Docs, Thesis & Papers with L A T EX Marion Lammarsch April - - PowerPoint PPT Presentation

Docs, Thesis & Papers with L

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Marion Lammarsch April 2017

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Table of Contents

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EX Why is L

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EX great for a thesis? Course precon – act – postcon General Information Example documents Update of Installation Programming Environ- ment Bibliography Links Homework

Why is L

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EX great for a thesis?

1 Separate content from style 2 Good layout (usually) 3 Perfect mathematical typesetting 4 Easy managing of references (including bibliography)

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Course syllabus

1 L

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EX basic information

2 Components of a scientific thesis with L

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3 Bibliographic references 4 Producing graphics with L

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EX and R

5 L

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EX for different scientific diciplines

6 Presentations with L

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Course preconditions

1 L

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EX software (distribution adapted for operating system)

2 Editor or development environment for L

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EX documents (T EXstudio or T EXmaker, T EXshop not recommended)

3 Demo files 4 Knowledge of rules for your own thesis

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Course act

1 Theory by examples and exercises 2 Please ask as many questions as you can 3 Homework assignment (see end of document)

Please send in your document via email (if possible not later than two days before next session)

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T EX special characters (german keyboard, qwertz)

Character Win Mac Backslash: \ AltGr+ß Alt+Shift+7 Curly Braces: { } AltGr+7 / AltGr+0 Alt+8 / Alt+9 Brackets: [ ] AltGr+8 / AltGr+9 Alt+5 / Alt+6 Ampersand: & Shift+6 Shift+6 Tilde: ~ AltGr++ Alt+n+Space Quote sign start: ‘ Shift+‘ Quote sign end: ’ Shift+’ (above #)

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T EX special characters (int./english keyboard, qwerty)

Character Win Mac Backslash: \ (left from return) (left from return) Curly Braces: { } Shift+[ / Shift+] Brackets: [ ] (left from return) (left from return) Ampersand: & Shift+7 Shift+7 Tilde: ~ AltGr+] Quote sign start: ‘ Shift+= Quote sign end: ’ Shift+\

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T EX 8

Quoting commands controlled by package babel

Character Type English Language (every language option): Single Quotation: ‘abc’

‘ ’

Double Quotation: “abc”

‘‘ ’’

German Language (language option ngerman): Single Quotation: ‚abc‘

\glq{} \grq{}

Double Quotation: „abc“

"‘ "’ / \glqq{} \grqq{}

French Language (language option french or ngerman): Single Quotation: ‹ abc ›

\flq{} \frq{}

Double Quotation: « abc »

"< "> / \flqq{} \frqq{}

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T EX 9

Hyphenation commands controlled by package babel

L

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EX won’t hyphenate a word that’s already been hyphenated, viz. the word contains a dash, e.g. multi-disciplinary. This is correct English typesetting style but sometimes you like to change that: Every Language: Discretionary hyphen (no other hypen valid): \- English Language (package hyphenat) Adding hyphen: \hyp e.g. multi-disci\hyp plinary German Language (language ngerman): Adding hyphen: "- Dash with hyphenation allowed: "= Non breakable dash "~ Break without dash: ""

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Macro typography (see doc16c)

new paragraph: empty line newline: \\ linebreak: \linebreak new page: \newpage page break: \pagebreak new page with shiping out all floating material: \clearpage enlarge a single page: \enlargethispage{<amount unit>}

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Micro typography

en-dash: – (type --), e.g. For ages 3–5 em-dash: — (type ---), e.g. Red, white, and blue—these are the colors of the flag. thin space (type \,), e.g. 5 mi tie between two words (non-breakable space): (type ~), e.g.

• Dr. Müller

(if the Dr. occurred near a line-break, it would never end up at the end of the line, only at the start) dots: . . . (type \dots{}, equivalent to \ldots{}) More infos (German): http://www.dante.de/DTK/Ausgaben/komoedie19964.pdf

• p. 23 ff. and http://www.dante.de/DTK/Ausgaben/komoedie19971.

pdf p. 25 ff. See also the siunitx package (doc25).

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Example documents beginners course I

doc00 Test for T EX installation doc01 Text and paragraphs doc02 Heading commands – chapter, section, subsection, . . . doc03 Title and table of contents doc04 List environments – enumeration, itemization doc05 Typefaces doc06 Simple math formulas doc07 KOMA-Script document classes scr. . . doc08 Footnotes doc09 Color – xcolor doc10 Cross references & hyperlinks – hyperref doc10a URLs doc10b Layout of hyperlinks with hypersetup

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Example documents beginners course II

doc11a Including figures – graphicx Commands includegraphics & graphicspath doc11b Disable floating of figures – float doc11c Changing figure names and references doc11d Changing figure caption style doc11e Changing figure caption to be beside figure doc11f Changing figure caption to be formatted raggedright doc12 Document class scrbook – suggested for thesis doc12a Head and foot of page, i.e. running title doc13 L

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EX thinking in boxes, horizontal and vertical doc14 Including source code listings – listings doc15 Including pages from a PDF file – pdfpages doc16 Sample thesis doc16a Figure numbering throughout whole thesis doc16b Change the page layout – geometry

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Example documents beginners course III

doc16c Page breaks, new page vs. page break doc16d Headings paragraph and subparagraph similar to sections doc16e Enumeration enhanced – enumitem doc17 Self designed title page doc18a Specify your own commands doc18b Specify your own environments doc18c Specify your own counters doc18d Building a to-do list for the thesis with own commands doc19a Material in columns – tabular doc19b Typesetting tables, horizontal lines – booktabs doc19c Material in columns extended – array doc19d Complex material in columns - tabularx doc19e Columnwidth automatically calculated - tabulary doc19f Color in tables – colortbl

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Example documents beginners course IV

doc20 Split a thesis into separate files; running title doc21 Changing the master file: including only parts for a build; modified running title doc22 Changing the master file: onehalfspacing – setspace protrusion – microtype; adding a CV; pagelayout – geometry; modified running title doc23 Using different font families doc24 Example for separate CV doc25 Units in Système international d’unités – siunitx doc26a Subfigures – subfig doc26b Subfigures – subcaption doc26c Figures surrounded by text – floatflt doc26d Figures surrounded by text – wrapfig doc30 Bibliographic references

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Example documents beginners course V

doc30a Bibliographic references with program bibtex doc30b Bib file doc30c Bibliographic references with program biber doc30d Bibliographic references export from endnote doc30e Bibliographic references export from mendely doc30f Bibliography oldstyle plain, unsrt, abbrev, alpha doc31 Typesetting abbreviations with an automatically generated list of abbreviations – acro doc40 Presentation – beamer

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Update of installed T EX-Version I

Start Tool T EX-Live-Utility in the T EX folder. Update T EX-Live-Utility itself Update T EX system (usually take long) Every year in April the T EX live system will be frozen and in order to get the new system a new installation is recommended in May.

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T EXstudio I

Manual http://texstudio.sourceforge.net/manual/current/ usermanual_en.html Configuration

Win: menu Options → Preferences Mac: menu TeXstudio → Preferences Default Bibliography Tool: Bib(la)TeX or Biber – submenu Build force packages to be used by auto completion (normally commands/environments from loaded packages show up automatically) – submenu Completion switch on line numbers – submenu Advanced Editor (check mark in left lower corner for Advanced Options)

Delete the auxiliary files generated by L

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EX – menu Tools → Clean Auxiliary Files . . . T EXstudio identify a master (root) document automatically

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T EXstudio II

A configuration can be saved in a profile (menu Options) Wizards for e.g. tabulated material (tabular), beamer presentations One can use SVN

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T EXmaker I

Configuration: engl: Menu texmaker → Preferences german: Menu Options → Texmaker konfigurieren Submenu Commands/Befehle Headline PDF-Viewer (right side): Choose Build-in-Viewer and Embedded Menu Options → Define current document as ‘Master Document’ / Aktuelle Datei zur ‘Masterdatei’ erklären engl: Menu texmaker → Preferences german: Menu Options → Texmaker konfigurieren Submenu Quick Build/Schnelles Übersetzen PdfLaTeX + Bib(la)tex + PdfLaTeX (x2) + View PDF

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T EXmaker II

engl: Menu texmaker → Preferences german: Menu Options → Texmaker konfigurieren Submenu Commands/Befehle Mac/Linux: Bib(la)TeX: "/usr/texbin/biber" % Win: Bib(la)TeX: "biber" % http://texwelt.de/wissen/fragen/1909/wie-verwende-ich-biber- in-meinem-editor Menu User/Benutzer → Custom Completion/ Wortvervollständigung anpassen → Examples: \glqq @\grqq{} \autoref{#label#} engl: Define your own Shortcuts for Commands and Macros german: Eigene Makros oder Befehle als Tastaturkürzel definieren: Menu User/Benutzer → User Commands/Eigene Makros

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T EXmaker III

Menu Help → TeXDoc → commands, packages search the local T EXDoc folder and the internet

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BibT EX/BibL

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EX I

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BibT EX/BibL

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Don’t mixup the external program BibTeX with the package biblatex. (Remark: There exist also an older package named bibtex, which should not be used any longer.) In the Internet you’ll find a lot of hints to use the package natbib, this is superseded by biblatex. There exists another external program named biber (as an alternative to the external program bibtex) which is more

• powerful. For styles like APA you are forced to use it.

It must be configured in your programming environment (see above). You can use programs to edit and manage your citations with a GUI, e.g. Bibdesk, Jabref.

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BibT EX/BibL

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Where to get bibliographic information? Export from software like Endnote1, Mendely2, Citavi, etc. into BibT EX format A lot of websites e.g. Google Scholar, Wikipedia3, etc. have a cite button, choose format BibT EX T EXMed – a BibT EX interface for PubMed http://www.bioinformatics.org/texmed/

1Download the latest Endnote Style from http://endnote.com/downloads/style/bibtex-export 2http://ramblingacademic.com/2016/06/fixing-bibtex-files-mendeley 3Tools→Cite Site

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Alternative L

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EX document classes I

memoir – based on book but more flexible, provides a variety

• f predefined page, chapter and caption styles

amsart, amsbook, and amsproc – papers for the American Mathematical Association revtex – American Physical Society refman – technical reference manuals with wide left margin for notes to the reader scrjura – law papers apa6 – American Psychological Association rules tufte-handout, tufte-book – inspired by the work of Edward Tufte bgteubner – producing books for the publisher Teubner Verlag exam – examinations with questions and possible answers

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Alternative L

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EX document classes II

leaflet – hand-outs that fit on a single sheet of paper which is then folded twice scrlttr2, letter, dinbrief – letters See http://texcatalogue.ctan.org/bytopic.html#classes

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L

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EX packages for different scientific disciplines

Natural Sciences: siunitx Biology: textopo, texshade, pfgmolbio Chemistry: chemtex, mhchem, chemfig, chemschemex Computer Science: listings, forest, svn Humanities: forest Mathematics: amsmath, amssymb, amsfonts, amsthm, gauss, mathabx, xy Physics: physics

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Links concerning the Software

T EX for different operating systems: http://tug.org/texlive Comprehensive T EX Archive Network (everything you’ll need) http://www.ctan.org Programming Environment: Recommended T EXstudio (others are T EXmaker, T EXnicCenter, T EXshop, T EXworks, Kile, WinEdt, Lyx) http://texstudio.sourceforge.net/ Using L

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EX Online (1) (“The easy to use, online, collaborative L

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EX editor.”) https://de.sharelatex.com Using L

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EX Online (2) (“Collaborative writing and publishing for the whole process of producing academic papers.”) https://www.overleaf.com

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Links concerning L

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Using L

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EX to Write a PhD Thesis http://www.dickimaw-books.com/latex/thesis/ Tips on Writing a Thesis in L

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EX http://www.khirevich.com/latex/ German: Ferienkurs L

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EX Grundlagen – Abschlussarbeit mit L

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EX http://www2.hs-esslingen.de/~dhommel/ German: Professionelle Dokumente und Arbeiten verfassen mit L

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EX http://www.fadi-semmo.de/latex/workshop/ German: L

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EX-Blog http://uweziegenhagen.de German: Das L

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EX Sündenregister http://www.ctan.org/tex-archive/info/l2tabu/german

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Links concerning symbols

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EX symbol catalog http://tug.ctan.org/info/symbols/comprehensive/ symbols-a4.pdf TikZ (portable graphics format) symbols http://www.ctan.org/tex-archive/graphics/pgf/ contrib/tikzsymbols Detexify – finding symbols by drawing them http://detexify.kirelabs.org/classify.html

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Links concerning the bibliography

Documentation to the biblatex package English: http://mirrors.ctan.org/macros/latex/ contrib/biblatex/doc/biblatex.pdf German: http://mirrors.ctan.org/info/translations/ biblatex/de/biblatex-de-Benutzerhandbuch.pdf Bibliography / References http://www.khirevich.com/latex/bibliography/ Biblatex customization http://www.khirevich.com/latex/biblatex/ Wikibook https://en.wikibooks.org/wiki/LaTeX/Bibliography_ Management German: Bibliographien erstellen mit biblatex http://biblatex.dominik-wassenhoven.de/download/ DTK-2_2008-biblatex-Teil1.pdf http://biblatex.dominik-wassenhoven.de/download/ DTK-4_2008-biblatex-Teil2.pdf German: biblatex-Stile eines Historikers

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Links concerning presentations

Themes https://mpetroff.net/files/beamer-theme-matrix/ Examples http://www2.informatik.uni-freiburg.de/ ~frank/ENG/latex-course/latex-course-3/ latex-course-3_en.html Tutorial http://www.uncg.edu/cmp/reu/presentations/ Charles%20Batts%20-%20Beamer%20Tutorial.pdf

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Link concerning L

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EX Tools for Life Scientists

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EX Tools for Life Scientists https: //www.tug.org/pracjourn/2007-4/senthil/senthil.pdf Eric Beitz, Das texshade-Paket: Setzen von Nukleotid- und Proteinalignments http: //www.dante.de/DTK/Ausgaben/komoedie19994.pdf,

• S. 38 ff.

Biopython Tutorial and Cookbook http: //biopython.org/DIST/docs/tutorial/Tutorial.html

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Link concerning Typography

Fonts http://www.tug.dk/FontCatalogue/ German: Philip Taylor, Eine pragmatische Herangehensweise an den Absatzumbruch: http: //www.dante.de/DTK/Ausgaben/komoedie19994.pdf,

• S. 50 ff.

German: Marion Neubauer (heute Lammarsch), Feinheiten bei wissenschaftlichen Publikationen – Mikrotypographie-Regeln, Teil I http: //www.dante.de/DTK/Ausgaben/komoedie19964.pdf,

• S. 23 ff.

German: Marion Neubauer (heute Lammarsch), Feinheiten bei wissenschaftlichen Publikationen – Mikrotypographie-Regeln, Teil II http: //www.dante.de/DTK/Ausgaben/komoedie19971.pdf,

• S. 25 ff.

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Homework for 1st L

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EX session I

Send in one document created from scratch containing a titlepage, at least 4 different level of headings, as many paragraphs of text in order to produce a pdf file which is at least 3 pages long (you can copy the text from elsewhere but have a closer look at special characters), a word with a German umlaut, some emphasized words, a quotation, a footnote, a nested enumeration. What happen when you change the document class to scrbook? Please make an error on purpose in your file and try to understand the error message in the log window.

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Homework for 1st L

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EX session II

Optional task: Write down a sentence for each of the following terms documentclass command environment package preambel of a T EX file \textrm vs. \mathrm width=0.8\textwidth

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Homework for 2nd L

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Send in one document with document class scrbook containing single sided, A4 paper, chapters can start on any page titlepage in the style of your own thesis table of contents, list of figures, list of tables, all listed in the table of contents some math, inline and displayed

• ne or two figures left aligned, captions left aligned as well,
• ne with hanging indent, the other one without, figure

numbers throughout the whole document cross reference to headings and figures which are clickable but not visible,

• ptional tasks: list some source code of a programming

language, e.g. python or mathlab, or statistic language, e.g. SPSS, R or a page from a PDF produced by Excel or Matlab

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Homework for 3rd L

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Send in one compressed file with a master file containing document class scrbook and toc, lot, lof, running title, as well as common page numbering as closest as possible to your own thesis page layout with running head/foot right, textwidth 18cm, textheight 25 cm a titlepage, CV and two chapters, each in separate files

• ne or two nicely formatted tables with aligned material,

including captions and references some bibliographic references, headline for the bibliography “Bibliographic References” please avoid overfull boxes of more than 4 pt

• ptional task: add some acronyms and a list of acronyms

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Homework for 3rd L

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• ptional task: add a complex math formula of 2 or 3 lines and

a cross reference to that, like this one from the webpage https://en.wikipedia.org/wiki/Fourier_transform# Analysis_of_differential_equations under the headline „Second, note that therefore any integral“

• ptional task: typeset some numbers with units in the

Système International d’Unités (SI)

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