Auto-generate citations and references.

git-svn-id: https://svn.r-project.org/R/trunk@88500 00db46b3-68df-0310-9c12-caf00c1e9a41

Author: hornik

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 1995-2024 R Core Team
+% Copyright 1995-2025 R Core Team
 % Distributed under GPL 2 or later
 
 \name{Random}
@@ -65,14 +65,16 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
       30323)}.
     The \I{Wichmann}--\I{Hill} generator has a cycle length of
     \eqn{6.9536 \times 10^{12}}{6.9536e12} (=
-    \code{prod(p-1)/4}, see \emph{Applied Statistics} (1984)
-    \bold{33}, 123 which corrects the original article).
+    \code{prod(p-1)/4}, see
+    \bibcitet{R:Wichmann+Hill:1984}
+    which corrects the original article).
     It exhibits 12 clear failures in the \I{TestU01} Crush suite and 22
-    in the \I{BigCrush} suite (\bibcite{L'Ecuyer, 2007}).}
+    in the \I{BigCrush} suite \bibcitep{R:L_Ecuyer+Simard:2007}.}
 
     \item{\code{"Marsaglia-Multicarry"}:}{
     A \emph{multiply-with-carry} RNG is used, as recommended by George
-    \I{Marsaglia} in his post to the mailing list \file{sci.stat.math}.
+    \I{Marsaglia} in his post to the mailing list \file{sci.stat.math}
+    \bibcitep{R:Marsaglia:1997}.
     It has a period of more than \eqn{2^{60}}{2^60}.
 
     It exhibits 40 clear failures in \I{L'Ecuyer}'s \I{TestU01} Crush suite.
@@ -89,17 +91,17 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
       4.6*10^18} for most initial seeds.  The seed is two integers (all
     values allowed for the first seed: the second must be odd).
 
-    We use the implementation by Reeds \abbr{et al.}\sspace(1982--84).
+    We use the implementation by \bibcitet{R:Reeds+Hubert+Abrahams:1982-4}.
 
     The two seeds are the \I{Tausworthe} and congruence long integers,
     respectively.
 
     It exhibits 25 clear failures in the \I{TestU01} Crush suite
-    (\bibcite{L'Ecuyer, 2007}). 
+    \bibcitep{R:L_Ecuyer+Simard:2007}. 
     }
 
     \item{\code{"Mersenne-Twister"}:}{
-      From \bibcite{Matsumoto and Nishimura (1998)}; code updated in 2002.
+      From \bibcitet{R:Matsumoto+Nishimura:1998}; code updated in 2002.
       A twisted \abbr{GFSR} with period
       \eqn{2^{19937} - 1}{2^19937 - 1} and equidistribution in 623
       consecutive dimensions (over the whole period).  The \sQuote{seed} is a
@@ -110,8 +112,8 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
       not affected by the initialization issue in the 1998 code of
       \I{Matsumoto} and \I{Nishimura} addressed in a 2002 update.
 
-      It exhibits 2 clear failures in each of the \I{TestU01} Crush and the
-      \I{BigCrush} suite (\bibcite{L'Ecuyer, 2007}).
+      It exhibits 2 clear failures in each of the \I{TestU01} Crush and
+      the \I{BigCrush} suite \bibcitep{R:L_Ecuyer+Simard:2007}.
     }
 
     \item{\code{"Knuth-TAOCP-2002"}:}{
@@ -125,7 +127,7 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
     }
 
     \item{\code{"Knuth-TAOCP"}:}{
-      An earlier version from Knuth (1997).
+      An earlier version from \bibcitet{R:Knuth:1997}.
 
       The 2002 version was not backwards compatible with the earlier
       version: the initialization of the \abbr{GFSR} from the seed was altered.
@@ -139,14 +141,11 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
 
       It exhibits 3 clear failure in the \I{TestU01} Crush suite and
       4 clear failures in the \I{BigCrush} suite
-      (\emph{\I{L'Ecuyer}}, 2007).
+      \bibcitep{R:L_Ecuyer+Simard:2007}.
     }
     \item{\code{"L'Ecuyer-CMRG"}:}{
       A \sQuote{combined multiple-recursive generator} from
-      %% <FIXME: bibcite>
-      %% \I{L'Ecuyer} (1999),
       \bibcitet{R:L_Ecuyer:1999},
-      %% </FIXME>
       each element of which is a feedback multiplicative
       generator with three integer elements: thus the seed is a (signed)
       integer vector of length 6. The period is around
@@ -161,8 +160,8 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
       basis for the multiple streams used in package \pkg{parallel}.
       % See \code{\link{RngStream}}.
 
-      It exhibits 6 clear failures in each of the \I{TestU01} Crush and the
-      \I{BigCrush} suite (\emph{\I{L'Ecuyer}}, 2007).
+      It exhibits 6 clear failures in each of the \I{TestU01} Crush and
+      the \I{BigCrush} suite \bibcitep{R:L_Ecuyer+Simard:2007}.
     }
 
     \item{\code{"user-supplied"}:}{
@@ -255,99 +254,30 @@ set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)
   \code{set.seed} returns \code{NULL}, invisibly.
 }
 \references{
-  Ahrens, J. H. and Dieter, U. (1973).
-  Extensions of Forsythe's method for random sampling from the normal
-  distribution.
-  \emph{Mathematics of Computation}, \bold{27}, 927--937.
-
-  Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988).
-  \emph{The New S Language}.
-  Wadsworth & Brooks/Cole.
-  (\code{set.seed}, storing in \code{.Random.seed}.)
-
-  Box, G. E. P. and Muller, M. E. (1958).
-  A note on the generation of normal random deviates.
-  \emph{Annals of Mathematical Statistics}, \bold{29}, 610--611.
-  \doi{10.1214/aoms/1177706645}.
-
-  De Matteis, A. and Pagnutti, S. (1993).
-  Long-range Correlation Analysis of the Wichmann-Hill Random Number
-  Generator.
-  \emph{Statistics and Computing}, \bold{3}, 67--70.
-  \doi{10.1007/BF00153065}.
-
-  Kinderman, A. J. and Ramage, J. G. (1976).
-  Computer generation of normal random variables.
-  \emph{Journal of the American Statistical Association}, \bold{71},
-  893--896.
-  \doi{10.2307/2286857}.
-
-  Knuth, D. E. (1997).
-  \emph{The Art of Computer Programming}.
-  Volume 2, third edition.\cr
-  Source code at \url{https://www-cs-faculty.stanford.edu/~knuth/taocp.html}.
-
-  Knuth, D. E. (2002).
-  \emph{The Art of Computer Programming}.
-  Volume 2, third edition, ninth printing.
-
-  \I{L'Ecuyer}, P. (1999).
-  Good parameters and implementations for combined multiple recursive
-  random number generators.
-  \emph{Operations Research}, \bold{47}, 159--164.
-  \doi{10.1287/opre.47.1.159}.
-
-  %% <FIXME bibcite>  
-  %% \I{L'Ecuyer}, P. and Simard, R. (2007).
-  %% \I{TestU01}: A C Library for Empirical Testing of Random Number Generators
-  %% \emph{ACM Transactions on Mathematical Software}, \bold{33}, Article 22.
-  %% \doi{10.1145/1268776.1268777}.
-  %% \cr The \I{TestU01} C library is available from
-  %% \url{https://simul.iro.umontreal.ca/testu01/tu01.html} or also
-  %% \url{https://github.com/umontreal-simul/TestU01-2009}.
-  %% </FIXME>
-  
-  %% <FIXME bibcite>
-  \bibinfo{R:Simard+L_Ecuyer:2007}{footer}{
+  \bibinfo{R:Becker+Chambers+Wilks:1988}{footer}{
+    (\\\\\\code{set.seed}, storing in \\\\\\code{.Random.seed}.)}
+  \bibinfo{R:Knuth:1997}{footer}{
+    Source code at \\\\\\url{https://www-cs-faculty.stanford.edu/~knuth/taocp.html}.}
+  \bibinfo{R:L_Ecuyer+Simard:2007}{footer}{
     The \\\\\\I{TestU01} C library is available from
     \\\\\\url{https://simul.iro.umontreal.ca/testu01/tu01.html} or also
     \\\\\\url{https://github.com/umontreal-simul/TestU01-2009}.
   }
-  \bibshow{R:Simard+L_Ecuyer:2007}
-  %% </FIXME>
-
-  Marsaglia, G. (1997).
-  \emph{A random number generator for C}.
-  Discussion paper, posting on Usenet newsgroup \code{sci.stat.math} on
-  September 29, 1997.
-
-  Marsaglia, G. and Zaman, A. (1994).
-  Some portable very-long-period random number generators.
-  \emph{Computers in Physics}, \bold{8}, 117--121.
-  \doi{10.1063/1.168514}.
-
-  Matsumoto, M. and Nishimura, T. (1998).
-  Mersenne Twister: A 623-dimensionally equidistributed uniform
-  pseudo-random number generator,
-  \emph{ACM Transactions on Modeling and Computer Simulation},
-  \bold{8}, 3--30.\cr
-  Source code formerly at \code{http://www.math.keio.ac.jp/~matumoto/emt.html}.\cr
-  Now see \url{https://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/VERSIONS/C-LANG/c-lang.html}.
-
-  Reeds, J., Hubert, S. and Abrahams, M. (1982--4).
-  C implementation of SuperDuper, University of California at Berkeley.
-  (Personal communication from Jim Reeds to Ross Ihaka.)
-
-  Wichmann, B. A.  and Hill, I. D. (1982).
-  Algorithm AS 183: An Efficient and Portable Pseudo-random Number
-  Generator.
-  \emph{Applied Statistics}, \bold{31}, 188--190; Remarks:
-  \bold{34}, 198 and \bold{35}, 89.
-  \doi{10.2307/2347988}.
-
-  %% <FIXME bibcite>
-  \bibshow{*}
-  %% </FIXME>
+  \bibinfo{R:Matsumoto+Nishimura:1998}{footer}{
+    Source code formerly at \\\\\\code{http://www.math.keio.ac.jp/~matumoto/emt.html}.
+    Now see \\\\\\url{https://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/VERSIONS/C-LANG/c-lang.html}.}
+  \bibinfo{R:Wichmann+Hill:1982}{note}{Remarks:
+    \\\\\\bold{34}, 198 and \\\\\\bold{35}, 89.}
+
+  \bibshow{*,
+    R:Ahrens+Dieter:1973,
+    R:Becker+Chambers+Wilks:1988,
+    R:Box+Muller:1958,
+    R:De_Matteis+Pagnutti:1993,
+    R:Kinderman+Ramage:1976,
+    R:Knuth:2002,
+    R:Marsaglia+Zaman:1994,
+    R:Wichmann+Hill:1982}
 }
 \author{of RNGkind: Martin Maechler. Current implementation, B. D. Ripley
   with modifications by Duncan Murdoch.}

src/library/base/man/sort.Rd

@@ -1,6 +1,6 @@
 % File src/library/base/man/sort.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2022 R Core Team
+% Copyright 1995-2025 R Core Team
 % Distributed under GPL 2 or later
 
 \name{sort}
@@ -78,20 +78,13 @@ sort.int(x, partial = NULL, na.last = NA, decreasing = FALSE,
   are more than 10.)  Names are discarded for partial sorting.
 
   Method \code{"shell"} uses Shellsort (an \eqn{O(n^{4/3})} variant from
-  %% <FIXME bibcite>
-  %% \bibcite{Sedgewick (1986)}).
-  \bibcitet{R:Sedgewick:1986}.
-  %% </FIXME>
-  If \code{x} has names a stable modification is
+  \bibcitet{R:Sedgewick:1986}.  If \code{x} has names a stable modification is
   used, so ties are not reordered.  (This only matters if names are
   present.)
 
   Method \code{"quick"} uses
-  %% FIXME bibcite
-  %% Singleton (1969)'s implementation of \I{Hoare}'s Quicksort method
   the implementation of \I{Hoare}'s Quicksort method from
   \bibcitet{R:Singleton:1969}
-  %% </FIXME>  
   and is only available when \code{x} is
   numeric (double or integer) and \code{partial} is \code{NULL}.  (For
   other types of \code{x} Shellsort is used, silently.)  It is normally
@@ -156,10 +149,7 @@ sort.int(x, partial = NULL, na.last = NA, decreasing = FALSE,
   \code{\link{order}} if you want the original element numbers.
 
   All attributes are removed from the return value
-  %% <FIXME bibcite>
-  %% (see Becker \abbr{et al.}, 1988, p.146)
   \bibcitep{|R:Becker+Chambers+Wilks:1988|p.\\\\\\sspace{}146}
-  %% </FIXME>
   except names, which are sorted.  (If
   \code{partial} is specified even the names are removed.)  Note that
   this means that the returned value has no class, except for factors
@@ -168,36 +158,7 @@ sort.int(x, partial = NULL, na.last = NA, decreasing = FALSE,
 }
 
 \references{
-  %% <FIXME bibcite>
   \bibshow{*, R:Knuth:1998}
-  %% </FIXME>
-  
-  %% <FIXME bibcite>  
-  %% Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988).
-  %% \emph{The New S Language}.
-  %% Wadsworth & Brooks/Cole.
-  %% </FIXME>
-  
-  %% <FIXME bibcite>    
-  %% Knuth, D. E. (1998).
-  %% \emph{The Art of Computer Programming, Volume 3: Sorting and
-  %%   Searching}, 2nd ed.
-  %% Addison-Wesley.
-  %% </FIXME>
-
-  %% <FIXME bibcite>
-  %% Sedgewick, R. (1986).
-  %% A new upper bound for Shellsort.
-  %% \emph{Journal of Algorithms}, \bold{7}, 159--173.
-  %% \doi{10.1016/0196-6774(86)90001-5}.
-  %% </FIXME>
-
-  %% <FIXME bibcite>
-  %% Singleton, R. C. (1969).
-  %% Algorithm 347: an efficient algorithm for sorting with minimal storage.
-  %% \emph{Communications of the ACM}, \bold{12}, 185--186.
-  %% \doi{10.1145/362875.362901}.
-  %% </FIXME>
 }
 \seealso{
   \sQuote{\link{Comparison}} for how character strings are collated.

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

@@ -1,6 +1,6 @@
 % File src/library/stats/man/fisher.test.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2024 R Core Team
+% Copyright 1995-2025 R Core Team
 % Distributed under GPL 2 or later
 
 \name{fisher.test}
@@ -87,8 +87,8 @@ fisher.test(x, y = NULL, workspace = 200000, hybrid = FALSE,
   using the (central or non-central) hypergeometric
   distribution. Otherwise, computations are based on a C version of the
   FORTRAN subroutine \code{FEXACT} which implements the network developed by
-  \bibcite{Mehta and Patel (1983, 1986)} and improved by
-  \bibcite{Clarkson, Fan and Joe (1993)}.
+  \bibcitet{R:Mehta+Patel:1983, R:Patel+Mehta:1986} and improved by
+  \bibcitet{R:Clarkson+Joe+Fan:1993}.
   The FORTRAN code can be obtained from
   \url{https://netlib.org/toms/643}.  Note this fails (with an error
   message) when the entries of the table are too large.  (It transposes
@@ -101,11 +101,11 @@ fisher.test(x, y = NULL, workspace = 200000, hybrid = FALSE,
   equals one.  \sQuote{Exact} inference can be based on observing that in
   general, given all marginal totals fixed, the first element of the
   contingency table has a non-central hypergeometric distribution with
-  non-centrality parameter given by the odds ratio (Fisher, 1935).  The
-  alternative for a one-sided test is based on the odds ratio, so
+  non-centrality parameter given by the odds ratio \bibcitep{R:Fisher:1935}.
+  The alternative for a one-sided test is based on the odds ratio, so
   \code{alternative = "greater"} is a test of the odds ratio being bigger
   than \code{or}.
-%
+
   Two-sided tests are based on the probabilities of the tables, and take
   as \sQuote{more extreme} all tables with probabilities less than or
   equal to that of the observed table, the p-value being the sum of such
@@ -130,62 +130,18 @@ fisher.test(x, y = NULL, workspace = 200000, hybrid = FALSE,
 
   Simulation is done conditional on the row and column marginals, and
   works only if the marginals are strictly positive.  (A C translation
-  of the algorithm of \bibcite{Patefield (1981)} is used.)
+  of the algorithm of \bibcitet{R:Patefield:1981} is used.)
   Note that the default number of replicates (\code{B = 2000}) implies a
   minimum p-value of about 0.0005 (\eqn{1/(B+1)}).
 }
 \references{
-  Agresti, A. (1990).
-  \emph{Categorical data analysis}.
-  New York: Wiley.
-  Pages 59--66.
-
-  Agresti, A. (2002).
-  \emph{Categorical data analysis}. Second edition.
-  New York: Wiley.
-  Pages 91--101.
-
-  Fisher, R. A. (1935).
-  The logic of inductive inference.
-  \emph{Journal of the Royal Statistical Society Series A}, \bold{98},
-  39--54.
-  \doi{10.2307/2342435}.
-
-  Fisher, R. A. (1962).
-  Confidence limits for a cross-product ratio.
-  \emph{Australian Journal of Statistics}, \bold{4}, 41.
-  \doi{10.1111/j.1467-842X.1962.tb00285.x}.
-
-  Fisher, R. A. (1970).
-  \emph{Statistical Methods for Research Workers}.
-  Oliver & Boyd.
-
-  Mehta, Cyrus R. and Patel, Nitin R. (1983).
-  A network algorithm for performing Fisher's exact test in \eqn{r
-  \times c}{r x c} contingency tables.
-  \emph{Journal of the American Statistical Association}, \bold{78},
-  427--434.
-  \doi{10.1080/01621459.1983.10477989}.
-
-  Mehta, C. R. and Patel, N. R. (1986).
-  Algorithm 643: FEXACT, a FORTRAN subroutine for Fisher's exact test
-  on unordered \eqn{r \times c}{r x c} contingency tables.
-  \emph{ACM Transactions on Mathematical Software}, \bold{12},
-  154--161.
-  \doi{10.1145/6497.214326}.
-
-  Clarkson, D. B., Fan, Y. and Joe, H. (1993)
-  A Remark on Algorithm 643: FEXACT: An Algorithm for Performing
-  Fisher's Exact Test in \eqn{r \times c}{r x c} Contingency Tables.
-  \emph{ACM Transactions on Mathematical Software}, \bold{19},
-  484--488.
-  \doi{10.1145/168173.168412}.
-
-  Patefield, W. M. (1981).
-  Algorithm AS 159: An efficient method of generating r x c tables
-  with given row and column totals.
-  \emph{Applied Statistics}, \bold{30}, 91--97.
-  \doi{10.2307/2346669}.
+  \bibinfo{R:Agresti:1990}{note}{pages 59--66}
+  \bibinfo{R:Agresti:2002}{note}{pages 91--101}
+  \bibshow{*,
+    R:Agresti:1990,
+    R:Agresti:2002,
+    R:Fisher:1962,
+    R:Fisher:1970}
 }
 \seealso{
   \code{\link{chisq.test}}