Overview. Dynamic documents with R and L A TEX (while citing properly) Outline. Software for your Statistical Analysis (1) knitr.

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1 Overview Dynamic documents with R and L A TEX (while citing properly) Michael Höhle 1 1 Department of Mathematics Stockholm University, Sweden Kandidatarbete i matematisk statistik VT-14 Seminarium, 25 Apr Dynamic Report Generation with R knitr BibTeX Dynamic documents & citations with LATEX Michael Höhle 1 / 29 Dynamic documents & citations with LATEX Michael Höhle 2 / 29 Software for your Statistical Analysis (1) 1 Dynamic Report Generation with R knitr is a free open source software environment for statistical computing and graphics available from runs on a wide variety of UNIX platforms, Windows and Mac OS. is an implementation of the S language (programming language oriented). produces high-quality graphics in a variety of formats, including JPEG, PNG, EPS and PDF. can be combined with Sweave/odfWeave/knitr for automatic report generation using L A TEX/OpenOffice. Dynamic documents & citations with LATEX Michael Höhle 3 / 29 Dynamic documents & citations with LATEX Michael Höhle 4 / 29

2 Software for your Statistical Analysis (2) Debugging We recommend programming in R using an integrated desktop environment (IDE). Currently, the best choice is RStudio the preview release version even contains debugging functionality! If you are an Emacs fan, then Emacs-Speaks-Statistics is the add-on package you want. R offers a number of functions for debugging your code browser(<condition>), e.g. browser(i==10) in a loop. Entire functions can be put into debug-mode by calling browser(<functionname>) n advance to the next step. c continue to the end of the current context where print a stack trace of all active function calls. Q exit the browser and the current evaluation and return to the top-level prompt. A number of packages exists for making debugging R code more comfortable here I shall only mention the debugging capabilities of RStudio. 1 Available from Dynamic documents & citations with LATEX Michael Höhle 5 / 29 Dynamic documents & citations with LATEX Michael Höhle 6 / 29 knitr knitr 2 is an R package for the elegant, flexible and fast dynamic report generation with R. 1 Dynamic Report Generation with R knitr The idea is to integrate text and R programming in one document literature programming A minimal example: library("knitr") knit('knitr-minimal.rnw') The resulting L A TEX file knitr-minimal.tex is then processed using, e.g., pdflatex Note: RStudio has a nice interface for automatizing the knitr/l A TEX compilation workflow 2 See for more information Dynamic documents & citations with LATEX Michael Höhle 7 / 29 Dynamic documents & citations with LATEX Michael Höhle 8 / 29

3 knitr (2) knitr (3) The built-in ability to cache the result of code blocks (e.g. blocks with heavy computations) makes knitr suitable even for documents requiring lengthy computations However, a divide and conquer strategy may be beneficial, e.g. outsourcing data pre-processing or lengthy computations into separate R files. These files are then included using knitr s read_chunk function or by simply loading R objects stored by these functions using save. Bachelor s or Master s thesis benefit from having dynamically generated contents while being reproducible! One can also extract the R code from a corresponding Rnw file using purl( knitr-minimal.rnw ) knitr has a very flexible choice of graphical output system, i.e. you can decide (even at the per-figure level) if you want output as PDF, PNG, tikzdevice, etc. Alternative document output formats of knitr are markdown or HTML. Dynamic documents & citations with LATEX Michael Höhle 9 / 29 Dynamic documents & citations with LATEX Michael Höhle 10 / 29 Non R users The best suggestion is of course to change to R! However, there might be a number of reasons that you can t For SAS there is also a program SASweave available: The program requires that you have gawk utility installed (handles data-reformatting). See the SASweave homepage for more details. 1 Dynamic Report Generation with R BibTeX Dynamic documents & citations with LATEX Michael Höhle 11 / 29 Dynamic documents & citations with LATEX Michael Höhle 12 / 29

4 Citations One of the great challenges of writing your thesis is to appropriately acknowledge the work of others when you use it Hence, your work procedure should require a different input device than: About Citations (1) 3 Citation has several important purposes: to uphold intellectual honesty (or avoiding plagiarism) to attribute prior or unoriginal work and ideas to the correct sources to allow the reader to determine whether the referenced material supports the author s argument in the claimed way to help the reader gauge the strength and validity of the material the author has used Image source: However, I m not a librarian so this is a personal account of how I think you should do this in a mathematical context Dynamic documents & citations with LATEX Michael Höhle 13 / 29 About Citations (2) 5 Broadly speaking, there are two types of citation systems: The Vancouver system uses sequential numbers in the text, either bracketed or superscript or both The five stages of grief are denial, anger, bargaining, depression, and acceptance. 4 Parenthetical referencing has full or partial, in-text, citations enclosed in parentheses The five stages of grief are denial, anger, bargaining, depression, and acceptance. (Kübler-Ross, 1969, p 45 60) 3 Copy & paste from Dynamic documents & citations with LATEX Michael Höhle 14 / 29 Author-Date Parenthetical Referencing (1) 6 In the author-date method, the in-text citation is placed in parentheses after the sentence or the part thereof that the citation supports, The citation includes the author s name, year of publication, and page number(s) when a specific part of the source is referred to (Smith 2008, p. 1) or (Smith 2008:1). A full citation is given in the references section: Smith, John (2008). Name of Book. Name of Publisher. 4 Elisabeth Kübler-Ross, On Death and Dying (New York: Macmillan, 1969) Copy & paste from Dynamic documents & citations with LATEX Michael Höhle 15 / 29 6 Copy & paste from Dynamic documents & citations with LATEX Michael Höhle 16 / 29

5 Author-Date Parenthetical Referencing (2) Author-Date Parenthetical Referencing (2) Especially the style for in-text references in the Chicago Manual of Style is of interest: 7 A complete guide on how to do author-date citations can be found in Chicago Manual of Style accessible electronically through the Stockholm University Library ch15_toc.html The manual also provides guidance on style and usage of, e.g., grammar, numbers, abbreviations Especially chapter 12 on Mathematics in Type is a must to read for any would-be B.Sc. in Mathematics Dynamic documents & citations with LATEX Michael Höhle 17 / 29 7 Screenshot of: Dynamic documents & citations with LATEX Michael Höhle 18 / 29 BibTeX (1) 8 BibTeX BibTeX is reference management software for formatting lists of references. The BibTeX tool is typically used together with the L A TEX document preparation system BibTeX makes it easy to cite sources in a consistent manner, by separating bibliographic information from the presentation of this information 8 Copy & paste from Dynamic documents & citations with LATEX Michael Höhle 19 / 29 Dynamic documents & citations with LATEX Michael Höhle 20 / 29

6 BibTeX (2) BibLaTeX (1) The BibTeX program takes the following input a.bib text file in BibTeX format containing a database of all reference-list entries each identified by an unique Title = {Non-life insurance pricing with generalized linear models}, Author = {Ohlsson, Esbj{\"o}rn and Johansson, Bj{\"o}rn}, Publisher = {Springer}, Year = {2010}, } an.aux file produced by L A TEX on an earlier run containing calls to the keys \abx@aux@cite{ohlsson_johansson2010} a style file, which specifies how to format individual entries BibLaTeX is a complete re-implementation of BibTeX with Biber used as its back-end. The comprehensive BibLaTeX manual can be found as: biblatex/doc/biblatex.pdf See http: //tex.stackexchange.com/questions/13509/biblatex-for-idiots as a quick starting point to BibLateX. Dynamic documents & citations with LATEX Michael Höhle 21 / 29 BibLaTeX (2) Dynamic documents & citations with LATEX Michael Höhle 22 / 29 BibLaTeX (3) \documentclass[11pt,a4paper]{article} \usepackage{etex} %Prepare for citations using biblatex \usepackage[natbib=true,style=authoryear,maxcitenames=6]{biblatex} \addbibresource{literature.bib} \begin{document} Blah blah blah \citep{xxx} and bla bla bla \citet{yyy} bla bla bla. % Add bibliography \printbibliography \end{document} Especially Section 3.7 of the BibLaTeX manual provides important information on how to cite in practice: \cite: Ohlsson and Johansson, 2010 \citeauthor: Ohlsson and Johansson \citetitle: Non-life insurance pricing with generalized linear models In particular, the natbib option is useful to get proper in-text citation: \citep: (Ohlsson and Johansson, 2010) \citet: Ohlsson and Johansson (2010) Dynamic documents & citations with LATEX Michael Höhle 23 / 29 Dynamic documents & citations with LATEX Michael Höhle 24 / 29

7 BibLaTeX (4) Minimal workflow if you are working with L A TEX on the shell: > pdflatex thesis.tex > biber thesis > pdflatex thesis.tex > pdflatex thesis.tex If you are using a L A TEX IDE, e.g. TeXShop or TeXnicCenter, the workflow might be more comfortable BibTeX Dynamic documents & citations with LATEX Michael Höhle 25 / 29 Dynamic documents & citations with LATEX Michael Höhle 26 / 29 Working with JabRef It is advisable to use a reference manager program to keep track of all your literature sources Proprietary reference managers are for example EndNote, or Mendeley. They are nice for interacting with Microsoft Word. However, as a mathematician you should be using L A TEX and here bibtex support is important. A good choice 9 available under the Gnu Public License is JabRef: 9 See for a comparison. Dynamic documents & citations with LATEX Michael Höhle 27 / 29 Dynamic documents & citations with LATEX Michael Höhle 28 / 29

8 Literature I Ohlsson, Esbjörn and Björn Johansson (2010). Non-life insurance pricing with generalized linear models. Springer. Dynamic documents & citations with LATEX Michael Höhle 29 / 29