# Texshop Bibliography Meaning

## LaTeX forum ⇒ BibTeX, biblatex and biber ⇒ can't make the bibliography ...

Information and discussion about BiBTeX - the bibliography tool for LaTeX documents.

paulosousa
Posts:90
Joined: Sun Jun 24, 2012 8:48 pm

### can't make the bibliography ...

Postby paulosousa » Thu Jun 19, 2014 2:30 pm

Hello all, I need some help...

I want this output for the bibliography

and this in the text: Write here the text (Hyder et al, 2007).

What I must do?

minimal example:
1. \documentclass[12pt, twoside, a4paper]{book}
2. \usepackage[portuguese,english]{babel}
3. \usepackage[applemac]{inputenc}
4. \usepackage{amsmath,amssymb,amsfonts,textcomp}
5. \bibliographystyle{plainnat}
6. Write here the text \citep{Hyder2007}.
7. \begin{thebibliography}{}
8. \bibitem{Hyder2007} Hyder, Adnan A. \emph{et al}. The impact of traumatic brain injuries: A global perspective. \emph{NeuroRehabilitation} 2007; 22(5): 341--353

Tags:
Johannes_B
Site Moderator
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Joined: Thu Nov 01, 2012 4:08 pm

Postby Johannes_B » Thu Jun 19, 2014 2:46 pm

If you have the freedom of choice, use biblatex in conjunction with biber. It will be much easier to change the look of entries.

Using natbib this could be quite hard.
The smart way: Calm down and take a deep breath, read posts and provided links attentively, try to understand and ask if necessary.
Johannes_B
Site Moderator
Posts:3638
Joined: Thu Nov 01, 2012 4:08 pm

Postby Johannes_B » Thu Jun 19, 2014 3:34 pm

I just realised you typed in your bibliographic information directly. Are you doing this everytime, or was that just an example? If you are doing this by hand every time, it is an awful lot of work.

The bib file is a simple text database including the bibliographic information. You can usually download the entries along with the articles pdf.
The database can be modified using any text or teX-editor or using a specialised tool like Jabref.
The smart way: Calm down and take a deep breath, read posts and provided links attentively, try to understand and ask if necessary.
paulosousa
Posts:90
Joined: Sun Jun 24, 2012 8:48 pm

Postby paulosousa » Thu Jun 19, 2014 3:41 pm

Don't understand what you mean with
Johannes_B wrote:I just realised you typed in your bibliographic information directly. Are you doing this everytime, or was that just an example? If you are doing this by hand every time, it is an awful lot of work.

Now I am changing the bibliography style, before I used only

and in the text typing I got [1], but now I need to get (Hyder et al, 2007)
1. \begin{thebibliography}{}
2. \bibitem{Hyder2007} Hyder Adnan A. \emph{et al}. The impact of traumatic brain injuries: A global perspective. \emph{NeuroRehabilitation} 2007; 22(5): 341--353
3. \bibitem{Mazzeo2011} Mazzeo A T. \emph{et al}. Heart rate variability: a diagnostic and prognostic tool in anesthesia and intensive care. \emph{Acta Anaesthesiologica Scandinavica} 2011; 55(7): 797--811
4. \bibitem{Lingsma2010} Lingsma H F \emph{et al}. Early prognosis in traumatic brain injury: from prophecies to predictions. \emph{The Lancet Neurology}, 2010; 9(5): 543--554
5. \bibitem{Shoukri2011} Shoukri MM. Measures of Interobserver Agreement and Reliability. Chapman $\&$ Hall/CRC \emph{Biostatistics Series}, 2nd ed. 2011; 91--117
Johannes_B
Site Moderator
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Joined: Thu Nov 01, 2012 4:08 pm

Postby Johannes_B » Thu Jun 19, 2014 7:13 pm

You can use the optional argument for .
But i really don't understand, why you are doing the bibliography by hand.

1. Write here the text \cite{Hyder2007}.
2. \begin{thebibliography}{}
3. \bibitem[Hyder et al, 2007]{Hyder2007} Hyder, Adnan A. \emph{et al}. The impact of traumatic brain injuries: A global perspective. \emph{NeuroRehabilitation} 2007; 22(5): 341--353
The smart way: Calm down and take a deep breath, read posts and provided links attentively, try to understand and ask if necessary.
Johannes_B
Site Moderator
Posts:3638
Joined: Thu Nov 01, 2012 4:08 pm

Postby Johannes_B » Fri Jun 20, 2014 4:56 pm

Prepare a database in key-value-pairs for the single entries.
Please have a look at TeX.SX.

But i think it is a little late to change now. But you should give it a try for your next project.

Johannes
The smart way: Calm down and take a deep breath, read posts and provided links attentively, try to understand and ask if necessary.
paulosousa
Posts:90
Joined: Sun Jun 24, 2012 8:48 pm

Postby paulosousa » Fri Jun 20, 2014 6:27 pm

It's not late because I have only 10 references at the moment...
Please let me know what I must do to print the references (must be named References)in the document and to have exactly (Hyder, 2007) after "have here the text " in the abstract.

In the bibfile.bib I have:

1. \documentclass[12pt, twoside, a4paper]{book}
2. \usepackage[portuguese,english]{babel}
3. \usepackage[applemac]{inputenc}
4. \usepackage{amsmath,amssymb,setspace,color}
5. \usepackage[style=authoryear,sorting=nyt]{biblatex}
7. \renewcommand{\bibname}{References}}
8. have here the text \cite{Hyder2007}.
1. title={The impact of traumatic brain injuries: a global perspective},
2. author={Hyder, Adnan A and Wunderlich, Colleen A and Puvanachandra, Prasanthi and Gururaj, G and Kobusingye, Olive C},
3. journal={NeuroRehabilitation},
Johannes_B
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Postby Johannes_B » Fri Jun 20, 2014 8:32 pm

I used the filecontents environment to keep my testing dir nice an clean. Everybody is naming his/her file somelithing like bib.bib or lit.bib.

This is just the basic, which should come close to what you want. See the link inside the MWE to find out how to customize biblatex styles. I ususally don't see any reason to tinker with the default.

There are many more useful commands described in the documentation of package biblatex. Be sure to update both biblatex and biber to get the best results.
1. \begin{filecontents}{\jobname.bib}
2. title={The impact of traumatic brain injuries: a global perspective},
3. author={Hyder, Adnan A and Wunderlich, Colleen A and Puvanachandra, Prasanthi and Gururaj, G and Kobusingye, Olive C},
4. journal={NeuroRehabilitation},
5. \documentclass{article}%just for the mwe
6. \usepackage[portuguese,english]{babel}
7. \usepackage[style=authoryear,sorting=nyt,backend=biber]{biblatex}
9. \renewcommand{\bibname}{References}}
10. have here the text \cite{Hyder2007}.\par
11. Or with parenthesis \parencite{Hyder2007}\par
12. Or cite the author: \citeauthor{Hyder2007},
13. or just cite the title: \citetitle{Hyder2007}.\par
14. You can find guidelines on how to change biblatex styles
15. at \url{http://tex.stackexchange.com/questions/12806/}
16. \printbibliography[title=References]
The smart way: Calm down and take a deep breath, read posts and provided links attentively, try to understand and ask if necessary.

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## Installation of LaTeX and TeXShop on a MAC

Last Edited: Dec 8, 2017

WARNING: MAKE SURE YOUR MAC IS CONNECTED TO THE POWER LINE OR FULLY CHARGED.

2. Click MacTeX-2017.pkg to install it. It may take several minutes. At the last phase, installation of Command Line Developer Tools is propsed and it is suggested to install them. It includes many unix commands to be used mainly in CLI.
3. Move TeXShop to your application folder.
4. Execute TeXShop, choose 'Preference ( 環境設定)'.
1. In the 'Source (書類)' tab, there is 'Set Default Values ( 設定プロファイル)' at the left bottom. Choose 'pTeX (ptex2pdf)'.
2. In the middle right side, there is 'Encoding (エンコーディング)' setting. Make sure it has been set as 'Unicode (UTF-8)'.
3. In the 'Engine (内部設定)' tab, make sure '(pdf)TeX Make sure that 'Latex' field under 'TeX+dvips+distiller' (located in the center left). is as follows:
ptex2pdf -l -ot "-synctex=1 -file-line-error"
4. Make sure if the 'BibTeX Engine/(BibTeX エンジン)' is set as 'pbibtex'.
5. Click 'OK' to save the configuration.
6. Then 'Quit TeXShop/(TeXShop を終了)' once to complete your configuration.

Invoke TeXShop, type in the following text:
\documentclass[a4j]{jarticle} \begin{document} \section{Introduction} Hello World. \end{document}

Oops, if you happen to use Japanese keyboard, you can input a \ by Option+¥.

Save it with a file name such as "sample.tex", then click "typeset" button. TeXShop executes LaTeX and generates "sample.dvi" file. If no error happens, it continues to create a PDF file "sample.pdf" and displays the generated PDF file. If you are able to input Japanese characters, add some Japanese words before the line of \end{document}. Save the file and click the "Typeset" button again to see what happens.

Note that multiple spaces in LaTeX are usually intepreted as a single space, and paragraphs are separated by blank lines. A comment starts with % and continues to the end of line. This is very convenient to leave your memo on the text which is not published in the document. However, you should be careful when you write something like

in the analysis, 45% of the users felt ...
All characters after % are ignored. In this case, you should write as
in the analysis, 45\% of the users felt ...
When you emphasize a word by a doublequote, you specify two backquotes as well as two apostrophies:
In order to emphasize'' a word
Some other special characters may have special meaning, and you prepend a \ to each of such characters in the text. Please refer the LaTeX documentation.

Before start using TeXShop, creating a new directory is highly recommended as TeX system generates several control/log files there. You can also split the text intro several files, and main tex file can include the definitions (such as \documentclass and \begin{document}) as well as inclusion directives of other files (such as \input{intro.tex}). Note: all of TeX files should have suffix of ".tex".

When you create a file to be included by the main file, you should specify the main file by Macro->Root for each new file. The TeXShop always starts with the main file when you click "Typeset" button (you don't have to search main file window).

When you start writing your thesis, it is recommended to use a TeX Macro Files maintained by Masato Yamanouchi, Daisuke Uriu, and others. Please check the following URL:

KMD Thesis Template maintained by Dr. Charith Fernando

If you are going to write a thesis in Science and Engineering style, I'd suggest to comment out the following lines at the end of each TeX file:

\section*{注}
\begin{footnotesize}
\theendnotes
\end{footnotesize}

If you are going to write in Japanese Science and Engineering style thesis, you may want to replace

\bibliographystyle{acm-sigchi}
at the end part of document.tex with the followings:
%\bibliographystyle{acm-sigchi}
\bibliographystyle{junsrt}
and move
%
% 謝辞
%
\acknowledgements

...
to after a line
%\input{conclusion.tex}

Make sure you periodically (daily) backup all of your files to an USB memory - don't override the old files as long as the remaining capacity allows. According to Murphy's Law, closer the deadline, higher the disk crash possibility. It is also vital to keep the USB memories to a secure place if they contain confidential information. If you have a remote server accessible via ssh, it is suggested to use remote version management tools such as cvs, svn, or git.

In your thesis, every figure and table is required to be referred in the main text, such as "As shown in Figure 2.12". Use \label{label-name} to define a label associated with a figure or a table, then use \ref{label-name} to refer it.

In some cases, you may want to add a citation to the caption such as

\begin{figure}[hbt] \begin{center} \includegraphics[width=10cm]{figs/sample-figure.eps} \end{center} \label{fig:sample-figure} \caption{Sample Figure~\cite{sample-figure}} \end{figure}
This is good, however, the citation marks such as [12] appear on the "List of Figures" page, which should be avoided. In this case, you can specify an alternate caption by using [ ] such as
\caption[Sample Figure]{Sample Figure~\cite{sample-figure}}
This is convenient as well when the caption is too long; you can specify an abbrevation version in [ ] to make the list of figure page more beautiful.
In TeX, it is possible to divide your thesis into several files (for example, a separate file for a chapter). But you may need to click the "Typeset" button of the top level file rather than the button of the file under editing in TeXshop. This is a little bit troublesome. You specify the root file once for every non-root file by "macro" -> "root"; then specify the top level file such as "thesis.tex" or "document.tex". It will add a line
% !TEX root = thesis.tex
at the top of the file. Now you can click "Typeset" to run LaTeX of the file under editing without seeking the top level file window.
Please keep in mind that you may need to run LaTeX (click the "Typeset" button) TWICE. The first run generates ".aux" file to record the chapter/section/subsection numbers, labels, caption of figures, etc. The output PDF file at this stage may include the following:
it is illustrated in Figure ??.
In this case, you may notify something like followings in the console window:
LaTeX warning: Reference `sample-figure' on page 8 undefined on input line 48. ... LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
In the second run, LaTeX refers the ".aux" file generated in the previous run to resolve the references to generate correct output such as
it is illustrated in Figure 2.11.
The full course execution of LaTeX would be:
"Typeset LaTeX", "Typeset BibTeX", "Typeset LaTeX", then "Typeset LaTeX".
You should execute this process before submission of your document.
It is essential to browse .log file to make sure
• No duplicated label is defined.
• No undefined label is referred.
• No undefined reference is cited.
• No TeX error occured (some warnings can be ignored, but not all!)

In LaTeX, you may specify more than one bibliography files such as
\bibliography{project.bib,rfc.bib,my.bib}

When you are to share a project bib file with your colleagues, entry name convention is important to avoid confusion and conflict.

When you need a bibliography file for RFC (Request for Comments), there are many automatically generated ones available. One of them is rfc.bib.gz maintained by Dr. -Ing. Roland Bless from Karlsruhe Institute of Technology.