Tweaks.

git-svn-id: https://svn.r-project.org/R/trunk@87736 00db46b3-68df-0310-9c12-caf00c1e9a41

Author: hornik

src/library/graphics/man/contour.Rd

@@ -91,7 +91,7 @@ contour(x, \dots)
   Vector (of length \eqn{> 1}) \code{col}, \code{lty}, and \code{lwd} are
   applied along \code{levels} and recycled, see the Examples.
 
-  Alternatively, use \code{\link[lattice:levelplot]{contourplot}} from the
+  Alternatively, use \code{\link[lattice]{contourplot}} from the
   \CRANpkg{lattice} package where the \code{\link{formula}} notation allows
   to use vectors \code{x}, \code{y}, and \code{z} of the same length.
 
@@ -111,7 +111,7 @@ contour(x, \dots)
 
   \code{\link{contourLines}}, \code{\link{filled.contour}}
   for color-filled contours,
-  \code{\link[lattice:levelplot]{contourplot}} (and
+  \code{\link[lattice]{contourplot}} (and
   \code{\link[lattice]{levelplot}}) from package \CRANpkg{lattice}.
   Further, \code{\link{image}} and the graphics demo which can be
   invoked as \code{demo(graphics)}.

src/library/graphics/man/filled.contour.Rd

@@ -108,7 +108,7 @@ filled.contour(x = seq(0, 1, length.out = nrow(z)),
 \seealso{
   \code{\link{contour}}, \code{\link{image}},
   \code{\link{hcl.colors}}, \code{\link{gray.colors}},
-  \code{\link{palette}}; \code{\link[lattice:levelplot]{contourplot}}
+  \code{\link{palette}}; \code{\link[lattice]{contourplot}}
   and \code{\link[lattice]{levelplot}} from package \CRANpkg{lattice}.
 }
 \examples{

src/library/methods/man/cbind2.Rd

@@ -74,9 +74,9 @@ rbind2(x, y, ...)
   from deparsing argument names such as in \code{\link{cbind}(...,
     deparse.level = d)} for \eqn{d \ge 1}{d >= 1}).
 }
-\seealso{\code{\link{cbind}}, \code{\link{rbind}};
-  further, \code{\link[Matrix]{cBind}}, \code{\link[Matrix:cBind]{rBind}} in
-  the \CRANpkg{Matrix} package.
+\seealso{
+  \code{\link{cbind}},
+  \code{\link{rbind}}
 }
 \examples{
 cbind2(1:3, 4)

src/library/stats/man/cor.Rd

@@ -120,7 +120,7 @@ cov2cor(V)
   Some people have noted that the code for Kendall's tau is slow for
   very large datasets (many more than 1000 cases).  It rarely makes
   sense to do such a computation, but see function
-  \code{\link[pcaPP:cor.fk]{cor.fk}} in package \CRANpkg{pcaPP}.
+  \code{\link[pcaPP]{cor.fk}} in package \CRANpkg{pcaPP}.
 }
 \references{
   Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988).

src/library/stats/man/cor.test.Rd

@@ -129,12 +129,12 @@ cor.test(x, \dots)
 }
 
 \seealso{
-  \code{\link[Kendall:Kendall]{Kendall}} in package \CRANpkg{Kendall}.
+  \code{\link[Kendall]{Kendall}} in package \CRANpkg{Kendall}.
 
   \code{\link[SuppDists]{pKendall}} and
   \code{\link[SuppDists]{pSpearman}} in package
   \CRANpkg{SuppDists},
-  \code{\link[pspearman:spearman.test]{spearman.test}} in package
+  \code{\link[pspearman]{spearman.test}} in package
   \CRANpkg{pspearman},
   which supply different (and often more accurate) approximations.
 }

src/library/stats/man/logLik.Rd

@@ -71,7 +71,7 @@ logLik(object, \dots)
   the restrictions if \code{REML = TRUE}).
 }
 \seealso{
-  \code{\link[nlme:logLik.lme]{logLik.gls}}, \code{\link[nlme]{logLik.lme}}, in
+  \code{\link[nlme]{logLik.gls}}, \code{\link[nlme]{logLik.lme}}, in
   package \CRANpkg{nlme}, etc.
 
   \code{\link{AIC}}

src/library/stats/man/princomp.Rd

@@ -44,8 +44,8 @@ princomp(x, \dots)
   \item{scores}{a logical value indicating whether the score on each
     principal component should be calculated.}
   \item{covmat}{a covariance matrix, or a covariance list as returned by
-    \code{\link{cov.wt}} (and \code{\link[MASS:cov.rob]{cov.mve}} or
-    \code{\link[MASS:cov.rob]{cov.mcd}} from package \CRANpkg{MASS}).
+    \code{\link{cov.wt}} (and \code{\link[MASS]{cov.mve}} or
+    \code{\link[MASS]{cov.mcd}} from package \CRANpkg{MASS}).
     If supplied, this is used rather than the covariance matrix of
     \code{x}.}
   \item{fix_sign}{Should the signs of the loadings and scores be chosen

src/library/stats/man/simulate.Rd

@@ -64,7 +64,7 @@ simulate(object, nsim = 1, seed = NULL, \dots)
   Poisson, for which prior weights are ignored with a warning.
 
   For a gamma GLM the shape parameter is estimated by maximum likelihood
-  (using function \code{\link[MASS:gamma.shape.glm]{gamma.shape}} in package
+  (using function \code{\link[MASS]{gamma.shape}} in package
   \CRANpkg{MASS}).  The interpretation of weights is as multipliers to a
   basic shape parameter, since dispersion is inversely proportional to
   shape.

src/library/stats4/man/plot-methods.Rd

@@ -33,7 +33,7 @@
 \section{Methods}{
   \describe{
     \item{\code{signature(x = "ANY", y = "ANY")}}{Generic function: see
-      \code{\link[graphics:plot.default]{plot}}.}
+      \code{\link[graphics]{plot}}.}
     \item{\code{signature(x = "profile.mle", y = "missing")}}{Plot
       likelihood profiles for \code{x}.}
   }

src/library/tools/man/check_packages_in_dir.Rd

@@ -131,7 +131,7 @@ check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRUE, ...)
 
   Installation and checking is performed in parallel if \code{Ncpus} is
   greater than one: this will use \code{\link[parallel]{mclapply}} on
-  Unix and \code{\link[parallel:clusterApply]{parLapply}} on Windows.
+  Unix and \code{\link[parallel]{parLapply}} on Windows.
 
   \code{check_packages_in_dir} returns an object inheriting from class
   \code{"check_packages_in_dir"} which has \code{\link{print}} and