1. Rolando V. RaqueñoThursday, April 23, 2015 1 Referencing in LaTex Recall the following method of referencing

2. Rolando V. RaqueñoThursday, April 23, 2015 2 Making references in LaTeX (fish.tex) \documentclass{article} \begin{document} \emph{My mother} is a \underline{fish} \cite{WF}. \begin{thebibliography}{99} \bibitem{WF} William Falkner, \emph{As I Lay Dying} \end{thebibliography} \end{document}

3. Rolando V. RaqueñoThursday, April 23, 2015 3 Need to compile the document twice Because we are using symbolic references, e.g., \cite{WF}, –a second pass is necessary The second pass will resolve references

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5. Rolando V. RaqueñoThursday, April 23, 2015 5 Problem with this method User is burdened with deciding how to format article titles, journal names, proceeding references Difficult to reuse references in other documents

6. Rolando V. RaqueñoThursday, April 23, 2015 6 Quick BibTex Tutorial

7. Rolando V. RaqueñoThursday, April 23, 2015 7 BibTex Tutorial Why do you want to learn BibTex? Nuts and Bolts of BibTex Examples

8. Rolando V. RaqueñoThursday, April 23, 2015 8 Why you want to learn BibTex Complements LaTeX documents by managing bibliography and references Minimizes the drudgery of formatting, numbering, and referencing Disadvantage: –Steep Learning Curve

9. Rolando V. RaqueñoThursday, April 23, 2015 9 The BibTex Process 1.Create a BibTex file with Rerefence entries 2.Get a *.bst file (bibliographic style file) 3.“Compile” or “Build” your LaTeX document to create an *.aux file 4.Run BibTeX on your LaTeX file 5.Run LaTeX twice on your updated file 6.View the dvi or pdf file

10. Rolando V. RaqueñoThursday, April 23, 2015 10 Types of Documents BibTex can handle ARTICLE BOOK BOOKLET INBOOK INCOLLECTION INPROCEEDINGS MANUAL MISC PHDTHESIS PROCEEDINGS TECHREPORT UNPUBLISHED

11. Rolando V. RaqueñoThursday, April 23, 2015 11 Each Document type can have the following entries address author booktitle chapter crossref edition editor howpublished institution journal key language month note number organization pages publisher school series title type=“Ph.D. dissertation” volume year

12. Rolando V. RaqueñoThursday, April 23, 2015 12 Sample BibTex Book Entry (mybib.bib) @BOOK{Press, author="W.H. Press", title="Numerical Recipes in C: The Art of Scientific Computing", publisher="Cambridge University Press", year=1992, }

13. Rolando V. RaqueñoThursday, April 23, 2015 13 Sample BibTex Technical Report Entry @TECHREPORT{Berk, author="Lex A. Berk and L.S. Bernstein and D.C. Robertson", title="MODTRAN: a moderate resolution model for LOWTRAN 7", number="GL-TR-89-0122", institution="Spectral Science", address = "Burlington, MA", year = 1989 }

14. Rolando V. RaqueñoThursday, April 23, 2015 14 Sample BibTex Ph.D. Dissertation Entry @PHDTHESIS{Kuo, author="Jan-Tai Kuo", title="The Influence of Hydrodynamic Transport on Phytoplankton Dynamics in Homogeneous Lakes", school="Cornell University", address="Ithaca, NY", year=1981, }

15. Rolando V. RaqueñoThursday, April 23, 2015 15 Sample BibTex Master’s Thesis Entry @MASTERSTHESIS{Knobelspiesse, author="Kirk D. Knobelspiesse", title="Atmospheric Compensation for SeaWIFS Images of Lake Superior Utilizing Spatial Information", school="Rochester Institute of Technology", addess="Rochester, NY", month=Sep, year=2000, }

16. Rolando V. RaqueñoThursday, April 23, 2015 16 Sample BibTex Article Entry @ARTICLE{Vodacek, author="Anthony Vodacek and F.E. Hoge and R.N. Swift and J.K. Yungel and E.T. Peltzer and N.V. Blough", title="The use of in situ and airborne fluorescence measurements to determine UV absorption coefficients and DOC concentrations in surface waters", journal="Limnology and Oceanography", volume=40, number=2, year=1995, pages="411--415", }

17. Rolando V. RaqueñoThursday, April 23, 2015 17 Sample BibTex Booklet Entry @BOOKLET{Sherwood, author="D.A. Sherwood", title="Phosphorus Loads Entering Long Pond, A Small Embayment of Lake Ontario near Rochester, New York", howpublished="USGS Fact Sheet 128-99", pages=4, month="November", year=1999, }

18. Rolando V. RaqueñoThursday, April 23, 2015 18 Sample BibTex Proceedings Entry @INPROCEEDINGS{Stoermer, author="E.F. Stoermer", title="Nearshore phytoplankton populations in the Grand Haven, Michigan vicinity during thermal bar conditions", booktitle="Proceedings of the 11th Conference on Great Lakes Research", pages="137--150", year=1968, }

19. Rolando V. RaqueñoThursday, April 23, 2015 19 Sample BibTex Manual Entry @MANUAL{RSI, author="RSI", title="ENVI User's Guide", publisher="Reasearch Systems Incorporated", organization="Research Systems Incorporated", howpublished="PDF File", address="Boulder, CO", month="September", year=2001, }

20. Rolando V. RaqueñoThursday, April 23, 2015 20 Different Formatting Styles To invoke a particular style, go to –http://www.ctan.orghttp://www.ctan.org Document styles are defined in *.sty files –mla.sty –bmsplain.sty Bibliography styles are defined in *.bst files –mla.bst –amsplain.bst

21. Rolando V. RaqueñoThursday, April 23, 2015 21 To invoke these styles in your document Copy them to your current working directory with your LaTeX and BibTex document Edit your LaTeX file to appropriately reference these style guides

22. Rolando V. RaqueñoThursday, April 23, 2015 22 Sample LaTeX document listing Bibliography in MLA Style ( bib.tex ) \documentclass{report} \usepackage{mla} \begin{document} \bibliographystyle{mla} \bibliography{mybib} \nocite{*} \end{document}

23. Rolando V. RaqueñoThursday, April 23, 2015 23 Commands to Build and View Document To use xdvi viewer % latex bib.tex % bibtex bib.aux % latex bib.tex % xdvi bib.dvi

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25. Rolando V. RaqueñoThursday, April 23, 2015 25 Sample LaTeX document listing Bibliography in AMS Style ( bib.tex ) \documentclass{report} \begin{document} \bibliographystyle{amsplain} \bibliography{mybib} \nocite{*} \end{document}

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27. Rolando V. RaqueñoThursday, April 23, 2015 27 To include only cited articles we remove the \nocite{*} command \documentclass{report} \begin{document} We want to get the documents \cite{RSI} and \cite{Kuo} for our collection \bibliographystyle{amsplain} \bibliography{mybib} \end{document}

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29. Rolando V. RaqueñoThursday, April 23, 2015 29 Cross-referencing in Proceedings @PROCEEDINGS{Narayanan, editor="Ram Mohan Narayanan and James E. Kalshoven, Jr.", title="Advances in Laser Remote Sensing for Terrestrial and Oceanographic Applications", booktitle="Proceeding of SPIE", publisher="SPIE", volume=3059, year=1997, }

30. Rolando V. RaqueñoThursday, April 23, 2015 30 Article in Proceedings @INPROCEEDINGS{Ulrich, author="B.L. Ulrich and P. Lacovara and S.E. Moran and M.J. DeWeert", title="Recent results in imaging lidar", crossref="Narayanan", pages="95--108", }

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32. Rolando V. RaqueñoThursday, April 23, 2015 32 Miscellaneous LaTeX Topics

33. Rolando V. RaqueñoThursday, April 23, 2015 33 Comments in LaTeX % –Ignores the rest of the line

34. Rolando V. RaqueñoThursday, April 23, 2015 34 To protect special characters Use the \ character –e.g. My\_Cat.raw To typeset a section as typed \begin{verbatim} \end{verbatim}

35. Rolando V. RaqueñoThursday, April 23, 2015 35 Verbatim command OK for small sections that can be typed into document What about including entire source code of programs –Use verbatim package

36. Rolando V. RaqueñoThursday, April 23, 2015 36 Including Source code in LaTeX documents \documentclass{article} \usepackage{verbatim} \begin{document} \begin{equation} \label{E:sum} s = \sum_{i=1}^{n}x_{i} \end{equation} The code as implemented in idl in vectorized form looks like \verbatiminput{sum.pro} \end{document}

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38. Rolando V. RaqueñoThursday, April 23, 2015 38 Including image graphics into you LaTeX document Need to convert your image graphics into EPS For images, use pnmtops, e.g. % pnmtops –norotate –nosetpage MyCat.pgm > MyCat.ps -norotate keeps from auto-rotating the image -nosetpage keeps from setting to a specific device Need to include an extension package to LaTeX called graphics using command \usepackage{graphics}

39. Rolando V. RaqueñoThursday, April 23, 2015 39 Image Graphics Example (image.tex) \documentclass{article} \usepackage{graphics} \begin{document} \begin{figure} \includegraphics{MyCat.ps} \caption{This is My Cat} \label{F:MyCat} \end{figure} \end{document}

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41. Rolando V. RaqueñoThursday, April 23, 2015 41 Flowchart Figures Create Flowchart in PowerPoint Export as a bmp file Convert from bmp to postscript % bmptoppm figure.bmp | pnmtops – norotate –nosetpage > figure.ps OR User xfig because it will export to EPS Shareware utility called WMF2EPS –Windows clipboard objects to EPS

42. Rolando V. RaqueñoThursday, April 23, 2015 42 Because current pdflatex cannot include Encapsulated Postscript Files (EPS)… Need to go from dvi to postscript to pdf using the following commands % dvips image.dvi % ps2pdf image.ps Some degradation in quality is observed

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