remove historical remarks about S-PLUS compatibility

git-svn-id: https://svn.r-project.org/R/trunk@85835 00db46b3-68df-0310-9c12-caf00c1e9a41

src/library/base/man/Random.Rd

@@ -1,6 +1,6 @@
 % File src/library/base/man/Random.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2021 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{Random}
@@ -92,9 +92,7 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
     We use the implementation by Reeds \emph{et al} (1982--84).
 
     The two seeds are the Tausworthe and congruence long integers,
-    respectively.  A one-to-one mapping to S's \code{.Random.seed[1:12]}
-    is possible but we will not publish one, not least as this generator
-    is \bold{not} exactly the same as that in recent versions of S-PLUS.
+    respectively.
 
     It exhibits 25 clear failures in the TestU01 Crush suite (\emph{L'Ecuyer}, 2007).
     }

src/library/base/man/cbind.Rd

@@ -1,6 +1,6 @@
 % File src/library/base/man/cbind.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2023 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{cbind}
@@ -100,13 +100,13 @@ rbind(\dots, deparse.level = 1)
   The \code{rbind} data frame method first drops all zero-column and
   zero-row arguments.  (If that leaves none, it returns the first
   argument with columns otherwise a zero-column zero-row data frame.)
-  It then takes the classes of the columns from the
-  first data frame, and matches columns by name (rather than by
-  position).  Factors have their levels expanded as necessary (in the
-  order of the levels of the level sets of the factors encountered) and
-  the result is an ordered factor if and only if all the components were
-  ordered factors.  (The last point differs from S-PLUS.)  Old-style
-  categories (integer vectors with levels) are promoted to factors.
+  It then takes the classes of the columns from the first data frame,
+  and matches columns by name (rather than by position).  Factors have
+  their levels expanded as necessary (in the order of the levels of the
+  level sets of the factors encountered) and the result is an ordered
+  factor if and only if all the components were ordered factors.
+  Old-style categories (integer vectors with levels) are promoted to
+  factors.
 
   Note that for result column \code{j}, \code{\link{factor}(., exclude = X(j))}
   is applied, where \preformatted{  X(j) := if(isTRUE(factor.exclude)) {

src/library/base/man/chartr.Rd

@@ -1,6 +1,6 @@
 % File src/library/base/man/chartr.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2020 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{chartr}
@@ -44,7 +44,7 @@ casefold(x, upper = FALSE)
   to a single upper-case character.
 
   \code{casefold} is a wrapper for \code{tolower} and \code{toupper}
-  provided for compatibility with S-PLUS.
+  originally written for compatibility with S-PLUS.
 }
 \value{
   A character vector of the same length and with the same attributes as

src/library/base/man/class.Rd

@@ -121,8 +121,6 @@ oldClass(x) <- value
 }
 
 \note{
-  Functions \code{oldClass} and \code{oldClass<-} behave in the same way
-  as functions of those names in S-PLUS 5/6, \emph{but} in \R
   \code{\link{UseMethod}} dispatches on the class as returned by
   \code{class} (with some interpolated classes: see the link) rather
   than \code{oldClass}.  \emph{However}, \link{group generic}s dispatch

src/library/base/man/file.access.Rd

@@ -1,6 +1,6 @@
 % File src/library/base/man/file.access.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2023 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{file.access}
@@ -54,10 +54,10 @@ file.access(names, mode = 0)
 }
 
 \note{
-  This is intended as a replacement for the S-PLUS function
+  This was written as a replacement for the S-PLUS function
   \code{access}, a wrapper for the C function of the same name, which
-  explains the return value encoding.  Note that
-  the return value is \bold{false} for \bold{success}.
+  explains the return value encoding.  Note that the return value is
+  \bold{false} for \bold{success}.
 }
 
 \seealso{

src/library/base/man/make.names.Rd

@@ -1,6 +1,6 @@
 % File src/library/base/man/make.names.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2013 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{make.names}
@@ -51,8 +51,7 @@ make.names(names, unique = FALSE, allow_ = TRUE)
   work. Use \code{allow_ = FALSE} for back-compatibility.
 
   \code{allow_ = FALSE} is also useful when creating names for export to
-  applications which do not allow underline in names (for example,
-  S-PLUS and some DBMSes).
+  applications which do not allow underline in names (such as some DBMSes).
 }
 \seealso{
   \code{\link{make.unique}},

src/library/datasets/man/iris.Rd

@@ -1,6 +1,6 @@
 % File src/library/datasets/man/iris.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2023 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{iris}
@@ -25,7 +25,7 @@ iris3
   \code{Petal.Length}, \code{Petal.Width}, and \code{Species}.
 
   \code{iris3} gives the same data arranged as a 3-dimensional array
-  of size 50 by 4 by 3, as represented by S-PLUS.  The first dimension
+  of size 50 by 4 by 3, as once provided by S-PLUS.  The first dimension
   gives the case number within the species subsample, the second the
   measurements with names \code{Sepal L.}, \code{Sepal W.},
   \code{Petal L.}, and \code{Petal W.}, and the third the species.

src/library/datasets/man/longley.Rd

@@ -1,6 +1,6 @@
 % File src/library/datasets/man/longley.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2014 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{longley}
@@ -43,7 +43,7 @@
 }
 \examples{
 require(stats); require(graphics)
-## give the data set in the form it is used in S-PLUS:
+## give the data set in the form it was used in S-PLUS:
 longley.x <- data.matrix(longley[, 1:6])
 longley.y <- longley[, "Employed"]
 pairs(longley, main = "longley data")

src/library/datasets/man/stackloss.Rd

@@ -1,6 +1,6 @@
 % File src/library/datasets/man/stackloss.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2007 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{stackloss}
@@ -31,10 +31,10 @@ stack.loss
     [,4] \tab  \code{stack.loss} \tab Stack loss\cr
   }
 
-  For compatibility with S-PLUS, the data sets \code{stack.x}, a matrix
-  with the first three (independent) variables of the data frame, and
-  \code{stack.loss}, the numeric vector giving the fourth (dependent)
-  variable, are provided as well.
+  For historical compatibility with S-PLUS, the data sets
+  \code{stack.x}, a matrix with the first three (independent) variables
+  of the data frame, and \code{stack.loss}, the numeric vector giving
+  the fourth (dependent) variable, are also provided.
 }
 \source{
   Brownlee, K. A. (1960, 2nd ed.\sspace{}1965)

src/library/stats/man/ar.Rd

@@ -108,7 +108,7 @@ ar.mle(x, aic = TRUE, order.max = NULL, na.action = na.fail,
   \code{ar.burg} allows two methods to estimate the innovations
   variance and hence AIC. Method 1 is to use the update given by
   the Levinson-Durbin recursion (Brockwell and Davis, 1991, (8.2.6)
-  on page 242), and folloeds S-PLUS. Method 2 is the mean of the sum
+  on page 242), and follows S-PLUS.  Method 2 is the mean of the sum
   of squares of the forward and backward prediction errors
   (as in Brockwell and Davis, 1996, page 145). Percival and Walden
   (1998) discuss both. In the multivariate case the estimated

src/library/stats/man/arima.Rd

@@ -108,14 +108,14 @@ arima(x, order = c(0L, 0L, 0L),
   \deqn{X_t= a_1 X_{t-1}+\cdots+ a_p X_{t-p} + e_t + b_1 e_{t-1}+\cdots+b_q e_{t-q}
   }{X[t] = a[1]X[t-1] + \dots + a[p]X[t-p] + e[t] + b[1]e[t-1] + \dots + b[q]e[t-q]}
 
-  and so the MA coefficients differ in sign from those used by S-PLUS.
-  Further, if \code{include.mean} is true (the default for an ARMA
-  model), this formula applies to \eqn{X - m} rather than \eqn{X}.  For
-  ARIMA models with differencing, the differenced series follows a
-  zero-mean ARMA model. If an \code{xreg} term is included, a linear
-  regression (with a constant term if \code{include.mean} is true and
-  there is no differencing) is fitted with an ARMA model for the error
-  term.
+  and so the MA coefficients differ in sign from those used in
+  documentation written for S-PLUS.  Further, if \code{include.mean} is
+  true (the default for an ARMA model), this formula applies to \eqn{X -
+  m} rather than \eqn{X}.  For ARIMA models with differencing, the
+  differenced series follows a zero-mean ARMA model. If an \code{xreg}
+  term is included, a linear regression (with a constant term if
+  \code{include.mean} is true and there is no differencing) is fitted
+  with an ARMA model for the error term.
 
   The variance matrix of the estimates is found from the Hessian of
   the log-likelihood, and so may only be a rough guide.
@@ -234,11 +234,6 @@ arima(x, order = c(0L, 0L, 0L),
 }
 
 \note{
-  The results are likely to be different from S-PLUS's
-  \code{arima.mle}, which computes a conditional likelihood and does
-  not include a mean in the model.  Further, the convention used by
-  \code{arima.mle} reverses the signs of the MA coefficients.
-
   \code{arima} is very similar to \code{\link{arima0}} for
   ARMA models or for differenced models without missing values,
   but handles differenced models with missing values exactly.

src/library/stats/man/cor.Rd

@@ -90,9 +90,8 @@ cov2cor(V)
   and gives an error in the other cases.
 
   The denominator \eqn{n - 1} is used which gives an unbiased estimator
-  of the (co)variance for i.i.d. observations.
-  These functions return \code{\link{NA}} when there is only one
-  observation (whereas S-PLUS returned \code{NaN}).
+  of the (co)variance for i.i.d. observations.  These functions return
+  \code{\link{NA}} when there is only one observation.
 
   For \code{cor()}, if \code{method} is \code{"kendall"} or
   \code{"spearman"}, Kendall's \eqn{\tau}{tau} or Spearman's

src/library/stats/man/cov.wt.Rd

@@ -44,8 +44,7 @@ cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE,
   The covariance matrix is divided by one minus the sum of squares of
   the weights, so if the weights are the default (\eqn{1/n}) the conventional
   unbiased estimate of the covariance matrix with divisor \eqn{(n - 1)}
-  is obtained.  This differs from the behaviour in S-PLUS which
-  corresponded to \code{method = "ML"} and does not divide.
+  is obtained.
 }
 \seealso{\code{\link{cov}} and \code{\link{var}}.
 }

src/library/stats/man/density.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/density.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2023 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{density}
@@ -27,7 +27,7 @@ density(x, \dots)
 
   \item{bw}{the smoothing bandwidth to be used.  The kernels are scaled
     such that this is the standard deviation of the smoothing kernel.
-    (Note this differs from the reference books cited below, and from S-PLUS.)
+    (Note this differs from the reference books cited below.)
 
     \code{bw} can also be a character string giving a rule to choose the
     bandwidth.  See \code{\link{bw.nrd}}. \cr The default,

src/library/stats/man/kernel.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/kernel.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2014 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{kernel}
@@ -45,8 +45,7 @@ is.tskernel(k)
 }
 \details{
   \code{kernel} is used to construct a general kernel or named specific
-  kernels.  The modified Daniell kernel halves the end coefficients (as
-  used by S-PLUS).
+  kernels.  The modified Daniell kernel halves the end coefficients.
 
   The \code{\link{[}} method allows natural indexing of kernel objects
   with indices in \code{(-m) : m}.  The normalization is such that for

src/library/stats/man/plot.spec.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/plot.spec.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2007 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{plot.spec}
@@ -40,7 +40,7 @@ plot.spec.coherency(x, ci = 0.95,
   \item{ci}{coverage probability for confidence interval.  Plotting of
     the confidence bar/limits is omitted unless \code{ci} is strictly
     positive.}
-  \item{log}{If \code{"dB"}, plot on log10 (decibel) scale (as S-PLUS),
+  \item{log}{If \code{"dB"}, plot on log10 (decibel) scale,
     otherwise use conventional log scale or linear scale.  Logical
     values are also accepted.  The default is \code{"yes"} unless
     \code{options(ts.S.compat = TRUE)} has been set, when it is

src/library/stats/man/ppr.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/ppr.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2018 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 % file stats/man/ppr.Rd
@@ -137,9 +137,9 @@ method functions.
 \item{model}{(only if \code{model = TRUE}) the model frame.}
 }
 \details{
-  The basic method is given by Friedman (1984), and is essentially the
-  same code used by S-PLUS's \code{ppreg}.  This code is extremely
-  sensitive to the compiler used.
+  The basic method is given by Friedman (1984) and based on his
+  code. This code has been shown to be extremely sensitive to the
+  Fortrancompiler used.
 
   The algorithm first adds up to \code{max.terms} ridge terms one at a
   time; it will use less if it is unable to find a term to add that makes

src/library/stats/man/princomp.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/princomp.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2018 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{princomp}
@@ -90,9 +90,9 @@ princomp(x, \dots)
   \code{princomp} is a generic function with \code{"formula"} and
   \code{"default"} methods.
 
-  The calculation is done using \code{\link{eigen}} on the correlation or
-  covariance matrix, as determined by \code{\link{cor}}.  This is done for
-  compatibility with the S-PLUS result.  A preferred method of
+  The calculation is done using \code{\link{eigen}} on the correlation
+  or covariance matrix, as determined by \code{\link{cor}}.  (This was
+  done for compatibility with the S-PLUS result.)  A preferred method of
   calculation is to use \code{\link{svd}} on \code{x}, as is done in
   \code{prcomp}.
 

src/library/stats/man/smooth.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/smooth.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2016 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{smooth}
@@ -48,8 +48,6 @@ smooth(x, kind = c("3RS3R", "3RSS", "3RSR", "3R", "3", "S"),
   smoothed values with additional attributes.
 }
 \note{
-  S and S-PLUS used a different (somewhat better) Tukey smoother in
-  \code{smooth(*)}.
   Note that there are other smoothing methods which provide
   rather better results.  These were designed for hand calculations
   and may be used mainly for didactical purposes.

src/library/stats/man/smooth.spline.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/smooth.spline.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2023 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{smooth.spline}
@@ -148,11 +148,12 @@ smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE,
 %%   = 1/3 - log(r)/{24 log(2)} +  log(lam) / {24 log(2)}
 %%   =               s0         + 0.0601 * log(lam)
   Note that from the above relation,
-  \code{spar} is \eqn{s = s0 + 0.0601 \cdot \log\lambda}{spar = s0 + 0.0601 * log(\lambda)},
-  which is intentionally \emph{different} from the S-PLUS implementation
-  of \code{smooth.spline} (where \code{spar} is proportional to
-  \eqn{\lambda}).  In \R's (\eqn{\log \lambda}{log \lambda}) scale, it makes more
-  sense to vary \code{spar} linearly.
+  \code{spar} is \eqn{s = s0 + 0.0601 \cdot \log\lambda}{spar = s0 + 0.0601 * log(\lambda)}.
+  %% which is intentionally \emph{different} from the S-PLUS implementation
+  %% of \code{smooth.spline} (where \code{spar} is proportional to
+  %% \eqn{\lambda}).
+  %% In \R's (\eqn{\log \lambda}{log \lambda}) scale, it makes more
+  %% sense to vary \code{spar} linearly.
 
   Note however that currently the results may become very unreliable
   for \code{spar} values smaller than about -1 or -2.  The same may

src/library/stats/man/spectrum.Rd

@@ -1,6 +1,6 @@
 % File src/library/stats/man/spectrum.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2008 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{spectrum}
@@ -57,11 +57,11 @@ spectrum(x, \dots, method = c("pgram", "ar"))
   \code{spectrum} is a wrapper function which calls the methods
   \code{\link{spec.pgram}} and \code{\link{spec.ar}}.
 
-  The spectrum here is defined with scaling \code{1/\link{frequency}(x)},
-  following S-PLUS.  This makes the spectral density a density over the
-  range \code{(-frequency(x)/2, +frequency(x)/2]}, whereas a more common
-  scaling is \eqn{2\pi}{2pi} and range \eqn{(-0.5, 0.5]} (e.g., Bloomfield)
-  or 1 and range \eqn{(-\pi, \pi]}{(-pi, pi]}.
+  The spectrum here is defined (for historical compatibility) with
+  scaling \code{1/\link{frequency}(x)}.  This makes the spectral density
+  a density over the range \code{(-frequency(x)/2, +frequency(x)/2]},
+  whereas a more common scaling is \eqn{2\pi}{2pi} and range \eqn{(-0.5,
+  0.5]} (e.g., Bloomfield) or 1 and range \eqn{(-\pi, \pi]}{(-pi, pi]}.
 
   If available, a confidence interval will be plotted by
   \code{plot.spec}: this is asymmetric, and the width of the centre