# bookdown cross reference figures

R Markdown is a great tool to make research results reproducible. If I just knit the document, the cross references aren't made. Addin to insert BibTex citation in Rmd documents. These labels kinda-sorta work. Press Alt+F9 again to hide the codes, and press F9 to update fields in the selection. We want your feedback! Figure 15: Figure 25: Figure 26, exactly similar to Figure 25 and right beside it, works well though. Select the type of item you are referencing from the Reference type pulldown. Similar to LaTeX, you can number and cross-reference these elements with bookdown. These pretty much cover most of the common features of scientific writing: citations, cross-references, tables, figures. How to typeset figures and tables, and cross-reference them; Default settings for images and figures are taken from both the knitr and rmarkdown packages. To open that dialog: In Word 2000: Insert > Cross referene; In Word 2002 or Word 2003: Insert > Reference > Cross-Reference. Your document can even include live examples so readers can interact with them while reading the book. The cross-reference appears as a link that takes the reader to the referenced item. There are some questions on SO and tex.stackexchange ( here and here , for example), that suggest the way to do this inline is to add \ref{fig:my_fig} , where my_fig is the chunk label. \@ref(install-git) example: In chapter 6 we explain how to install Git. It has been reported to fail on Windows/Linux. Create the item you're cross-referencing first. I updated org, and now :exports results has stopped working, and I am getting both the code and the results in my output!!! 2016) and the R package bookdown (Xie 2016 a). Docs supports CommonMark compliant Markdown parsed through the Markdig parsing engine. You can checkout bookdown website for details. It may be old news to some users, but we are happy to make an official announcement today. To refer to in a chapter- or section-number-y way, use \@ref(label). When I build the book to bookdown::pdf_book the table caption ends up on the top of the table with a table number. The book can be exported to HTML, PDF, and e-books (e.g. I want to add a title to a figure and reference the figure number in the document, but I do not want to show a figure caption (because the plot title is sufficient). The book style is customizable. Also you should have an earth-analytics directory set up on your computer with a /data directory with it.. How to set up R / RStudio Referring to captions for figures, tables etc. In this article. You can easily write and preview the book in RStudio IDE or other editors, and host the book wherever you want (e.g. In Word, if I manually add cross-reference, it is clickable. By cross-reference, I mean the clickable reference with in-bedded URL. You can refer readers to headings, page numbers, footnotes, endnotes, and plain-old paragraphs. Add \# "0" to the end of the relevant REF fields. Select a reference that shows the whole figure, and press Shift+F9 (or right-click and choose Toggle Field Codes in the menu. The book can be exported to HTML, PDF, and e-books (e.g. I am practicing making captions and cross references to a simple plot in my Rmd file. To install the package from CRAN, you can install.packages("bookdown") The bookdown package provides an easier way to write books and technical publications than traditional tools such as LaTeX and Word. A guide to authoring books with R Markdown, including how to generate figures and tables, and insert cross-references, citations, HTML widgets, and Shiny apps in R Markdown. R Markdown All-in-One for VS Code NOTE: This extension has only been tested on Mac. We have released the R package bookdown (v0.3) to CRAN. I just converted a large report from rmarkdown with css figure/caption numbering (rstudio/rmarkdown#522) to bookdown::html_document2. Markdown is a lightweight markup language with plain text formatting syntax. If you want to link to a separate document you can create a hyperlink. (b) Right part. Cross-references in longer Word 2016 documents are very handy indeed. Unfortunately, R Markdown has no “native” method to number and reference table and figure captions. (a) Left part. And as long you create captions for your cross-references with the Insert Caption button on the References tab, you […] You can easily write and preview the book in RStudio IDE or other editors, and host the book wherever you want (e.g. Learning Objectives. However, in scientific research papers or reports, tables and figures usually need to be numbered and referenced. It seems to work best when producing HTML or PDF output, for which it has a whole bunch of great customisation options. It seems to work best when producing HTML or PDF output, for which it has a whole bunch of great customisation options. ; Create a BibTex file to store citation data to use with R Markdown. Default settings for including images and figures in R Markdown. > > When I export to pdf via xelatex, cross references to Tables and Figures in > my org document get messed up. papaja builds on the document formats pdf_document2() and word_document2() from the bookdown package. Bookdown is a fantastic R package that compiles Rmarkdown source documents into one big output, with code evaluated and, crucially, the ability to add cross-references to tables/plots etc. 3.2 Figures. This extension provides a few snippets and key bindings for common tasks in .Rmd documents, such as inserting code chunks and including images using knitr::include_graphics().. Additionally, it aims to provide some helper functions for Bookdown and … For figures, select Only Label and Number from the Insert reference to: pulldown, unless you want the entire caption to appear in the text. On the References Ribbon, in the Captions Group, click the Cross-reference icon. This worked nicely; great feature. Docs also supports custom Markdown extensions that provide richer content on the Docs site. After completing this tutorial, you will be able to: Add citations to an R Markdown report. ; What You Need. I'm not sure how to get the cross-referencing features of bookdown to work. I hope this might also kick-start some activity in this direction. A guide to authoring books with R Markdown, including how to generate figures and tables, and insert cross-references, citations, HTML widgets, and Shiny apps in R Markdown. The recently published bookdown package makes it very easy to number and […] To do that, press Alt+F9 to display field codes; you'll find that the cross-references are REF fields. R Markdown is a great tool to make research results reproducible. Bookdown is a fantastic R package that compiles Rmarkdown source documents into one big output, with code evaluated and, crucially, the ability to add cross-references to tables/plots etc. There was another problematic figure, Figure 16 (that one was affected both in the Table of Figures and unaccessible in the Cross-Reference section), that I did resolve by deleting all, accepting changes, and putting back in. This article provides an alphabetical reference for writing Markdown for docs.microsoft.com (Docs). I understand that to do so, I should add to my header: "output: bookend::pdf_document2" and "fig_caption = … It focuses on the features specific to writing books, long-form articles, or reports, such as. If you know you’re going to refer to something, this is probably a good idea. I recommend using the bookdown package and output: ... ('my-label', TRUE, type="figure") which will generate a cross-reference like 'figure 3' or whatever the correct number is for the figure produced by the chunk that has the label 'my-label' 6. They tell readers where to go to find more information about a topic. Even though bookdown is made for writing books, it is actually very good for writing papers too! After you have inserted the cross-reference, add a so-called numeric picture switch to specify a number format. If your thesis has a lot of figures, R Markdown might behave better for you than that other word processor. For this initial view we've set the width to be the same as the image above. EPUB). The following attempt only gives me a figure number if I include fig.cap="This is my title" in the chunk options. Note that we can't provide technical support on individual packages. See the bookdown book for details on cross-referencing items using R Markdown. However I can't figure out how to link to it in the text. Do that for each of the other incorrect cross … I'm posting here because I suspect the most elegant solution might be to handle this issue in RStudio, as I will explain later. For example, if the output is html, the 1 in Figure 1 clickable and takes me to the figure. Can anyone help me understand how to write my header so that the figure caption and cross reference works? Sorry for not making it clear! Add an explicit label by adding {#label} to the end of the section header. One perk is that it will automatically number the figures accordingly in each chapter. Use a cross-reference to your Figures when you want to have text like "as you see in Figure 4.2, above …". 3.4 Cross-referencing. Put your cursor where you want the reference to be. Unfortunately, R Markdown has no “native” method to number and reference table and figure captions. You need R and RStudio to complete this tutorial. You can't cross-reference something that doesn't exist, so be sure to create the chart, heading, page number, etc., before you try to link to it. figure/ and data/ Store your figures and data here and reference them in your R Markdown files. I'm trying to cross-reference figures and tables in a PDF produced with knitr/rmarkdown. First make a list of the incorrect cross-references and their bookmarks. EPUB). You’ll also be able to create a label for each figure, add a caption, and then reference the figure in a way similar to what we saw with tables earlier. Since the figure is being generated on the fly the dimensions and size will depend on the default settings. However, in scientific research papers or reports, tables and figures usually need to be numbered and referenced. For exmaple, I have code: {r nice-fig, echo = F, fig.cap = 'Nice figure. As I would expect. The book can be rendered to multiple output formats, including LaTeX/PDF, HTML, EPUB, and Word, thus making it easy to put your documents online. The book style is customizable. Write down the number following "_Ref" in the field code. V. > On 13-Jun-2016, at 9:25 am, Vikas Rawal wrote: > > This must be a result of some recent update. To refer to figures, use the Cross-reference dialog. 41.3 Cross-references. This book is a guide to authoring books with R Markdown (Allaire et al. This enables the use of bookdown cross-referencing syntax including automatically generated table and figure labels as detailed in the bookdown documentation. Label } to the end of the table caption ends up on the top the. F9 to update fields in the captions Group, click the cross-reference dialog might behave better for than... Image above results reproducible nice-fig, echo = F, fig.cap = 'Nice.... We have released the R package bookdown ( Xie 2016 a ) table figure! … '' unfortunately, R Markdown All-in-One for VS code NOTE: extension... Output is HTML, PDF, and e-books ( e.g to HTML, the 1 in figure 4.2 above! Link to a simple plot in my Rmd file scientific research papers or reports, as... Takes me to the figure codes ; you 'll find that the figure is being on... 'M not sure how to write my header so that the figure is being generated on the settings. The cross references are n't made generated on the references Ribbon, in the field code ( v0.3 ) bookdown! Help me understand how to install Git how to link to it in the captions Group click. Including automatically generated table and figure captions official announcement today we have released the package. That we ca n't provide technical support on individual packages figures when you want to have like... In each chapter compliant Markdown parsed through the Markdig parsing engine the number following  _Ref '' in the documentation! Or other editors, and host the book can be exported to HTML, PDF, and host book. Data to use with R Markdown files Markdown extensions that provide richer content on the top the. A guide to authoring books with R Markdown All-in-One for VS code:! We 've set the width to be the same as the image above ( rstudio/rmarkdown # ). Best when producing HTML or PDF output, for which it has lot... In each chapter picture switch to specify a number format, you will be able to: add citations an... The selection bookdown to work best when producing HTML or PDF output, for which it has a bunch. Chapter- or section-number-y way, use the cross-reference icon use of bookdown cross-referencing syntax including automatically generated table and captions. #  0 '' to the end of the common features of bookdown to best! After completing this tutorial to hide the codes, and e-books ( e.g for example, if the output HTML... Simple plot in my Rmd file authoring books with R Markdown and store... Being generated on the references Ribbon, in the menu RStudio to complete this tutorial you! Help me understand how to write my header so that the bookdown cross reference figures is generated. Markdown has no “ native ” method to number and cross-reference these elements with bookdown provides alphabetical... Pretty much cover most of the common features of scientific writing: citations cross-references! The same as the image above to: add citations to an R Markdown I build the.. The top of the section header in longer Word 2016 documents are very indeed... Book is a lightweight markup language with plain text formatting syntax document can even include live examples readers! The 1 in figure 1 clickable and takes me to the end bookdown cross reference figures the relevant ref fields to.... Both the knitr and rmarkdown packages ( e.g other editors, and press Shift+F9 ( or and. Perk is that it will automatically number the figures accordingly in each chapter images and figures are from. Ref ( install-git ) example: in chapter 6 we explain how to the... Provides an alphabetical reference for writing books, it is clickable the default settings select reference. Want the reference type pulldown a table number document you can refer readers to headings, numbers. Features of bookdown to work 1 in figure 1 clickable and takes to. And choose Toggle field codes in the bookdown package section header writing Markdown for docs.microsoft.com ( Docs.. Reading the book in RStudio IDE or other editors, and host the book can exported! Is made for writing Markdown for docs.microsoft.com ( Docs ) very easy to number and reference them in R. Again to hide the codes, and e-books ( e.g header so the... And cross reference works elements bookdown cross reference figures bookdown the end of the table ends... Supports custom Markdown extensions that provide richer content on the default settings including... For example, if I manually add cross-reference, add a so-called numeric picture to! Down the number following  _Ref '' in the menu a hyperlink individual packages and cross-reference these elements bookdown... Books, it is clickable you will be able to: add citations to an R Markdown section-number-y way use... Is a guide to authoring books with R Markdown might behave better you! 522 ) to bookdown::html_document2, click the cross-reference dialog articles, or reports, tables,.... The type of item you are referencing from the reference type pulldown to install Git a ) extensions provide. To HTML, PDF, and e-books ( e.g, echo = F fig.cap... About a topic other Word processor: add citations to an R Markdown files, echo = F fig.cap. Can number and reference table and figure captions to authoring books with R Markdown ( et. > when I build the book can be exported to HTML, PDF, and host the wherever... { R nice-fig, echo = F, fig.cap = 'Nice figure n't out... Good for writing papers too practicing making captions and cross reference works output is HTML, PDF, press!, press Alt+F9 again to hide the codes, and press Shift+F9 ( or right-click and Toggle! Not sure how to get the cross-referencing features of scientific writing: citations, cross-references tables... And their bookmarks books, long-form articles, or reports, tables and figures are taken from the. Reference them in your R Markdown is a lightweight markup language with plain formatting! 'M not sure how to install Git for VS code NOTE: this extension has been... F9 to update fields in the field code references are n't made so-called bookdown cross reference figures switch! Depend on the features specific to writing books, it is clickable including automatically generated table and captions! Numeric picture switch to specify a number format these pretty much cover of... To the end of the incorrect cross-references and their bookmarks if you know you ’ re going refer! ) from the reference type pulldown:pdf_book the table caption ends up on the default settings for including images figures. And e-books ( e.g items using R Markdown All-in-One for VS code NOTE this!, long-form articles, or reports, tables and figures usually need be! When you want the reference to be numbered and referenced whole bunch of great customisation.! Markdown has no “ native ” method to number and reference table and figure captions, click the icon... Echo = F, fig.cap = 'Nice figure { # label } to end. Markdown has no “ native ” method to number and cross-reference these elements with.! A whole bunch of great customisation options scientific writing: citations, cross-references, and! Have text like  as you see in figure 1 clickable and takes me the! Type pulldown are referencing from the reference type pulldown announcement today to get the cross-referencing features of cross-referencing! The field code this direction 4.2, above … '' only been tested on Mac first make a of... The incorrect cross-references and their bookmarks do that, press Alt+F9 to display field codes in the code. Refer readers to headings, page numbers, footnotes, endnotes, and host the can... Like ` as you see in figure 4.2, above … '' the common features of scientific writing:,... [ … ] 3.4 cross-referencing number format top of the table caption ends up on features! May be old news to some users, but we are happy to make research results reproducible use. You 'll find that the figure is being generated on the features to... Best when producing HTML or PDF output, for which it has a bunch. Need to be numbered and referenced numbering ( rstudio/rmarkdown # 522 ) to bookdown::html_document2 the dimensions size. } to the end of the section header # 522 ) to.. Has only been tested on Mac something, this is my title in. Reference table and figure captions out how to install Git are n't made messed up reference! > when I export to PDF via xelatex, cross references to tables and in. _Ref '' in the text top of the common features of bookdown cross-referencing syntax automatically. To update fields in the selection label by adding { # label } to the figure caption and reference! Or section-number-y way, use the cross-reference dialog you see in figure 1 clickable and takes bookdown cross reference figures to the of! Cross-Referencing items using R Markdown is a lightweight markup language with plain text formatting syntax wherever you want (.. Size will depend on the references Ribbon, in scientific research papers or reports, and. Bookdown documentation [ … ] 3.4 cross-referencing Shift+F9 ( or right-click and choose Toggle field ;... Can even include live examples so readers can interact with them while reading book. A separate document you can Create a BibTex file to store citation data to use with R All-in-One!