[Pomp-commits] r264 - in pkg: . inst inst/doc src

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed May 26 20:16:06 CEST 2010


Author: kingaa
Date: 2010-05-26 20:16:05 +0200 (Wed, 26 May 2010)
New Revision: 264

Added:
   pkg/inst/doc/fullnat.bst
Removed:
   pkg/inst/doc/ecology.bst
Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
   pkg/inst/doc/intro_to_pomp.Rnw
   pkg/inst/doc/intro_to_pomp.pdf
   pkg/src/dmeasure.c
   pkg/src/pomp_fun.c
   pkg/src/rmeasure.c
Log:
- slight improvements to dmeasure & rmeasure methods
- change bibliography style in vignettes


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-05-23 15:30:55 UTC (rev 263)
+++ pkg/DESCRIPTION	2010-05-26 18:16:05 UTC (rev 264)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.29-2
-Date: 2010-05-23
+Version: 0.29-3
+Date: 2010-05-26
 Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Description: Inference methods for partially-observed Markov processes

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2010-05-23 15:30:55 UTC (rev 263)
+++ pkg/inst/ChangeLog	2010-05-26 18:16:05 UTC (rev 264)
@@ -1,5 +1,16 @@
+2010-05-23  kingaa
+
+	* [r263] man/mif-class.Rd, man/mif-methods.Rd, man/mif.Rd: - trying
+	  to get Carles' name right
+	* [r257] DESCRIPTION:
+
+2010-05-22  kingaa
+
+	* [r256] DESCRIPTION:
+
 2010-05-21  kingaa
 
+	* [r255] inst/ChangeLog:
 	* [r254] inst/NEWS: - documenting changes
 	* [r253] inst/CHANGES_0.29-1.txt: - word wrap
 	* [r252] inst/CHANGES_0.29-1.txt: - describe the changes in version

Deleted: pkg/inst/doc/ecology.bst
===================================================================
--- pkg/inst/doc/ecology.bst	2010-05-23 15:30:55 UTC (rev 263)
+++ pkg/inst/doc/ecology.bst	2010-05-26 18:16:05 UTC (rev 264)
@@ -1,1471 +0,0 @@
-%%
-%% This is file `ecology.bst',
-%% generated with the docstrip utility.
-%%
-%% The original source files were:
-%%
-%% merlin.mbs  (with options: `ay,nat,nm-rev1,xlab-it,keyxyr,dt-beg,yr-per,note-yr,jttl-rm,vol-bf,vnum-x,numser,btit-rm,bt-rm,xedn')
-%% ----------------------------------------
-%% *** Ecology/Ecological Monographs ***
-%% 
-%% Copyright 1994-2004 Patrick W Daly
- % ===============================================================
- % IMPORTANT NOTICE:
- % This bibliographic style (bst) file has been generated from one or
- % more master bibliographic style (mbs) files, listed above.
- %
- % This generated file can be redistributed and/or modified under the terms
- % of the LaTeX Project Public License Distributed from CTAN
- % archives in directory macros/latex/base/lppl.txt; either
- % version 1 of the License, or any later version.
- % ===============================================================
- % Name and version information of the main mbs file:
- % \ProvidesFile{merlin.mbs}[2004/02/09 4.13 (PWD, AO, DPC)]
- %   For use with BibTeX version 0.99a or later
- %-------------------------------------------------------------------
- % This bibliography style file is intended for texts in ENGLISH
- % This is an author-year citation style bibliography. As such, it is
- % non-standard LaTeX, and requires a special package file to function properly.
- % Such a package is    natbib.sty   by Patrick W. Daly
- % The form of the \bibitem entries is
- %   \bibitem[Jones et al.(1990)]{key}...
- %   \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}...
- % The essential feature is that the label (the part in brackets) consists
- % of the author names, as they should appear in the citation, with the year
- % in parentheses following. There must be no space before the opening
- % parenthesis!
- % With natbib v5.3, a full list of authors may also follow the year.
- % In natbib.sty, it is possible to define the type of enclosures that is
- % really wanted (brackets or parentheses), but in either case, there must
- % be parentheses in the label.
- % The \cite command functions as follows:
- %   \citet{key} ==>>                Jones et al. (1990)
- %   \citet*{key} ==>>               Jones, Baker, and Smith (1990)
- %   \citep{key} ==>>                (Jones et al., 1990)
- %   \citep*{key} ==>>               (Jones, Baker, and Smith, 1990)
- %   \citep[chap. 2]{key} ==>>       (Jones et al., 1990, chap. 2)
- %   \citep[e.g.][]{key} ==>>        (e.g. Jones et al., 1990)
- %   \citep[e.g.][p. 32]{key} ==>>   (e.g. Jones et al., p. 32)
- %   \citeauthor{key} ==>>           Jones et al.
- %   \citeauthor*{key} ==>>          Jones, Baker, and Smith
- %   \citeyear{key} ==>>             1990
- %---------------------------------------------------------------------
-
-ENTRY
-  { address
-    author
-    booktitle
-    chapter
-    edition
-    editor
-    eid
-    howpublished
-    institution
-    journal
-    key
-    month
-    note
-    number
-    organization
-    pages
-    publisher
-    school
-    series
-    title
-    type
-    volume
-    year
-  }
-  {}
-  { label extra.label sort.label short.list }
-INTEGERS { output.state before.all mid.sentence after.sentence after.block }
-FUNCTION {init.state.consts}
-{ #0 'before.all :=
-  #1 'mid.sentence :=
-  #2 'after.sentence :=
-  #3 'after.block :=
-}
-STRINGS { s t}
-FUNCTION {output.nonnull}
-{ 's :=
-  output.state mid.sentence =
-    { ", " * write$ }
-    { output.state after.block =
-        { add.period$ write$
-          newline$
-          "\newblock " write$
-        }
-        { output.state before.all =
-            'write$
-            { add.period$ " " * write$ }
-          if$
-        }
-      if$
-      mid.sentence 'output.state :=
-    }
-  if$
-  s
-}
-FUNCTION {output}
-{ duplicate$ empty$
-    'pop$
-    'output.nonnull
-  if$
-}
-FUNCTION {output.check}
-{ 't :=
-  duplicate$ empty$
-    { pop$ "empty " t * " in " * cite$ * warning$ }
-    'output.nonnull
-  if$
-}
-FUNCTION {fin.entry}
-{ add.period$
-  write$
-  newline$
-}
-
-FUNCTION {new.block}
-{ output.state before.all =
-    'skip$
-    { after.block 'output.state := }
-  if$
-}
-FUNCTION {new.sentence}
-{ output.state after.block =
-    'skip$
-    { output.state before.all =
-        'skip$
-        { after.sentence 'output.state := }
-      if$
-    }
-  if$
-}
-FUNCTION {add.blank}
-{  " " * before.all 'output.state :=
-}
-
-FUNCTION {date.block}
-{
-  new.block
-}
-
-FUNCTION {not}
-{   { #0 }
-    { #1 }
-  if$
-}
-FUNCTION {and}
-{   'skip$
-    { pop$ #0 }
-  if$
-}
-FUNCTION {or}
-{   { pop$ #1 }
-    'skip$
-  if$
-}
-FUNCTION {new.block.checkb}
-{ empty$
-  swap$ empty$
-  and
-    'skip$
-    'new.block
-  if$
-}
-FUNCTION {field.or.null}
-{ duplicate$ empty$
-    { pop$ "" }
-    'skip$
-  if$
-}
-FUNCTION {emphasize}
-{ duplicate$ empty$
-    { pop$ "" }
-    { "{\em " swap$ * "\/}" * }
-  if$
-}
-FUNCTION {bolden}
-{ duplicate$ empty$
-    { pop$ "" }
-    { "{\bf " swap$ * "}" * }
-  if$
-}
-FUNCTION {tie.or.space.prefix}
-{ duplicate$ text.length$ #3 <
-    { "~" }
-    { " " }
-  if$
-  swap$
-}
-
-FUNCTION {capitalize}
-{ "u" change.case$ "t" change.case$ }
-
-FUNCTION {space.word}
-{ " " swap$ * " " * }
- % Here are the language-specific definitions for explicit words.
- % Each function has a name bbl.xxx where xxx is the English word.
- % The language selected here is ENGLISH
-FUNCTION {bbl.and}
-{ "and"}
-
-FUNCTION {bbl.etal}
-{ "et~al." }
-
-FUNCTION {bbl.editors}
-{ "editors" }
-
-FUNCTION {bbl.editor}
-{ "editor" }
-
-FUNCTION {bbl.edby}
-{ "edited by" }
-
-FUNCTION {bbl.edition}
-{ "edition" }
-
-FUNCTION {bbl.volume}
-{ "volume" }
-
-FUNCTION {bbl.of}
-{ "of" }
-
-FUNCTION {bbl.number}
-{ "number" }
-
-FUNCTION {bbl.nr}
-{ "no." }
-
-FUNCTION {bbl.in}
-{ "in" }
-
-FUNCTION {bbl.pages}
-{ "pages" }
-
-FUNCTION {bbl.page}
-{ "page" }
-
-FUNCTION {bbl.chapter}
-{ "chapter" }
-
-FUNCTION {bbl.techrep}
-{ "Technical Report" }
-
-FUNCTION {bbl.mthesis}
-{ "Master's thesis" }
-
-FUNCTION {bbl.phdthesis}
-{ "Ph.D. thesis" }
-
-MACRO {jan} {"January"}
-
-MACRO {feb} {"February"}
-
-MACRO {mar} {"March"}
-
-MACRO {apr} {"April"}
-
-MACRO {may} {"May"}
-
-MACRO {jun} {"June"}
-
-MACRO {jul} {"July"}
-
-MACRO {aug} {"August"}
-
-MACRO {sep} {"September"}
-
-MACRO {oct} {"October"}
-
-MACRO {nov} {"November"}
-
-MACRO {dec} {"December"}
-
-MACRO {acmcs} {"ACM Computing Surveys"}
-
-MACRO {acta} {"Acta Informatica"}
-
-MACRO {cacm} {"Communications of the ACM"}
-
-MACRO {ibmjrd} {"IBM Journal of Research and Development"}
-
-MACRO {ibmsj} {"IBM Systems Journal"}
-
-MACRO {ieeese} {"IEEE Transactions on Software Engineering"}
-
-MACRO {ieeetc} {"IEEE Transactions on Computers"}
-
-MACRO {ieeetcad}
- {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}
-
-MACRO {ipl} {"Information Processing Letters"}
-
-MACRO {jacm} {"Journal of the ACM"}
-
-MACRO {jcss} {"Journal of Computer and System Sciences"}
-
-MACRO {scp} {"Science of Computer Programming"}
-
-MACRO {sicomp} {"SIAM Journal on Computing"}
-
-MACRO {tocs} {"ACM Transactions on Computer Systems"}
-
-MACRO {tods} {"ACM Transactions on Database Systems"}
-
-MACRO {tog} {"ACM Transactions on Graphics"}
-
-MACRO {toms} {"ACM Transactions on Mathematical Software"}
-
-MACRO {toois} {"ACM Transactions on Office Information Systems"}
-
-MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}
-
-MACRO {tcs} {"Theoretical Computer Science"}
-FUNCTION {bibinfo.check}
-{ swap$
-  duplicate$ missing$
-    {
-      pop$ pop$
-      ""
-    }
-    { duplicate$ empty$
-        {
-          swap$ pop$
-        }
-        { swap$
-          pop$
-        }
-      if$
-    }
-  if$
-}
-FUNCTION {bibinfo.warn}
-{ swap$
-  duplicate$ missing$
-    {
-      swap$ "missing " swap$ * " in " * cite$ * warning$ pop$
-      ""
-    }
-    { duplicate$ empty$
-        {
-          swap$ "empty " swap$ * " in " * cite$ * warning$
-        }
-        { swap$
-          pop$
-        }
-      if$
-    }
-  if$
-}
-STRINGS  { bibinfo}
-INTEGERS { nameptr namesleft numnames }
-
-FUNCTION {format.names}
-{ 'bibinfo :=
-  duplicate$ empty$ 'skip$ {
-  's :=
-  "" 't :=
-  #1 'nameptr :=
-  s num.names$ 'numnames :=
-  numnames 'namesleft :=
-    { namesleft #0 > }
-    { s nameptr
-      duplicate$ #1 >
-        { "{f.~}{vv~}{ll}{, jj}" }
-        { "{vv~}{ll}{, jj}{, f.}" }
-      if$
-      format.name$
-      bibinfo bibinfo.check
-      't :=
-      nameptr #1 >
-        {
-          namesleft #1 >
-            { ", " * t * }
-            {
-              numnames #2 >
-                { "," * }
-                'skip$
-              if$
-              s nameptr "{ll}" format.name$ duplicate$ "others" =
-                { 't := }
-                { pop$ }
-              if$
-              t "others" =
-                {
-                  " " * bbl.etal *
-                }
-                {
-                  bbl.and
-                  space.word * t *
-                }
-              if$
-            }
-          if$
-        }
-        't
-      if$
-      nameptr #1 + 'nameptr :=
-      namesleft #1 - 'namesleft :=
-    }
-  while$
-  } if$
-}
-FUNCTION {format.names.ed}
-{
-  'bibinfo :=
-  duplicate$ empty$ 'skip$ {
-  's :=
-  "" 't :=
-  #1 'nameptr :=
-  s num.names$ 'numnames :=
-  numnames 'namesleft :=
-    { namesleft #0 > }
-    { s nameptr
-      "{f.~}{vv~}{ll}{, jj}"
-      format.name$
-      bibinfo bibinfo.check
-      't :=
-      nameptr #1 >
-        {
-          namesleft #1 >
-            { ", " * t * }
-            {
-              numnames #2 >
-                { "," * }
-                'skip$
-              if$
-              s nameptr "{ll}" format.name$ duplicate$ "others" =
-                { 't := }
-                { pop$ }
-              if$
-              t "others" =
-                {
-
-                  " " * bbl.etal *
-                }
-                {
-                  bbl.and
-                  space.word * t *
-                }
-              if$
-            }
-          if$
-        }
-        't
-      if$
-      nameptr #1 + 'nameptr :=
-      namesleft #1 - 'namesleft :=
-    }
-  while$
-  } if$
-}
-FUNCTION {format.key}
-{ empty$
-    { key field.or.null }
-    { "" }
-  if$
-}
-
-FUNCTION {format.authors}
-{ author "author" format.names
-}
-FUNCTION {get.bbl.editor}
-{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ }
-
-FUNCTION {format.editors}
-{ editor "editor" format.names duplicate$ empty$ 'skip$
-    {
-      "," *
-      " " *
-      get.bbl.editor
-      *
-    }
-  if$
-}
-FUNCTION {format.note}
-{
- note empty$
-    { "" }
-    { note #1 #1 substring$
-      duplicate$ "{" =
-        'skip$
-        { output.state mid.sentence =
-          { "l" }
-          { "u" }
-        if$
-        change.case$
-        }
-      if$
-      note #2 global.max$ substring$ * "note" bibinfo.check
-    }
-  if$
-}
-
-FUNCTION {format.title}
-{ title
-  duplicate$ empty$ 'skip$
-    { "t" change.case$ }
-  if$
-  "title" bibinfo.check
-}
-FUNCTION {format.full.names}
-{'s :=
- "" 't :=
-  #1 'nameptr :=
-  s num.names$ 'numnames :=
-  numnames 'namesleft :=
-    { namesleft #0 > }
-    { s nameptr
-      "{vv~}{ll}" format.name$
-      't :=
-      nameptr #1 >
-        {
-          namesleft #1 >
-            { ", " * t * }
-            {
-              s nameptr "{ll}" format.name$ duplicate$ "others" =
-                { 't := }
-                { pop$ }
-              if$
-              t "others" =
-                {
-                  " " * bbl.etal *
-                }
-                {
-                  numnames #2 >
-                    { "," * }
-                    'skip$
-                  if$
-                  bbl.and
-                  space.word * t *
-                }
-              if$
-            }
-          if$
-        }
-        't
-      if$
-      nameptr #1 + 'nameptr :=
-      namesleft #1 - 'namesleft :=
-    }
-  while$
-}
-
-FUNCTION {author.editor.key.full}
-{ author empty$
-    { editor empty$
-        { key empty$
-            { cite$ #1 #3 substring$ }
-            'key
-          if$
-        }
-        { editor format.full.names }
-      if$
-    }
-    { author format.full.names }
-  if$
-}
-
-FUNCTION {author.key.full}
-{ author empty$
-    { key empty$
-         { cite$ #1 #3 substring$ }
-          'key
-      if$
-    }
-    { author format.full.names }
-  if$
-}
-
-FUNCTION {editor.key.full}
-{ editor empty$
-    { key empty$
-         { cite$ #1 #3 substring$ }
-          'key
-      if$
-    }
-    { editor format.full.names }
-  if$
-}
-
-FUNCTION {make.full.names}
-{ type$ "book" =
-  type$ "inbook" =
-  or
-    'author.editor.key.full
-    { type$ "proceedings" =
-        'editor.key.full
-        'author.key.full
-      if$
-    }
-  if$
-}
-
-FUNCTION {output.bibitem}
-{ newline$
-  "\bibitem[{" write$
-  label write$
-  ")" make.full.names duplicate$ short.list =
-     { pop$ }
-     { * }
-   if$
-  "}]{" * write$
-  cite$ write$
-  "}" write$
-  newline$
-  ""
-  before.all 'output.state :=
-}
-
-FUNCTION {n.dashify}
-{
-  't :=
-  ""
-    { t empty$ not }
-    { t #1 #1 substring$ "-" =
-        { t #1 #2 substring$ "--" = not
-            { "--" *
-              t #2 global.max$ substring$ 't :=
-            }
-            {   { t #1 #1 substring$ "-" = }
-                { "-" *
-                  t #2 global.max$ substring$ 't :=
-                }
-              while$
-            }
-          if$
-        }
-        { t #1 #1 substring$ *
-          t #2 global.max$ substring$ 't :=
-        }
-      if$
-    }
-  while$
-}
-
-FUNCTION {word.in}
-{ bbl.in capitalize
-  " " * }
-
-FUNCTION {format.date}
-{ year "year" bibinfo.check duplicate$ empty$
-    {
-      "empty year in " cite$ * "; set to ????" * warning$
-       pop$ "????"
-    }
-    'skip$
-  if$
-  extra.label *
-  before.all 'output.state :=
-  after.sentence 'output.state :=
-}
-FUNCTION {format.btitle}
-{ title "title" bibinfo.check
-  duplicate$ empty$ 'skip$
-    {
-    }
-  if$
-}
-FUNCTION {either.or.check}
-{ empty$
-    'pop$
-    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
-  if$
-}
-FUNCTION {format.bvolume}
-{ volume empty$
-    { "" }
-    { bbl.volume volume tie.or.space.prefix
-      "volume" bibinfo.check * *
-      series "series" bibinfo.check
-      duplicate$ empty$ 'pop$
-        { swap$ bbl.of space.word * swap$
-          emphasize * }
-      if$
-      "volume and number" number either.or.check
-    }
-  if$
-}
-FUNCTION {format.number.series}
-{ volume empty$
-    { number empty$
-        { series field.or.null }
-        { output.state mid.sentence =
-            { bbl.number }
-            { bbl.number capitalize }
-          if$
-          number tie.or.space.prefix "number" bibinfo.check * *
-          series empty$
-            { "there's a number but no series in " cite$ * warning$ }
-            { bbl.in space.word *
-              series "series" bibinfo.check *
-            }
-          if$
-        }
-      if$
-    }
-    { "" }
-  if$
-}
-
-FUNCTION {format.edition}
-{ edition duplicate$ empty$ 'skip$
-    {
-      output.state mid.sentence =
-        { "l" }
-        { "t" }
-      if$ change.case$
-      "edition" bibinfo.check
-      " " * bbl.edition *
-    }
-  if$
-}
-INTEGERS { multiresult }
-FUNCTION {multi.page.check}
-{ 't :=
-  #0 'multiresult :=
-    { multiresult not
-      t empty$ not
-      and
-    }
-    { t #1 #1 substring$
-      duplicate$ "-" =
-      swap$ duplicate$ "," =
-      swap$ "+" =
-      or or
-        { #1 'multiresult := }
-        { t #2 global.max$ substring$ 't := }
-      if$
-    }
-  while$
-  multiresult
-}
-FUNCTION {format.pages}
-{ pages duplicate$ empty$ 'skip$
-    { duplicate$ multi.page.check
-        {
-          bbl.pages swap$
-          n.dashify
-        }
-        {
-          bbl.page swap$
-        }
-      if$
-      tie.or.space.prefix
-      "pages" bibinfo.check
-      * *
-    }
-  if$
-}
-FUNCTION {format.journal.pages}
-{ pages duplicate$ empty$ 'pop$
-    { swap$ duplicate$ empty$
-        { pop$ pop$ format.pages }
-        {
-          ":" *
-          swap$
-          n.dashify
-          "pages" bibinfo.check
-          *
-        }
-      if$
-    }
-  if$
-}
-FUNCTION {format.journal.eid}
-{ eid "eid" bibinfo.check
-  duplicate$ empty$ 'pop$
-    { swap$ duplicate$ empty$ 'skip$
-      {
-          ":" *
-      }
-      if$
-      swap$ *
-    }
-  if$
-}
-FUNCTION {format.vol.num.pages}
-{ volume field.or.null
-  duplicate$ empty$ 'skip$
-    {
-      "volume" bibinfo.check
-    }
-  if$
-  bolden
-  eid empty$
-    { format.journal.pages }
-    { format.journal.eid }
-  if$
-}
-
-FUNCTION {format.chapter.pages}
-{ chapter empty$
-    'format.pages
-    { type empty$
-        { bbl.chapter }
-        { type "l" change.case$
-          "type" bibinfo.check
-        }
-      if$
-      chapter tie.or.space.prefix
-      "chapter" bibinfo.check
-      * *
-      pages empty$
-        'skip$
-        { ", " * format.pages * }
-      if$
-    }
-  if$
-}
-
-FUNCTION {format.booktitle}
-{
-  booktitle "booktitle" bibinfo.check
-}
-FUNCTION {format.in.ed.booktitle}
-{ format.booktitle duplicate$ empty$ 'skip$
-    {
-      editor "editor" format.names.ed duplicate$ empty$ 'pop$
-        {
-          "," *
-          " " *
-          get.bbl.editor
-          ", " *
-          * swap$
-          * }
-      if$
-      word.in swap$ *
-    }
-  if$
-}
-FUNCTION {format.thesis.type}
-{ type duplicate$ empty$
-    'pop$
-    { swap$ pop$
-      "t" change.case$ "type" bibinfo.check
-    }
-  if$
-}
-FUNCTION {format.tr.number}
-{ number "number" bibinfo.check
-  type duplicate$ empty$
-    { pop$ bbl.techrep }
-    'skip$
-  if$
-  "type" bibinfo.check
-  swap$ duplicate$ empty$
-    { pop$ "t" change.case$ }
-    { tie.or.space.prefix * * }
-  if$
-}
-FUNCTION {format.article.crossref}
-{
-  word.in
-  " \cite{" * crossref * "}" *
-}
-FUNCTION {format.book.crossref}
-{ volume duplicate$ empty$
-    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
-      pop$ word.in
-    }
-    { bbl.volume
-      capitalize
-      swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word *
-    }
-  if$
-  " \cite{" * crossref * "}" *
-}
-FUNCTION {format.incoll.inproc.crossref}
-{
-  word.in
-  " \cite{" * crossref * "}" *
-}
-FUNCTION {format.org.or.pub}
-{ 't :=
-  ""
-  address empty$ t empty$ and
-    'skip$
-    {
-      t empty$
-        { address "address" bibinfo.check *
-        }
-        { t *
-          address empty$
-            'skip$
-            { ", " * address "address" bibinfo.check * }
-          if$
-        }
-      if$
-    }
-  if$
-}
-FUNCTION {format.publisher.address}
-{ publisher "publisher" bibinfo.warn format.org.or.pub
-}
-
-FUNCTION {format.organization.address}
-{ organization "organization" bibinfo.check format.org.or.pub
-}
-
-FUNCTION {article}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title "title" output.check
-  new.block
-  crossref missing$
-    {
-      journal
-      "journal" bibinfo.check
-      "journal" output.check
-      format.vol.num.pages output
-    }
-    { format.article.crossref output.nonnull
-      format.pages output
-    }
-  if$
-  new.block
-  format.note output
-  fin.entry
-}
-FUNCTION {book}
-{ output.bibitem
-  author empty$
-    { format.editors "author and editor" output.check
-      editor format.key output
-    }
-    { format.authors output.nonnull
-      crossref missing$
-        { "author and editor" editor either.or.check }
-        'skip$
-      if$
-    }
-  if$
-  format.date "year" output.check
-  date.block
-  format.btitle "title" output.check
-  crossref missing$
-    { format.bvolume output
-      new.block
-      new.sentence
-      format.number.series output
-      format.publisher.address output
-    }
-    {
-      new.block
-      format.book.crossref output.nonnull
-    }
-  if$
-  format.edition output
-  new.block
-  format.note output
-  fin.entry
-}
-FUNCTION {booklet}
-{ output.bibitem
-  format.authors output
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title "title" output.check
-  new.block
-  howpublished "howpublished" bibinfo.check output
-  address "address" bibinfo.check output
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {inbook}
-{ output.bibitem
-  author empty$
-    { format.editors "author and editor" output.check
-      editor format.key output
-    }
-    { format.authors output.nonnull
-      crossref missing$
-        { "author and editor" editor either.or.check }
-        'skip$
-      if$
-    }
-  if$
-  format.date "year" output.check
-  date.block
-  format.btitle "title" output.check
-  crossref missing$
-    {
-      format.bvolume output
-      format.chapter.pages "chapter and pages" output.check
-      new.block
-      new.sentence
-      format.number.series output
-      format.publisher.address output
-    }
-    {
-      format.chapter.pages "chapter and pages" output.check
-      new.block
-      format.book.crossref output.nonnull
-    }
-  if$
-  format.edition output
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {incollection}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title "title" output.check
-  new.block
-  crossref missing$
-    { format.in.ed.booktitle "booktitle" output.check
-      format.bvolume output
-      format.chapter.pages output
-      new.sentence
-      format.number.series output
-      format.publisher.address output
-      format.edition output
-    }
-    { format.incoll.inproc.crossref output.nonnull
-      format.chapter.pages output
-    }
-  if$
-  new.block
-  format.note output
-  fin.entry
-}
-FUNCTION {inproceedings}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title "title" output.check
-  new.block
-  crossref missing$
-    { format.in.ed.booktitle "booktitle" output.check
-      format.bvolume output
-      format.pages output
-      new.sentence
-      format.number.series output
-      publisher empty$
-        { format.organization.address output }
-        { organization "organization" bibinfo.check output
-          format.publisher.address output
-        }
-      if$
-    }
-    { format.incoll.inproc.crossref output.nonnull
-      format.pages output
-    }
-  if$
-  new.block
-  format.note output
-  fin.entry
-}
-FUNCTION {conference} { inproceedings }
-FUNCTION {manual}
-{ output.bibitem
-  format.authors output
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.btitle "title" output.check
-  organization address new.block.checkb
-  organization "organization" bibinfo.check output
-  address "address" bibinfo.check output
-  format.edition output
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {mastersthesis}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.btitle
-  "title" output.check
-  new.block
-  bbl.mthesis format.thesis.type output.nonnull
-  school "school" bibinfo.warn output
-  address "address" bibinfo.check output
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {misc}
-{ output.bibitem
-  format.authors output
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title output
-  new.block
-  howpublished "howpublished" bibinfo.check output
-  new.block
-  format.note output
-  fin.entry
-}
-FUNCTION {phdthesis}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.btitle
-  "title" output.check
-  new.block
-  bbl.phdthesis format.thesis.type output.nonnull
-  school "school" bibinfo.warn output
-  address "address" bibinfo.check output
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {proceedings}
-{ output.bibitem
-  format.editors output
-  editor format.key output
-  format.date "year" output.check
-  date.block
-  format.btitle "title" output.check
-  format.bvolume output
-  new.sentence
-  format.number.series output
-  publisher empty$
-    { format.organization.address output }
-    { organization "organization" bibinfo.check output
-      format.publisher.address output
-    }
-  if$
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {techreport}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title
-  "title" output.check
-  new.block
-  format.tr.number output.nonnull
-  institution "institution" bibinfo.warn output
-  address "address" bibinfo.check output
-  new.block
-  format.note output
-  fin.entry
-}
-
-FUNCTION {unpublished}
-{ output.bibitem
-  format.authors "author" output.check
-  author format.key output
-  format.date "year" output.check
-  date.block
-  format.title "title" output.check
-  new.block
-  format.note "note" output.check
-  fin.entry
-}
-
-FUNCTION {default.type} { misc }
-READ
-FUNCTION {sortify}
-{ purify$
-  "l" change.case$
-}
-INTEGERS { len }
-FUNCTION {chop.word}
-{ 's :=
-  'len :=
-  s #1 len substring$ =
-    { s len #1 + global.max$ substring$ }
-    's
-  if$
-}
-FUNCTION {format.lab.names}
-{ 's :=
-  "" 't :=
-  s #1 "{vv~}{ll}" format.name$
-  s num.names$ duplicate$
-  #2 >
-    { pop$
-      " " * bbl.etal *
-    }
-    { #2 <
-        'skip$
-        { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
-            {
-              " " * bbl.etal *
-            }
-            { bbl.and space.word * s #2 "{vv~}{ll}" format.name$
-              * }
-          if$
-        }
-      if$
-    }
-  if$
-}
-
-FUNCTION {author.key.label}
-{ author empty$
-    { key empty$
-        { cite$ #1 #3 substring$ }
-        'key
-      if$
-    }
-    { author format.lab.names }
-  if$
-}
-
-FUNCTION {author.editor.key.label}
-{ author empty$
-    { editor empty$
-        { key empty$
-            { cite$ #1 #3 substring$ }
-            'key
-          if$
-        }
-        { editor format.lab.names }
-      if$
-    }
-    { author format.lab.names }
-  if$
-}
-
-FUNCTION {editor.key.label}
-{ editor empty$
-    { key empty$
-        { cite$ #1 #3 substring$ }
-        'key
-      if$
-    }
-    { editor format.lab.names }
-  if$
-}
-
-FUNCTION {calc.short.authors}
-{ type$ "book" =
-  type$ "inbook" =
-  or
-    'author.editor.key.label
-    { type$ "proceedings" =
-        'editor.key.label
-        'author.key.label
-      if$
-    }
-  if$
-  'short.list :=
-}
-
-FUNCTION {calc.label}
-{ calc.short.authors
-  short.list
-  "("
-  *
-  year duplicate$ empty$
-  short.list key field.or.null = or
-     { pop$ "" }
-     'skip$
-  if$
-  *
-  'label :=
-}
-
-FUNCTION {sort.format.names}
-{ 's :=
-  #1 'nameptr :=
-  ""
-  s num.names$ 'numnames :=
-  numnames 'namesleft :=
-    { namesleft #0 > }
-    { s nameptr
-      "{vv{ } }{ll{ }}{  f{ }}{  jj{ }}"
-      format.name$ 't :=
-      nameptr #1 >
-        {
-          "   "  *
-          namesleft #1 = t "others" = and
-            { "zzzzz" * }
-            { t sortify * }
-          if$
-        }
-        { t sortify * }
-      if$
-      nameptr #1 + 'nameptr :=
-      namesleft #1 - 'namesleft :=
-    }
-  while$
-}
-
-FUNCTION {sort.format.title}
-{ 't :=
-  "A " #2
-    "An " #3
-      "The " #4 t chop.word
-    chop.word
-  chop.word
-  sortify
-  #1 global.max$ substring$
-}
-FUNCTION {author.sort}
-{ author empty$
-    { key empty$
-        { "to sort, need author or key in " cite$ * warning$
-          ""
-        }
-        { key sortify }
-      if$
-    }
-    { author sort.format.names }
-  if$
-}
-FUNCTION {author.editor.sort}
-{ author empty$
-    { editor empty$
-        { key empty$
-            { "to sort, need author, editor, or key in " cite$ * warning$
-              ""
-            }
-            { key sortify }
-          if$
-        }
-        { editor sort.format.names }
-      if$
-    }
-    { author sort.format.names }
-  if$
-}
-FUNCTION {editor.sort}
-{ editor empty$
-    { key empty$
-        { "to sort, need editor or key in " cite$ * warning$
-          ""
-        }
-        { key sortify }
-      if$
-    }
-    { editor sort.format.names }
-  if$
-}
-FUNCTION {presort}
-{ calc.label
-  label sortify
-  "    "
-  *
-  type$ "book" =
-  type$ "inbook" =
-  or
-    'author.editor.sort
-    { type$ "proceedings" =
-        'editor.sort
-        'author.sort
-      if$
-    }
-  if$
-  #1 entry.max$ substring$
-  'sort.label :=
-  sort.label
-  *
-  "    "
-  *
-  title field.or.null
-  sort.format.title
-  *
-  #1 entry.max$ substring$
-  'sort.key$ :=
-}
-
-ITERATE {presort}
-SORT
-STRINGS { last.label next.extra }
-INTEGERS { last.extra.num number.label }
-FUNCTION {initialize.extra.label.stuff}
-{ #0 int.to.chr$ 'last.label :=
-  "" 'next.extra :=
-  #0 'last.extra.num :=
-  #0 'number.label :=
-}
-FUNCTION {forward.pass}
-{ last.label label =
-    { last.extra.num #1 + 'last.extra.num :=
-      last.extra.num int.to.chr$ 'extra.label :=
-    }
-    { "a" chr.to.int$ 'last.extra.num :=
-      "" 'extra.label :=
-      label 'last.label :=
-    }
-  if$
-  number.label #1 + 'number.label :=
-}
-FUNCTION {reverse.pass}
-{ next.extra "b" =
-    { "a" 'extra.label := }
-    'skip$
-  if$
-  extra.label 'next.extra :=
-  extra.label
-  emphasize
-  duplicate$ empty$
-    'skip$
-    { "{\natexlab{" swap$ * "}}" * }
-  if$
-  'extra.label :=
-  label extra.label * 'label :=
-}
-EXECUTE {initialize.extra.label.stuff}
-ITERATE {forward.pass}
-REVERSE {reverse.pass}
-FUNCTION {bib.sort.order}
-{ sort.label
-  "    "
-  *
-  year field.or.null sortify
-  *
-  "    "
-  *
-  title field.or.null
-  sort.format.title
-  *
-  #1 entry.max$ substring$
-  'sort.key$ :=
-}
-ITERATE {bib.sort.order}
-SORT
-FUNCTION {begin.bib}
-{ preamble$ empty$
-    'skip$
-    { preamble$ write$ newline$ }
-  if$
-  "\begin{thebibliography}{" number.label int.to.str$ * "}" *
-  write$ newline$
-  "\providecommand{\natexlab}[1]{#1}"
-  write$ newline$
-}
-EXECUTE {begin.bib}
-EXECUTE {init.state.consts}
-ITERATE {call.type$}
-FUNCTION {end.bib}
-{ newline$
-  "\end{thebibliography}" write$ newline$
-}
-EXECUTE {end.bib}
-%% End of customized bst file
-%%
-%% End of file `ecology.bst'.

Added: pkg/inst/doc/fullnat.bst
===================================================================
--- pkg/inst/doc/fullnat.bst	                        (rev 0)
+++ pkg/inst/doc/fullnat.bst	2010-05-26 18:16:05 UTC (rev 264)
@@ -0,0 +1,1429 @@
+%%
+%% This is file `fullnat.bst',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% merlin.mbs  (with options: `ay,nat,vonx,nm-init,ed-au,keyxyr,yr-par,note-yr,vol-bf,vnum-x,num-xser,jnm-x,pub-date,pp,ed,abr,xedn,etal-it,nfss,')
+%% ----------------------------------------
+%% ***  ***
+%% 
+%% Copyright 1994-2004 Patrick W Daly
+ % ===============================================================
+ % IMPORTANT NOTICE:
+ % This bibliographic style (bst) file has been generated from one or
+ % more master bibliographic style (mbs) files, listed above.
+ %
+ % This generated file can be redistributed and/or modified under the terms
+ % of the LaTeX Project Public License Distributed from CTAN
+ % archives in directory macros/latex/base/lppl.txt; either
+ % version 1 of the License, or any later version.
+ % ===============================================================
+ % Name and version information of the main mbs file:
+ % \ProvidesFile{merlin.mbs}[2004/02/09 4.13 (PWD, AO, DPC)]
+ %   For use with BibTeX version 0.99a or later
+ %-------------------------------------------------------------------
+ % This bibliography style file is intended for texts in ENGLISH
+ % This is an author-year citation style bibliography. As such, it is
+ % non-standard LaTeX, and requires a special package file to function properly.
+ % Such a package is    natbib.sty   by Patrick W. Daly
+ % The form of the \bibitem entries is
+ %   \bibitem[Jones et al.(1990)]{key}...
+ %   \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}...
+ % The essential feature is that the label (the part in brackets) consists
+ % of the author names, as they should appear in the citation, with the year
+ % in parentheses following. There must be no space before the opening
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 264


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