More LaTeX

An Extensive Sample Report

I thought I should also provide a sample, including the LaTeX code, that is more along the lines of an actual paper. Since making up stuff is way to hard, I took a published paper of mine and turned that into a sample-report. I made a few changes to make it about 90% understandable, hopefully. These changes aside, the report has essentially the scope of a published scientific paper and is thus quite a bit more extensive than is expected for your reports. It should give you some idea about the amount of details contained in experimental physics papers, the work that goes into motivating the research, and the extend of a background review.

The files that are associated with the sample report are:

• Report_illing_bpchaos.pdf - the compiled sample report.
• The source files in one neat zipped directory long-example.zip.

Compiling

I use BibTeX, that is, the references are pulled from a BibTeX data base (unimaginatively named references.bib) that is separate from the sample-report .tex file (Report_illing_bpchaos.tex). To properly include all the references in the report, you need to invoke in TexShop:

In TeXShop:
• Pick LaTeX, then do Typeset
• Pick BibTeX, then do Typeset
• Pick LaTeX, then do Typeset
• Pick LaTeX, then do Typeset

(Note that in most Macintosh programs, such as TeXShop, pdfTeX is invoked by default, so that in TexShop the LaTeX command actually implements pdflatex under the default setting. In general, latex and pdflatex are different. Therefore, to compile the sample report on other systems you need to invoke pdflatex.)

Example (e.g. compiling the source file from a terminal via command lines:)
• pdflatex Report_illing_bpchaos
• bibtex Report_illing_bpchaos
• pdflatex Report_illing_bpchaos
• pdflatex Report_illing_bpchaos

BibTeX

The disadvantage of using BibTeX is that you have to get a whole other program to work with your LaTeX file and you have to deal with errors that arise if the .bib file is not correctly formatted. (See the %-comments at the end of the sample file for an alternative.)

The advantage of using BibTeX is that you do not have to worry about correctly formatting the reference section, this is done for you by the chosen BibTeX stylefile (.bst extension).

The other advantage is, that you can use bibliography programs such as jabref or endnote to organize the bibliography file (I have used jabref and quite like it.). From online databases such as Web of Science you can directly export lists that can be read by endnote and jabref. Thus, you do not need to type in any of the information. Knowing how to do this might be handy when writing a thesis where you have to cite, potentially, many articles.

The main thing you have to do, once the reference information has been imported into a bibliogrphy .bib file using jabref, let's say, is to generate a citation-key (such as foo2008) for each reference. You can do this by hand or use the magic wand button in jabref. Then simply include `\cite{foo2008}' into your .tex file and the appropriate reference will be pulled from the .bib database, correctly formatted, and put at the end of your report when you compile your latex document as described above.

Here is a link to a description of how to interface endnote and BibTeX.

Jabref and Journal abbreviations

Some BibTeX stylefiles have included a list of abbreviations for the journals that are most often cited. Upon compiling the LaTeX file, BibTeX will attempt to replace the journal titles with the appropriate abbreviation. However, that only works if in the .bib database the journal names are in a `standard' form. Unfortunately, the journal names that are imported from the different databases, such as Web of Science or Inspec, are not always in the right form. It is therefore worthwhile to have more fine control over the journal names as written to the .bib-database.

I use jabref and a journal abbreviation file (see below) to make sure the journal names are saved in the correct abbreviated form to the .bib file (e.g. references.bib). In jabref, I use the Toogle abbreviation button to see if the journal title toogles between the full name and the abbreviated form. If so, then it is recognized in my journal abbreviation file. If not, one either needs to enter the correct abbreviated journal name in the Journal field or, alternatively, edit the journal abbreviation file.

To get started, here is a journal abbreviation file with a small list of common journals: In jabref go to Options>>Manage journal abbreviations and include in the personal journal list as an external file journal_abbreviations_general.txt.