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Casey Dunn committed 8f729f0

added to contrasts example

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analyses/character_evolution/Geospiza.nex

-#NEXUS
-[R-package APE, Tue Dec 11 10:25:04 2007]
-
-BEGIN TAXA;
-	DIMENSIONS NTAX = 14;
-	TAXLABELS
-		fuliginosa
-		fortis
-		magnirostris
-		conirostris
-		scandens
-		difficilis
-		pallida
-		parvulus
-		psittacula
-		pauper
-		Platyspiza
-		fusca
-		Pinaroloxias
-		olivacea
-	;
-END;
-BEGIN TREES;
-	TRANSLATE
-		1	fuliginosa,
-		2	fortis,
-		3	magnirostris,
-		4	conirostris,
-		5	scandens,
-		6	difficilis,
-		7	pallida,
-		8	parvulus,
-		9	psittacula,
-		10	pauper,
-		11	Platyspiza,
-		12	fusca,
-		13	Pinaroloxias,
-		14	olivacea
-	;
-	TREE * UNTITLED = [&R] ((((((((((1:0.055,2:0.055):0.055,3:0.11):0.07333,4:0.18333):0.00917,5:0.1925):0.0355,6:0.228):0.10346,(7:0.08667,((8:0.02,9:0.02):0.015,10:0.035):0.05167):0.24479):0.13404,11:0.4655):0.06859,12:0.53409):0.04924,13:0.58333):0.29744,14:0.88077);
-END;

analyses/character_evolution/Geospiza.txt

-"wingL" "tarsusL" "culmenL" "beakD" "gonysW"
-"magnirostris" 4.4042 3.03895 2.724667 2.823767 2.675983
-"conirostris" 4.349867 2.9842 2.6544 2.5138 2.360167
-"difficilis" 4.224067 2.898917 2.277183 2.0111 1.929983
-"scandens" 4.261222 2.929033 2.621789 2.1447 2.036944
-"fortis" 4.244008 2.894717 2.407025 2.362658 2.221867
-"fuliginosa" 4.132957 2.806514 2.094971 1.941157 1.845379
-"pallida" 4.265425 3.08945 2.43025 2.01635 1.949125
-"fusca" 3.975393 2.936536 2.051843 1.191264 1.401186
-"parvulus" 4.1316 2.97306 1.97442 1.87354 1.81334
-"pauper" 4.2325 3.0359 2.187 2.0734 1.9621
-"Pinaroloxias" 4.1886 2.9802 2.3111 1.5475 1.6301
-"Platyspiza" 4.419686 3.270543 2.331471 2.347471 2.282443
-"psittacula" 4.23502 3.04912 2.25964 2.23004 2.07394

analyses/character_evolution/README.md

-# Character evolution
-
-In these examples you will explore the evolution of characters on phylogenetic 
-trees. This is a bit different than our previous analyses, where we started 
-with character data and built a tree. In the present analyses, we will start 
-with both a tree and character data. In most situations the tree will have been 
-inferred from molecular sequence data, and the character data will be 
-morphological.
-
-In the previous exercises where we built trees, you used a variety of programs 
-at the command line. These programs were there themselves written in several 
-different languages. In the past decade, a large community of phylogenetic 
-biologists interested in character evolution have written many analysis tools 
-in the programming language R. This set of tools provides a rich environment 
-for the study of character evolution. All of our character evolution analyses 
-will be conducted as interactive R sessions. 
-
-
-## Getting oriented with R
-
-R, like python and many other languages, can be used interactively, where you 
-enter a few commands at a time, or in batch mode, where a series of commands are 
-placed in a file and executed all at once. We will use R interactively, and 
-load R code that others have already written for phylogenetic analyses as we 
-go.
-
-There are already *many* general introductions, tutorials, and quick-references 
-for R. I therefore won't provide a background on R itself, we will dive right 
-into some analyses.
-
-There is detailed information on phylogenetic analysis with R at both 
-(the R phylo wiki)[http://www.r-phylo.org/wiki/Main_Page] and the 
-(CRAN task page for phylogenetics)[http://cran.r-project.org/web/views/Phylogenetics.html].
-
-For the analyses below, you will need to install the `ape` library in R.
-
-
-## Phylogenetic Independent Contrast
-
-This example expands on that presented at the 
-(R phylogenetics wiki)[http://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts].
-The data files are also included in the same directory as this document. 
-
-Copy the data files (`Geospiza.txt` and `Geospiza.nex`) to a directory on your 
-computer. Open the R interface (which was installed alongside the rest of the 
-R components) or open a terminal window and launch an interactive R session 
-with the command `R`.
-
-Now, change to the directory where your data files are:
-
-    setwd('DATA_DIR')
-
-Where `DATA_DIR` is the directory where you put the data files. The R command 
-`setwd()` is much like the shell command `cd` - it controls your working 
-directory.
-
-Load and prepare the data:
-
-    geodata<-read.table("Geospiza.txt")
-    geotree<-read.nexus("Geospiza.nex")
-    geotree <- drop.tip(geotree, "olivacea")
-    
-That last command is necessary since there is one taxon in the tree that isn't 
-in the data file.

analyses/independent_contrasts/Geospiza.nex

+#NEXUS
+[R-package APE, Tue Dec 11 10:25:04 2007]
+
+BEGIN TAXA;
+	DIMENSIONS NTAX = 14;
+	TAXLABELS
+		fuliginosa
+		fortis
+		magnirostris
+		conirostris
+		scandens
+		difficilis
+		pallida
+		parvulus
+		psittacula
+		pauper
+		Platyspiza
+		fusca
+		Pinaroloxias
+		olivacea
+	;
+END;
+BEGIN TREES;
+	TRANSLATE
+		1	fuliginosa,
+		2	fortis,
+		3	magnirostris,
+		4	conirostris,
+		5	scandens,
+		6	difficilis,
+		7	pallida,
+		8	parvulus,
+		9	psittacula,
+		10	pauper,
+		11	Platyspiza,
+		12	fusca,
+		13	Pinaroloxias,
+		14	olivacea
+	;
+	TREE * UNTITLED = [&R] ((((((((((1:0.055,2:0.055):0.055,3:0.11):0.07333,4:0.18333):0.00917,5:0.1925):0.0355,6:0.228):0.10346,(7:0.08667,((8:0.02,9:0.02):0.015,10:0.035):0.05167):0.24479):0.13404,11:0.4655):0.06859,12:0.53409):0.04924,13:0.58333):0.29744,14:0.88077);
+END;

analyses/independent_contrasts/Geospiza.txt

+"wingL" "tarsusL" "culmenL" "beakD" "gonysW"
+"magnirostris" 4.4042 3.03895 2.724667 2.823767 2.675983
+"conirostris" 4.349867 2.9842 2.6544 2.5138 2.360167
+"difficilis" 4.224067 2.898917 2.277183 2.0111 1.929983
+"scandens" 4.261222 2.929033 2.621789 2.1447 2.036944
+"fortis" 4.244008 2.894717 2.407025 2.362658 2.221867
+"fuliginosa" 4.132957 2.806514 2.094971 1.941157 1.845379
+"pallida" 4.265425 3.08945 2.43025 2.01635 1.949125
+"fusca" 3.975393 2.936536 2.051843 1.191264 1.401186
+"parvulus" 4.1316 2.97306 1.97442 1.87354 1.81334
+"pauper" 4.2325 3.0359 2.187 2.0734 1.9621
+"Pinaroloxias" 4.1886 2.9802 2.3111 1.5475 1.6301
+"Platyspiza" 4.419686 3.270543 2.331471 2.347471 2.282443
+"psittacula" 4.23502 3.04912 2.25964 2.23004 2.07394

analyses/independent_contrasts/README.md

+# Character evolution
+
+In these examples you will explore the evolution of characters on phylogenetic 
+trees. This is a bit different than our previous analyses, where we started 
+with character data and built a tree. In the present analyses, we will start 
+with both a tree and character data. In most situations the tree will have been 
+inferred from molecular sequence data, and the character data will be 
+morphological.
+
+In the previous exercises where we built trees, you used a variety of programs 
+at the command line. These programs were there themselves written in several 
+different languages. In the past decade, a large community of phylogenetic 
+biologists interested in character evolution have written many analysis tools 
+in the programming language R. This set of tools provides a rich environment 
+for the study of character evolution. All of our character evolution analyses 
+will be conducted as interactive R sessions. 
+
+
+## Getting oriented with R
+
+R, like python and many other languages, can be used interactively, where you 
+enter a few commands at a time, or in batch mode, where a series of commands are 
+placed in a file and executed all at once. We will use R interactively, and 
+load R code that others have already written for phylogenetic analyses as we 
+go.
+
+There are already *many* general introductions, tutorials, and quick-references 
+for R. I therefore won't provide a background on R itself, we will dive right 
+into some analyses.
+
+There is detailed information on phylogenetic analysis with R at both 
+(the R phylo wiki)[http://www.r-phylo.org/wiki/Main_Page] and the 
+(CRAN task page for phylogenetics)[http://cran.r-project.org/web/views/Phylogenetics.html].
+
+For the analyses below, you will need to install the `ape` library in R.
+
+
+## Phylogenetic Independent Contrast 
+
+Copy the data files (`Geospiza.txt` and `Geospiza.nex`) to a directory on your 
+computer. Open the R interface (which was installed alongside the rest of the 
+R components) or open a terminal window and launch an interactive R session 
+with the command `R`.
+
+Now, change to the directory where your data files are:
+
+    setwd('DATA_DIR')
+
+Where `DATA_DIR` is the directory where you put the data files. The R command 
+`setwd()` is much like the shell command `cd` - it controls your working 
+directory.
+
+Load and prepare the data:
+
+    geodata<-read.table("Geospiza.txt")
+    geotree<-read.nexus("Geospiza.nex")
+    geotree <- drop.tip(geotree, "olivacea")
+    
+That last command is necessary since there is one taxon in the tree that isn't 
+in the data file.

analyses/independent_contrasts/knitr/amnat.bst

+%%
+%% This is file `amnatnat.bst',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% merlin.mbs  (with options: `ay,nat,nm-rev1,jnrlst,nmdash,nmd-3,xlab-it,keyxyr,dt-beg,yr-per,note-yr,jttl-rm,thtit-a,vnum-x,num-xser,jnm-x,btit-rm,bt-rm,pre-edn,in-it,ed,abr,ednx,ord,and-com,etal-xc,nfss,')
+%% ----------------------------------------
+%% *** Style file for _American Naturalist_. ***
+%% 
+%% Copyright 1994-2007 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}[2007/04/24 4.20 (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$ "" }
+    { "\emph{" 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}
+{ "eds." }
+
+FUNCTION {bbl.editor}
+{ "ed." }
+
+FUNCTION {bbl.edby}
+{ "edited by" }
+
+FUNCTION {bbl.edition}
+{ "ed." }
+
+FUNCTION {bbl.volume}
+{ "vol." }
+
+FUNCTION {bbl.of}
+{ "of" }
+
+FUNCTION {bbl.number}
+{ "no." }
+
+FUNCTION {bbl.nr}
+{ "no." }
+
+FUNCTION {bbl.in}
+{ "in" }
+
+FUNCTION {bbl.pages}
+{ "pages" }
+
+FUNCTION {bbl.page}
+{ "page" }
+
+FUNCTION {bbl.chapter}
+{ "chap." }
+
+FUNCTION {bbl.techrep}
+{ "Tech. Rep." }
+
+FUNCTION {bbl.mthesis}
+{ "M.S. thesis" }
+
+FUNCTION {bbl.phdthesis}
+{ "Ph.D. thesis" }
+
+FUNCTION {bbl.first}
+{ "1st" }
+
+FUNCTION {bbl.second}
+{ "2nd" }
+
+FUNCTION {bbl.third}
+{ "3rd" }
+
+FUNCTION {bbl.fourth}
+{ "4th" }
+
+FUNCTION {bbl.fifth}
+{ "5th" }
+
+FUNCTION {bbl.st}
+{ "st" }
+
+FUNCTION {bbl.nd}
+{ "nd" }
+
+FUNCTION {bbl.rd}
+{ "rd" }
+
+FUNCTION {bbl.th}
+{ "th" }
+
+MACRO {jan} {"Jan."}
+
+MACRO {feb} {"Feb."}
+
+MACRO {mar} {"Mar."}
+
+MACRO {apr} {"Apr."}
+
+MACRO {may} {"May"}
+
+MACRO {jun} {"Jun."}
+
+MACRO {jul} {"Jul."}
+
+MACRO {aug} {"Aug."}
+
+MACRO {sep} {"Sep."}
+
+MACRO {oct} {"Oct."}
+
+MACRO {nov} {"Nov."}
+
+MACRO {dec} {"Dec."}
+
+FUNCTION {eng.ord}
+{ duplicate$ "1" swap$ *
+  #-2 #1 substring$ "1" =
+     { bbl.th * }
+     { duplicate$ #-1 #1 substring$
+       duplicate$ "1" =
+         { pop$ bbl.st * }
+         { duplicate$ "2" =
+             { pop$ bbl.nd * }
+             { "3" =
+                 { bbl.rd * }
+                 { bbl.th * }
+               if$
+             }
+           if$
+          }
+       if$
+     }
+   if$
+}
+
+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$
+}
+INTEGERS { nameptr namesleft numnames }
+
+
+STRINGS  { bibinfo}
+
+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}{, f.}{, jj}" }
+      if$
+      format.name$
+      bibinfo bibinfo.check
+      't :=
+      nameptr #1 >
+        {
+          namesleft #1 >
+            { ", " * t * }
+            {
+              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 * }
+            {
+              s nameptr "{ll}" format.name$ duplicate$ "others" =
+                { 't := }
+                { pop$ }
+              if$
+              numnames #2 >
+              t "others" = not and
+                { "," * }
+                'skip$
+              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 {capword.in}
+{ bbl.in capitalize
+  emphasize
+  " " * }
+
+FUNCTION {word.in}
+{ bbl.in 
+  emphasize
+  " " * }
+
+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 }
+        { series empty$
+            { number "number" bibinfo.check }
+            { output.state mid.sentence =
+                { bbl.number }
+                { bbl.number capitalize }
+              if$
+              number tie.or.space.prefix "number" bibinfo.check * *
+              bbl.in space.word *
+              series "series" bibinfo.check *
+            }
+          if$
+        }
+      if$
+    }
+    { "" }
+  if$
+}
+FUNCTION {is.num}
+{ chr.to.int$
+  duplicate$ "0" chr.to.int$ < not
+  swap$ "9" chr.to.int$ > not and
+}
+
+FUNCTION {extract.num}
+{ duplicate$ 't :=
+  "" 's :=
+  { t empty$ not }
+  { t #1 #1 substring$
+    t #2 global.max$ substring$ 't :=
+    duplicate$ is.num
+      { s swap$ * 's := }
+      { pop$ "" 't := }
+    if$
+  }
+  while$
+  s empty$
+    'skip$
+    { pop$ s }
+  if$
+}
+
+FUNCTION {convert.edition}
+{ extract.num "l" change.case$ 's :=
+  s "first" = s "1" = or
+    { bbl.first 't := }
+    { s "second" = s "2" = or
+        { bbl.second 't := }
+        { s "third" = s "3" = or
+            { bbl.third 't := }
+            { s "fourth" = s "4" = or
+                { bbl.fourth 't := }
+                { s "fifth" = s "5" = or
+                    { bbl.fifth 't := }
+                    { s #1 #1 substring$ is.num
+                        { s eng.ord 't := }
+                        { edition 't := }
+                      if$
+                    }
+                  if$
+                }
+              if$
+            }
+          if$
+        }
+      if$
+    }
+  if$
+  t
+}
+
+FUNCTION {format.edition}
+{ edition duplicate$ empty$ 'skip$
+    {
+      convert.edition
+      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.cappages}
+{ pages duplicate$ empty$ 'skip$
+    { duplicate$ multi.page.check
+        {
+          bbl.pages capitalize swap$
+          n.dashify
+        }
+        {
+          bbl.page capitalize swap$
+        }
+      if$
+      tie.or.space.prefix
+      "pages" bibinfo.check
+      * *
+    }
+  if$
+}
+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$
+  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.capchapter.pages}
+{ chapter empty$
+    'format.cappages
+    { type empty$
+        { bbl.chapter capitalize }
+        { type "l" change.case$ capitalize
+          "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.capin.ed.booktitle}
+{ format.booktitle duplicate$ empty$ 'skip$
+    {
+      editor "editor" format.names.ed duplicate$ empty$ 'pop$
+        {
+          "," *
+          " " *
+          get.bbl.editor
+          ", " *
+          * swap$
+          * }
+      if$
+      capword.in swap$ *
+    }
+  if$
+}
+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}
+{
+  capword.in
+  " \cite{" * crossref * "}" *
+}
+FUNCTION {format.book.crossref}
+{ volume duplicate$ empty$
+    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
+      pop$ capword.in
+    }
+    { bbl.volume
+      capitalize
+      swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word *
+    }
+  if$
+  " \cite{" * crossref * "}" *
+}
+FUNCTION {format.incoll.inproc.crossref}
+{
+  capword.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
+}
+
+STRINGS {oldname}
+
+FUNCTION {name.or.dash}
+{ 's :=
+   oldname empty$
+     { s 'oldname := s }
+     { s oldname =
+         { "---{}---{}---" }
+         { s 'oldname := s }
+       if$
+     }
+   if$
+}
+
+FUNCTION {article}
+{ output.bibitem
+  format.authors "author" output.check
+  author format.key output
+  name.or.dash
+  format.date "year" output.check
+  date.block
+  format.title "title" output.check
+  new.block
+  crossref missing$
+    {
+      journal
+      "journal" bibinfo.check
+      "journal" output.check
+      add.blank
+      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
+      name.or.dash
+    }
+    { format.authors output.nonnull
+      name.or.dash
+      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
+      format.number.series output
+      format.edition output
+      new.sentence
+      format.publisher.address output
+    }
+    {
+      new.block
+      format.book.crossref output.nonnull
+    }
+  if$
+  new.block
+  format.note output
+  fin.entry
+}
+FUNCTION {booklet}
+{ output.bibitem
+  format.authors output
+  author format.key output
+  name.or.dash
+  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
+      name.or.dash
+    }
+    { format.authors output.nonnull
+      name.or.dash
+      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
+      format.number.series output
+      format.edition output
+      new.sentence
+      format.publisher.address output
+    }
+    {
+      format.chapter.pages "chapter and pages" output.check
+      new.block
+      format.book.crossref output.nonnull
+    }
+  if$
+  new.block
+  format.note output
+  fin.entry
+}
+
+FUNCTION {incollection}
+{ output.bibitem
+  format.authors "author" output.check
+  author format.key output
+  name.or.dash
+  format.date "year" output.check
+  date.block
+  format.title "title" output.check
+  new.block
+  crossref missing$
+    { pages empty$
+      { format.capin.ed.booktitle "booktitle" output.check }
+      { format.capchapter.pages output add.blank
+        format.in.ed.booktitle "booktitle" output.check }
+      if$
+      format.bvolume output
+      format.number.series output
+      format.edition output
+      new.sentence
+      format.publisher.address 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
+  name.or.dash
+  format.date "year" output.check
+  date.block
+  format.title "title" output.check
+  new.block
+  crossref missing$
+    { pages empty$ 
+      { format.capin.ed.booktitle "booktitle" output.check }
+      { format.cappages output add.blank
+        format.in.ed.booktitle "booktitle" output.check }
+      if$
+      new.block
+      format.bvolume capitalize output
+      format.number.series output
+      new.sentence
+      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
+  name.or.dash
+  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
+  name.or.dash
+  format.date "year" output.check
+  date.block
+  format.title
+  "title" output.check
+  new.block
+  bbl.mthesis format.thesis.type output.nonnull
+  new.block
+  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
+  name.or.dash
+  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
+  name.or.dash
+  format.date "year" output.check
+  date.block
+  format.title
+  "title" output.check
+  new.block
+  bbl.phdthesis format.thesis.type output.nonnull
+  new.block
+  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
+  name.or.dash
+  format.date "year" output.check
+  date.block
+  format.btitle "title" output.check
+  format.bvolume output
+  format.number.series output
+  new.sentence
+  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
+  name.or.dash
+  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
+  name.or.dash
+  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 `amnatnat.bst'.

analyses/independent_contrasts/knitr/independent_contrasts.Rnw

+\documentclass[11pt]{article}
+
+%% This document source is based on the excellent:
+%% http://www.math.smith.edu/~nhorton/sleuth/
+%%
+%% Specifically, 
+%% http://www.math.smith.edu/~nhorton/sleuth/chapter02.Rnw
+
+\usepackage{natbib}
+\usepackage[margin=1in,bottom=.5in,includehead,includefoot]{geometry}
+\usepackage{hyperref}
+\usepackage{language}
+\usepackage{alltt}
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{}
+
+%% Now begin customising things. See the fancyhdr docs for more info.
+
+\chead{}
+\lhead[\sf \thepage]{\sf \leftmark}
+\rhead[\sf \leftmark]{\sf \thepage}
+\lfoot{}
+\cfoot{Independent contrasts}
+\rfoot{}
+
+\newcounter{myenumi}
+\newcommand{\saveenumi}{\setcounter{myenumi}{\value{enumi}}}
+\newcommand{\reuseenumi}{\setcounter{enumi}{\value{myenumi}}}
+
+\pagestyle{fancy}
+
+\def\R{{\sf R}}
+\def\Rstudio{{\sf RStudio}}
+\def\RStudio{{\sf RStudio}}
+\def\term#1{\textbf{#1}}
+\def\tab#1{{\sf #1}}
+
+
+\usepackage{relsize}
+
+\newlength{\tempfmlength}
+\newsavebox{\fmbox}
+\newenvironment{fmpage}[1]
+     {
+   \medskip
+   \setlength{\tempfmlength}{#1}
+   \begin{lrbox}{\fmbox}
+     \begin{minipage}{#1}
+     \vspace*{.02\tempfmlength}
+		 \hfill
+	   \begin{minipage}{.95 \tempfmlength}}
+		 {\end{minipage}\hfill