Microsoft's version of Google Scholar?

I accidentally ran into this today. Microsoft has their own version of Google Scholar:

• Microsoft Academic Search (aka Journalogy(.com)?):
  • http://academic.research.microsoft.com/
  • http://journalogy.com/

Among other things, it will even generate aggregate statistics on a particular author you're interested in (number of publications, number of citations, etc.). In fact, it can even generate similar aggregates for journals and conferences (which augments the metrics you can already get from ISI databases).

Unfortunately, some of the candy tools (co-author graph and path – tools that have little functionality but lots of coolness) require Silverlight. I tried running them with Moonlight, which crashed Firefox but seemed to work in Chrome. I say "seemed" because the Silverlight/Moonlight applet loaded fine but was populated with no information. Moreover, doing searches within the applet also returned no information. However, I haven't tried it on a Windows (nor Wine) machine for comparison, and so maybe co-author graphs/paths just aren't ready for production yet. I realized yesterday that it might be wrong to interpret MAS as a product for research so much as a product still being developed within Microsoft Research.

LIBRARY ACCESS UPDATE: As of March 11, 2011, it is very possible that your university's library proxy is not yet configured to allow access through Microsoft Academic Search. If you try to access the search engine through your library proxy and it fails at the MAS address, try it again at the Journalogy address. Strangely, these two names resolve to the same address, but neither is a CNAME. Moreover, neither uses a HTTP redirect to the other. Regardless, many library proxies search their database of allowable hosts by name, and so trying either name may help. If neither name works, contact your library and have them add MAS.

rspublic.cls fixed to get rid of nasty Incomplete \if errors

Depending on how updated your LaTeX distribution is, if you try to use the Royal Society's rspublic.cls to build your compuscript, you may get nasty incomprehensible errors like:

! Incomplete \if; all text was ignored after line 7.

                \fi

I didn't get these errors on my home system (which has TeX Live 2007 installed), but I got them on Manuscript Central for Proc. R. Soc. B, and that's a major problem.

After two days of binary searching through possible sources of the problem, I found it. Jonathan Wainwright (the author of the document class) used a \phantom in both the \@oddhead and \@evenhead without preceding it by a \protect. The \phantom macro is fragile, which means that it can cause major problems when put in contexts that move around (like headers). So it needs to be protected.

I added \protect in front of each of the two \phantom calls, and all was well in the world.

I've posted a fixed version of the document class at:

• http://links.tedpavlic.com/cls/rspublic.cls

Give it a shot. That version also allows for 11pt and 12pt fonts, and it defines \@ptsize, which setspace needs to exist in order to work (i.e., for double spacing).

natbib-compatible BST file for Royal Socety journals

I just whipped up rspublicnat.bst, which is a natbib-compatible BibTeX style file (BST) for the Royal Society journals (e.g., Proceedings of the Royal Society A and B and others).

FYI, the BST can be regenerated by applying LaTeX (i.e., docstrip) to rspublicnat.dbj and then applying rspublicnatbst.patch (with patch) to the resulting BST file. The patched result should closely match the Royal Society's bibliographic conventions for both in-line and listed references.

Removing hyperref's space inside \autoref

Many journals (e.g., any of the Royal Society journals) prefer sections to be identified with the section symbol (§) rather than the word "section" followed by a space. If you use \auotref, one of the wonderful macros provided by the hyperref package, then you'll want to do something like...

\renewcommand*\sectionautorefname{\S}

Unfortunately, \autoref will still insert a space between the section symbol (\S, which renders as §) and the section number. So, as discussed in a comp.text.tex posting, you'll need to be more clever and do something like (the ~ character is the "tilde", which is on the upper-left of most keyboards; it's a LaTeX "tie"—a non-breaking space)...

\def\Snospace~{\S{}}
\renewcommand*\sectionautorefname{\Snospace}

instead. That will eat the space that \autoref inserts after the section. Voila!

Perl script that generates CSV and BerkeleyDB versions of LTWA list

UPDATE: If you're wondering why I just didn't save the LTWA database and search it every time I needed to abbreviate a journal, it's because I wanted to optimize for speed downstream. That is, I did all the possible processing now to speed things up later. I've also augmented the script to do the opposite (and save the results in other smaller files) so that I can tell the downstream process to take longer (and possibly have better results with less spurious entries in the hash table). I've also updated the downstream script to save any successful lookups locally to speed up successive runs. Again, contact me if you want more details.

I'm sick of looking up ISO 4 standard journal abbreviations from the List of Title Word Abbreviations (LTWA) hosted at ISSN's LTWA online. The most annoying thing about LTWA online is that you can't get one big list unless you have them mail you a paper copy (for a price). So you have to resort to clicking each letter and waiting for the list for that letter to come up.

So I wrote a Perl script that automatically cURLs each LTWA online page down, processes it, and generates both CSV and BerkeleyDB (BDB) hash files containing a list of words and their associated official LTWA abbreviation. I use the BDB file in another script to automatically generate BibTeX database files for each of my journal papers (that script first checks a list of known-good journal abbreviations before trying to generate the abbreviation itself).

There were several challenges to such a task, and the list isn't perfect. I focused on one-word entries. For more complicated abbreviations, I figured I'd lean on my list of known-good journal abbreviations. That still left LTWA entries like "psycholog-" and "bulletin-" which use "-" to imply "and any other character." So I used a typical /usr/share/dict/words list to generate a list of English words that matched each pattern. Because such lists don't usually include plurals, I used Lingua::EN::Inflect to generate plurals and then took all of the plurals that included the singular (i.e., that would also match the LTWA pattern).

So that works well for me. Someday I might put the script and/or the files it produces on-line. For the moment, if you want any of these, contact me and let me know. I'll share.

Journal Reviewer Review

A recent paper of mine was rejected from Journal of Theoretical Biology. For fun, lets compare and contrast and selection from the reviewer comments ("MS" = "manuscript"):

From Reviewer #1:

Overall I really liked the work presented in this MS - by generalising the traditional models of the ecological economics underpinning solitary foraging behaviour the authors offer a very interesting (& in retrospect) intuitively appealing justification for accepting that the concorde fallacy may not always be fallacious.

From Reviewer #2:

This result seems to be of significance in biology, psychology, economics, and business, and I think that the paper is deserving of publication in JTB. The paper is also very well written, and the mathematical presentation is clear and precise.

Those two were pretty nice, and suggest that I should resubmit the paper with a couple tiny revisions and I'll be off and running. Great! Wait... What's this?

From Reviewer #3:

I regret to say I have no idea what this paper is about. The mathematical lingo is completely unfamiliar to me (after about 50 years of teaching and research in maths)...(details omitted)...(I recently had a grad student who wrote in this vein. When I asked him to explain in ordinary math, he gave up.) I didn't read any further. My advice is reject.

HUH?!

American Naturalist BibTeX BST style file

The American Naturalist, a University of Chicago Press - Journals Division journal, specifies that AASTeX should be used to typeset submissions; however, it does not provide any BibTeX BST bibliography style file. That means that authors still have to manually manage their reference list rather than using BibTeX and a central BIB bibliography database.

The BST: I've tried to remedy this by creating amnatnat.bst, a natbib-compatible BibTeX Bibliography STyle (BST) file for the American Naturalist.

As far as I can tell, this BST will generate a properly formatted BBL file that should not require modifications. Note that American Naturalist requires authors to upload their BBL files and NOT their BIB files (i.e., they don't have the ability to run BibTeX on the server).

ONE CAVEAT: If you have titles that contain colons in them, you will have to manually (either in the BIB or the BBL) change the case of the letter following the colon. For example, if "Some Title: Subtitle" is the title, change the "S" in "Subtitle" to "s". A feature/bug of BibTeX is that its sentence case keeps letters following colons capitalized. This does not match the sentence case definition used by many journals, which considers the words after a colon being at the middle of a sentence rather than the start of a new sentence. As far as I know right now, there is no easy way to change the BST file to do this automatically for you.

FYI: This BST file was generated using amnatnat.dbj (for more details, see amnatnat_full.dbj) and amnatnat.patch.

LaTeX for generating Behavioral Ecology manuscript

UPDATE: Check out a more complete math-oriented template/example, that I posted as behavecol_math_template.tex. This is ready to use out of the box. It has comments. It is setup for AMS math. It has table, figure, and autoreferencing examples too.

IMPORTANT NOTE: If using amsmath environments, be sure to check out my information on making lineno compatible with amsmath environments.

UPDATE: I have put behavecol_template.tex and behavecol.bst on-line so that you don't have to do any of the following to get them.

The Oxford Journal Behavioral Ecology is not setup for LaTeX manuscript submissions. This baffles me.

So, I spent some time putting together some macros and a BibTeX style file to get up and running with this journal.

First, a template (that uses the article document class), which fixes incompatibilities between figcaps, caption, and anything that uses \ref (see behavecol_template.tex for what is below, or see behavecol_math_template.tex for a more complete example):

\documentclass[12pt]{article}

\usepackage[paper=letterpaper,margin=1.5in]{geometry}
\usepackage{setspace}\doublespacing

\usepackage{graphicx}

\usepackage[%
            labelsep=newline,
            justification=RaggedRight,
            singlelinecheck=false,
            labelfont=bf,
            tableposition=top,
           ]{caption}
\captionsetup[table]{textfont=bf,position=above}
\makeatletter
\let\oldmakecaption\@makecaption
\makeatother

\usepackage[figon,printfigures]{figcaps}
\def\figurecapname{Figure legends}
\def\tablepagename{Tables}
\def\figurepagename{Figures}
 
\makeatletter
% This lets figcaps work with \ref
% However, forces \label outside of \caption
\def\phantomsection{\relax}
\let\oldfigurepage\@figurepage
\def\@figurepage{%
        \@ifundefined{tf@pof}{}{%
        \let\oldlabel\label%
        \let\oldinput\@input%
        \def\@input{\def\label{\oldlabel}\oldinput}%
        \phantomsection%
        \addcontentsline{toc}{section}{\figurepagename}}%
        \oldfigurepage%
        }
\let\@makefcaption\@makecaption
\let\oldtablepage\@tablepage
\def\@tablepage{%
        \@ifundefined{tf@pot}{}{%
        \clearpage%
        \phantomsection%
        \addcontentsline{toc}{section}{\tablepagename}}%
        \oldtablepage%
        }
\makeatother
\usepackage[subrefformat=subparens,labelformat=parens]{subfig}
\captionsetup[subfloat]{position=top}

\setcounter{secnumdepth}{0}

% Lines are numbered, starting at 1 
% (add pagewise to reset at each page)
%\usepackage[modulo,pagewise,mathlines]{lineno}
\usepackage[modulo,mathlines]{lineno}
\modulolinenumbers[1]
\firstlinenumber{1}
\linenumbers

\usepackage{natbib}
\bibliographystyle{behavecol}
\setcitestyle{%
        authoryear,round,semicolon,%
        aysep={},%
        yysep={,},%
        notesep={, }%
        }

\usepackage{tocbibind}
\def\tocbibname{\refname}

\usepackage{varioref}
\labelformat{equation}{\textup{(#1)}}
\labelformat{enumi}{\textup{(#1)}}

\usepackage[%
            pdftitle={},
            pdfsubject={},
            pdfauthor={},
            pdfkeywords={},
            pdfstartview=FitH,
            bookmarks=true,bookmarksopen=true,
            breaklinks=true,
            colorlinks=false,
            pdfpagelabels=true,hypertexnames=true,
            plainpages=false,naturalnames=false,
            %draft,
            ]{hyperref}

% \Autoref is for the beginning of the sentence
\let\orgautoref\autoref
\providecommand{\Autoref}
    {\def\equationautorefname{Equation}%
     \def\figureautorefname{Figure}%
     \def\subfigureautorefname{Figure}%
     \def\Itemautorefname{Item}%
     \def\tableautorefname{Table}%
     \orgautoref}
 
% \Autorefs is plural for the beginning of the sentence
\providecommand{\Autorefs}
    {\def\equationautorefname{Equations}%
     \def\figureautorefname{Figures}%
     \def\subfigureautorefname{Figures}%
     \def\Itemautorefname{Items}%
     \def\tableautorefname{Tables}%
     \orgautoref}
 
% \autoref is used inside a sentence 
% (renew of the standard autoref)
\renewcommand{\autoref}{\Autoref}
 
% \autorefs is plural for inside a sentence
\providecommand{\autorefs}{\Autorefs}

\let\oldsection\section
\newcommand{\uppercasesection}[2][]{%
    \oldsection[#1]{\MakeUppercase{#2}}}
\newcommand{\uppercasesectionstar}[1]{%
    \oldsection*{\MakeUppercase{#1}}}
\makeatletter
\def\section{%
    \@ifstar{\uppercasesectionstar}%
            {\@dblarg{\uppercasesection}}}
\makeatother

\hypersetup{%
        pdftitle=
        {The title},
}
\title{The title}
\author{}
\date{}
     
\begin{document}
    
\maketitle
     
\begin{abstract}
% ...The abstract...
        \textit{Key words:} Keywords separated with comma+space, 
                            List ends with period.
        \hypersetup{%
        pdfkeywords=
        {Keywords separated with comma+space, 
         List ends with period},
        }
\end{abstract}
\newpage
     
% ...The document...
     
% The following line loads the references
\bibliography{the_bib_database_name}
     
\end{document}

Of course, remember to put table captions before the actual table insertion. In fact, it is important that the inside of a table environment has caption first, then label OUTSIDE of the caption, then the actual table content. Additionally, subfigures should be inserted (within a figure environment) with something like:

\subfloat[]{
% ... something like an \includegraphics ...
\label{fig:a}
}

Also, when you're ready to submit, get rid of the % on the %draft, line of the hyperref options. This will turn off all hyper linking, which will prevent strange little unlinked boxes from being drawn in your autogenerated proof.

Next, the bibliography style file, which I may end up posting later separately. As of right now, it has to be constructed from pieces. First, save the following as behavecol.dbj (see behavecol_full.dbj for more details):

%% Driver file to produce behavecol.bst from merlin.mbs
%% Generated with makebst, version 4.1 (2003/09/08)
%% Produced on 2007/08/23 at 12:02
%% 
\input docstrip
 
\preamble
----------------------------------------
*** Bibliography style for _Behavioral Ecology_. ***
 
\endpreamble
 
\postamble
End of customized bst file
\endpostamble
 
\keepsilent
 
\askforoverwritefalse
\def\MBopts{\from{merlin.mbs}{%
  ay,nat,nm-rvx,ed-rev,jnrlst,keyxyr,dt-beg,yr-per,note-yr,jxper,%
  jttl-rm,thtit-a,vnum-x,pp-last,num-xser,btit-rm,bt-rm,add-pub,%
  pre-edn,in-col,pp,abr,ednx,ord,jabr,xand,etal-xc,nfss,}}
\generate{\file{behavecol.bst}{\MBopts}}
\endbatchfile

and then run latex behavecol.dbj. Next, save the following to behavecol.patch:

--- behavecol.bst 2007-08-29 12:07:40.000000000 -0400
+++ behavecol_new.bst 2007-08-29 12:08:01.000000000 -0400
@@ -89,7 +89,7 @@
 FUNCTION {output.nonnull}
 { 's :=
   output.state mid.sentence =
-    { ", " * write$ }
+    { ". " * write$ }
     { output.state after.block =
         { add.period$ write$
           newline$
@@ -144,6 +144,9 @@
 FUNCTION {add.blank}
 {  " " * before.all 'output.state :=
 }
+FUNCTION {add.semicolon}
+{  ";" * before.all 'output.state :=
+}
 
 FUNCTION {date.block}
 {
@@ -248,7 +251,7 @@
 { "in" }
 
 FUNCTION {bbl.pages}
-{ "pp." }
+{ "p." }
 
 FUNCTION {bbl.page}
 { "p." }
@@ -260,10 +263,10 @@
 { "Tech. Rep." }
 
 FUNCTION {bbl.mthesis}
-{ "Master's thesis" }
+{ "[Master's thesis]" }
 
 FUNCTION {bbl.phdthesis}
-{ "Ph.D. thesis" }
+{ "[PhD thesis]" }
 
 FUNCTION {bbl.first}
 { "1st" }
@@ -488,6 +491,16 @@
     }
   if$
 }
+FUNCTION {format.book.pages}
+{ pages "pages" bibinfo.check
+  %duplicate$ empty$ 'skip$
+  empty$ 'skip$
+    { add.semicolon 
+      add.blank 
+      pages "pages" bibinfo.check 
+      " " * bbl.pages * }
+  if$
+}
 FUNCTION {format.note}
 {
  note empty$
@@ -950,6 +963,10 @@
     }
   if$
 }
+FUNCTION {format.university.address}
+{ school "school" bibinfo.warn format.org.or.pub
+}
+
 FUNCTION {format.publisher.address}
 { publisher "publisher" bibinfo.warn format.org.or.pub
 }
@@ -1148,12 +1165,11 @@
   author format.key output
   format.date "year" output.check
   date.block
-  format.title
-  "title" output.check
-  new.block
+  format.title "title" output.check
+  add.blank
   bbl.mthesis format.thesis.type output.nonnull
-  school "school" bibinfo.warn output
-  address "address" bibinfo.check output
+  format.university.address output
+  format.book.pages output
   new.block
   format.note output
   fin.entry
@@ -1178,12 +1194,11 @@
   author format.key output
   format.date "year" output.check
   date.block
-  format.title
-  "title" output.check
-  new.block
+  format.title "title" output.check
+  add.blank
   bbl.phdthesis format.thesis.type output.nonnull
-  school "school" bibinfo.warn output
-  address "address" bibinfo.check output
+  format.university.address output
+  format.book.pages output
   new.block
   format.note output
   fin.entry

Then run

patch < behavecol.patch

from the same directory that you ran the DBJ command in. That should generate the behavecol.bst file that is needed for the above template to work.

Broken sections in Elsevier elsart1p, elsart3p, and elsart5p

UPDATE: You should probably add

\def\@seccntformat#1{{\@secnumfont{}\csname the#1\endcsname.}\quad}

around line 128 (i.e., after the \@secnumfont definition) as well. Alternatively, you could add something similar (surrounded by \makeatletter and \makeatother) to your preamble.

Ever notice how section* is broken in elsart1p.cls, elsart3p.cls, and elsart5p.cls from Elsevier? Because of this, the section titles for the acknowledgments (i.e., from \ack) and the references look like normal text. Plus, the references do not show up in the PDF bookmarks. This "feature" is annoying; working with journals generally is.

How to fix this? You have to hack the document class files. In particular, you need to remove (or comment by placing a % on the beginning of the line) a chunk of lines from the document class of interest to you. In particular, remove

• elsart1p.cls - lines 144--196
• elsart3p.cls - lines 147--199
• elsart5p.cls - lines 144--196

These lines redefine the LaTeX internals \@startsection, \@sect, and \@ssect. However, it does not appear there is any good reason why Elsevier has done this, so just stick with the standard ones. This will make your document look much better too.

Until Elsevier does this for you, you should upload your modified document class with your article OR use the elsart document class in the version you send to Elsevier.

cleveref incompatibilities with Elsevier and Springer

elsart problems: If you try using cleveref with any of the elsart packages, you may get this error:

! TeX capacity exceeded, sorry [input stack size=5000].
\cl@part ->\cl@part 
                    \@elt {section}

This is due to a flaw in the elsart packages. They setup some part counters even though part isn't defined. This confuses cleveref. To fix this, add the following anywhere in your preamble:

\makeatletter \let\cl@part\relax \makeatother

Later, you can use cleveref's poorman option to strip all of the cleveref stuff from your document. After that, you can remove this line.

svjour problems: Similarly, if you try combining cleveref with Springer journal support files, you may get this error:

! TeX capacity exceeded, sorry [input stack size=5000].
\cl@chapter ->\cl@chapter
                          \@elt {theorem}

Again, this is due to a flaw in the Springer packages. They setup some chapter counters even though chapter isn't defined. To fix this, add the following anywhere in your preamble:

\makeatletter \let\cl@chapter\relax \makeatother

Again, this can be removed after cleveref's poorman procedure is applied.

Source and acknowledgments: The Springer solution was given by "Dan" in a comp.text.tex post. I used it to generate the elsart solution.

spmpscinat.bst: A natbib style file for Journal of Mathematical Biology (e.g., Springer journals)

UPDATE: I learned how to use custom-bib's makebst. I've updated the spmpscinat.bst file in a more proper way by using makebst. I also regenerated the spmpsci.bst file so it properly reverses editor names to match the JMB format. I will submit these to JMB and hopefully they'll use them. FYI, these were mostly generated from spmpscinat.dbj and spmpsci.dbj, respectively.

I was frustrated to find out that the Journal of Mathematical Biology (JMB) has been using some outdated LaTeX support files. In particular, they distribute a BiBTeX style file that has no support for natbib use (or anything similar, like apacite). This appears to be less of a problem with JMB and more of a problem with Springer in general (i.e., most of its journals). They actually expect people to type the names of the authors that they reference directly (either that or use references (e.g., [2]) as nouns, which is bad style even though it saves space)! Can you believe that?

Civilized people use a package like natbib to do something like \citet{SK86} on every textual citation, which will then generate "Stephens and Krebs (1986)" (in Harvard mode) or "Stephens and Krebs [61]" (in numerical mode). There are lots of good reasons to do this. For one, it prevents me from accidentally turning "Krebs" into "Krbes".

To deal with this, I took the abbrvnat.bst style file packaged with natbib and hacked its support into the spmpsci.bst file from Springer. The result is spmpscinat.bst, which seems to work as desired for most bibliography entries I have tried.

I don't have a lot of experience with working with BiBTeX support files, so I have a feeling that it would have been better to use custom-bib to generate a BiBTeX style file in the JMB format that would be compatible with natbib. I may do that later.

So basically, I reserve the right to update or changed spmpscinat.bst at any time and without any notice, so look out for updates.