial correlation.}
   \item{corGaus}{Gaussian spatial correlation.}
+% \item{corIdent}{Identity matrix (trivial zero) correlation. \bold{Deprecated}.}
   \item{corLin}{linear spatial correlation.}
   \item{corRatio}{Rational quadratics spatial correlation.}
   \item{corSpher}{spherical spatial correlation.}
   \item{corSymm}{general correlation matrix, with no additional
-    structure.} 
+    structure.}
 }
 
 \references{
   Pinheiro, J.C., and Bates, D.M. (2000) "Mixed-Effects Models
-  in S and S-PLUS", Springer.  
+  in S and S-PLUS", Springer.
 }
 \author{José Pinheiro and Douglas Bates \email{bates@stat.wisc.edu}}
 
@@ -40,7 +40,7 @@
   \code{constructor} function and, at a minimum, methods for the
   functions \code{corMatrix} and \code{coef}. For
   examples of these functions, see the methods for classes \code{corSymm}
-  and \code{corAR1}. 
+  and \code{corAR1}.
 }
 \seealso{
   \code{\link{corAR1}}, \code{\link{corARMA}},

nlme/man/corMatrix.corStruct.Rd

@@ -13,7 +13,6 @@
 \alias{corMatrix.corARMA}
 \alias{corMatrix.corCAR1}
 \alias{corMatrix.corCompSymm}
-\alias{corMatrix.corIdent}
 \alias{corMatrix.corNatural}
 \alias{corMatrix.corSpatial}
 \alias{corMatrix.corSymm}

nlme/man/logDet.corStruct.Rd

@@ -9,7 +9,6 @@
 \method{logDet}{corStruct}(object, covariate, \dots)
 }
 \alias{logDet.corStruct}
-\alias{logDet.corIdent}
 \arguments{
  \item{object}{an object inheriting from class \code{"\link{corStruct}"},
    representing a correlation structure.}

nlme/man/nlme-deprecated.Rd

@@ -9,18 +9,26 @@
 %% said to be deprecated in 2018-08, with warning since 2023-01
 \alias{nfGroupedData}
 \alias{nmGroupedData}
+\alias{corIdent}
 
 \usage{
 ## internal functions wrapped by groupedData()
 nfGroupedData(formula, data, order.groups, FUN, outer, inner,
               labels, units)
 nmGroupedData(formula, data, order.groups, FUN, outer, inner,
               labels, units)
+## trivial "identity" correlation:
+corIdent(form = NULL)
 }
 
 \description{
   These functions are provided for compatibility with older versions of
   \pkg{nlme} only, and may be defunct as soon as the next release.
 }
 
+\examples{
+tools::assertWarning(verbose=TRUE, csId <-  corIdent(~ 1 | Subject))
+tools::assertWarning(verbose=TRUE, csI. <- Initialize(csId, data = Orthodont))
+tools::assertCondition( corMatrix(csI.),  "error", "warning")# quietly, catching warning
+}
 \keyword{internal}

nlme/man/recalc.corStruct.Rd

@@ -13,7 +13,6 @@
 \alias{recalc.corCAR1}
 \alias{recalc.corCompSymm}
 \alias{recalc.corHF}
-\alias{recalc.corIdent}
 \alias{recalc.corNatural}
 \alias{recalc.corSpatial}
 \alias{recalc.corSymm}

nlme/man/summary.corStruct.Rd

@@ -14,7 +14,6 @@
 \alias{summary.corCompSymm}
 \alias{summary.corExp}
 \alias{summary.corGaus}
-\alias{summary.corIdent}
 \alias{summary.corLin}
 \alias{summary.corNatural}
 \alias{summary.corRatio}
@@ -27,9 +26,9 @@
  \item{structName}{an optional character string defining the type of
    correlation structure associated with \code{object}, to be used in
    the \code{print.summary} method. Defaults to
-   \code{class(object)[1]}.} 
+   \code{class(object)[1]}.}
  \item{\dots}{some methods for this generic require additional
-    arguments.  None are used in this method.} 
+    arguments.  None are used in this method.}
 }
 \description{
   This method function prepares \code{object} to be printed using the
@@ -44,10 +43,10 @@
 }
 \author{José Pinheiro and Douglas Bates }
 \seealso{
-  \code{\link{corClasses}}, 
+  \code{\link{corClasses}},
   \code{\link{corNatural}},
-  \code{\link{Initialize.corStruct}}, 
-  \code{\link{summary}} 
+  \code{\link{Initialize.corStruct}},
+  \code{\link{summary}}
 }
 
 %\seealso{\code{\link{print.summary.corStruct}}}