The marker can be seen as a name that we give to the object that we want to reference. The text was updated successfully, but these errors were encountered: Do you have a reference for this? You should never be copy-pasting or retyping data summaries into a table. In case you prefer the figures not to have the filename of your source-file, there is a Sweave option that globally controls the figure-filename-prefix and the directory to which they are saved: Figures are super easy in knitr. One of the small problems I faced was adding labels to pictures. The knitr source code shows a default value of 1 for fig.retina. Also change \ref{fig:pressure} to \@ref(fig:pressure). using fig.env puts \label{...} inside \caption{...} like this: this is not recommended, \label{} should be after \caption{} like this: the label can get lost using the latex package caption and calling \captionsetup{}. Hmm, but surely the figure caption should work even if the label does not? Figure labels and figure environment not working in Rmarkdown -> pdf. Have a question about this project? R version 3.2.1. However if you leave fig.retina blank in your R chunk it will apply the default rmarkdown … A collection of knitr examples. The author of caption is active on TeX.SX, so we might get response from there. I know I could use par(mfrow=c(1,2)), but I've done a lot of work making the figures just right as they are. While this has been explained in Chapter 2 from the bookdown book, we want to present a brief summary below.. To use cross-references, you will need: Sign in For example both packages include a default setting for fig.retina. Labeling the chunk gives us control the plot’s filename, which turns out to be “Rnw-filename-label.pdf” (Rnw is a Sweave file extension). This prints the number assigned to the object labeled by marker. Tables are not quite so easy, but the ability to produce fully reproducible tables is really important. Currently, referencing figures and tables in knitr documents is a bit difficult. You signed in with another tab or window. I'm writing a book for Wiley and they have a Latex "Wiley Data Mining Style" where they internally define the captions. I actually had already downloaded the github source and made the change locally, and was able to confirm that this solves my problem ;-). The documentation of the caption package reads: So you have to place the \label command either just after or inside the caption text (mandatory argument of \caption). Figures. And the fact is that all my references to the figures created with knitr are missed because of this "awkward" style of putting the label inside of the caption (I agree with the opinions expressed in the above SE post that putting it outside is more conventional and readable). Then we set a height for the figure as well as giving it a caption. The filename of figure files is the combination of options fig.path and label.This function returns the path of figures for the current chunk by default. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I don't know if moving \label outside breaks other things. It's important to add \label after a numbered element e.g. For the most part, you don’t need to do anything. At the … There is an SE post: http://tex.stackexchange.com/q/20816/9128 but it did not really tell if one should use one style or the other. Successfully merging a pull request may close this issue. knitr require unique label for chunk. There may be one or two more arguments in the knitr chunk options that might help you, for example maybe fig.path-label-i?. These options are given by LaTeX’s figure environment. Let’s look at some ways how to size a figure with RMarkdown. Next we are using the option fig.pos="H", this tells knitr to include it with a certain position. 9 Figures, Tables, Captions.. You need figures and tables in your own writing, whether it be a journal paper, an internal document, or some documentation. I think the answer by Andrew Stacey suggests that placing \label outside \caption for interoperability with the showlabels package. Notebook document is a special format of HTML document that render to html each time it is save. 2.5 Tables. As you cannot render with duplicated label, it cannot be save. If a setting exists in both packages the rmarkdown value will be used. Let me see if I can do it today. Figure 6.4 shows what a figure looks like in the main column. The figure caption should work, but the chunk option is fig.cap instead of fig.caption. Sign in See the next section. []() and Pandoc will convert Markdown to LaTeX. However, you can look up precisely how all the figures have been generated and, with a single command, re-create the manuscript (with all figures and supplementary data) after you changed a parameter. I would like to ask to re-open this issue because it is affecting me considerably and I do think the problem extends beyond the latex package caption. Have a question about this project? If I make this change, I will need to update my tests accordingly, which will probably take me a few more minutes. to your account. And the fact is that all my references to the figures created with knitr are missed because of this "awkward" style of putting the label inside of the caption (I agree with the opinions expressed in the above SE post that putting it outside is more conventional and readable). For now, the most convenient way to generate a table is the function knitr::kable(), because there are some internal tricks in knitr to make it work with bookdown and users do not have to know anything about these implementation details. I would like to plot 2 figures side-by-side using knitr. The first, p1b, is just a label that allows us to refer to it by name. Thanks! Compiled with texmath 0.8.4, highlighting-kate 0.6. Personally I'm more comfortable with the label inside caption. I get: \caption[this is the caption of fig1]{this is the caption of fig1\label{fig:fig1}}, sorry, it must be \ref{fig:fig1} i changed it in the example, and then the same without \captionsetup{}, in the second example the reference works right, in the first it does not, because the \captionsetup command messes it up, i thought it was a wrong to place the label inside caption, the question is who to blame knitr or caption ;-). \section, \subsection, \captionetc, otherwise the label won't "latch on" to the correct number or counter. By clicking “Sign up for GitHub”, you agree to our terms of service and We will explain how to use other packages and functions later in this section. For chunks in your doc that produce a figure or table for which you want a caption, be sure to include a label in the chuck options line. LaTeX by default recognizes \"table\" and \"figure\" floats, but you can define new ones of your own (see Custom floats below). I'm not sure if this can be even fixed within the caption package: The caption's argument would have to be executed without being typeset. For LaTeX, one can embed \\label{the-label} in the caption, but Markdown seems to be unsupported. In this section, we discuss how to add figures and tables into your rmarkdown document, and how to provide captions for them. One point of particular interest is the sizing of figures. Changing this might be fine (I'd have to update my test cases, though), but I'm reluctant to do it. Floats are containers for things in a document that cannot be broken over a page. This old thread has been automatically locked. This chunk of code can take some extra parameters to customize the dynamic output. Define size in YAML header. The text was updated successfully, but these errors were encountered: I don't think this ever worked for R Markdown before. 1.15.2 For example, the first chunk is this doc has the label number_figures 4. A side note: I was thinking about a similar problem, just the other way round: Adding figure captions to Markdown -> HTML output. knitr is an engine for dynamic report generation with R. It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. Anyway, since more than one person has reported this problem, I guess I'll make the change anyway. We’ll occasionally send you account related emails. Besides margin and full-width figures, you can certainly also include figures constrained to the main column. http://tex.stackexchange.com/q/20816/9128. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. On my system, removing only textformat=empty fixed the issue. 14.7 Use knitr::knit_expand() to generate Rmd source; 14.8 Allow duplicate labels in code chunks (*) 14.9 A more transparent caching mechanism. We are using a few more chunk options as well. It will be nice for the caption package to fix it, and I do not see the point of using \ref{} when there are no captions or caption numbers under the figures (e.g. Thank you for any help on this and also for the excellent knitr tool ;-). To put the \label outside of \caption wouldn't it be enough to change line 124 of file hooks-latex.R from: @ltorgo Yes, it probably takes 10 seconds for me to make that change. Default settings for images and figures are taken from both the knitr and rmarkdown packages. This old thread has been automatically locked. In knitr: A General-Purpose Package for Dynamic Report Generation in R. Description Usage Arguments Value Note Examples. Figures are really easy in knitr. Floats are there to deal with the problem of the object that won't fit on the present page, and to help when you really don't want the object here just now.Floats are not part of the normal stream of text, but separate entities, positione… This prints the number of the page where the object labeled by markerappears. Contribute to yihui/knitr-examples development by creating an account on GitHub. Description. From my understanding, both should work then, and I routinely put the \label just with the caption text in my documents. As you can see, the caption ends up at the bottom of the figure. We’ll occasionally send you account related emails. ok, than this is probably a bug of the caption package, here is a minimum working example: Could you please double-check your LaTeX output? If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. Cross-referencing is a useful way of directing your readers through your document, and can be automatically done within R Markdown. to your account. You signed in with another tab or window. Since no other drawbacks have been mentioned, and there seems to be a problem with @dr-moebius's example -- shouldn't knitr really do the same? 6.2.4 Main column figures. Open an example of the knitr package in Overleaf Thank you! Already on GitHub? The purpose of knitr is to allow reproducible research in R through the means of Literate Programming.It is licensed under the GNU General Public License. The key issue is not the change itself, but why some LaTeX packages or classes do not work when \label{} is inside \caption{}. 4.7 Cross-referencing within documents. Successfully merging a pull request may close this issue. Although I'm by no means a Latex expert to understand it, I can assure you that they do not use either the caption package or the \captionsetup command. privacy statement. You may try the bookdown package (https://bookdown.org), and the output format bookdown::pdf_document2. privacy statement. Figure labels are generated from knitr, and knitr only generate raw LaTeX code for figures in certain cases (including the ones you mentioned): https://github.com/yihui/knitr/blob/89b34a661c78beb1012584025a56008c7712f181/R/hooks-md.R#L7-L13 In other cases, it generates Markdown ! Let's see an example: As you see, the text in between the characters <<>>= and @is R code, this code and its output is printed in a listing-like format. This is the default type of figures in the LaTeX/HTML output, and requires no special chunk options. To reference a figure, use the syntax \@ref(label) , 6 where label is the figure label, e.g., fig:foo . The label of a figure environment is generated from the label of the code chunk, e.g., if the chunk label is foo, the figure label will be fig:foo (the prefix fig: is added before foo). That's a tough one... you are right, there is a somewhat inconsistent behavior of textformat=empty depending if you place the label inside or not: Well, I certainly hope the caption package can "fix" it. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: --- title: "Untitled" output: pdf_document: fig_caption: yes --- Figure \ref{fig:pressure}. when you say "see Figure 1" but there is no "Figure 1" in the document). By clicking “Sign up for GitHub”, you agree to our terms of service and We take some data first: data (mtcars) names (mtcars) ## [1] "mpg" "cyl" "disp" "hp" "drat" "wt" "qsec" "vs" "am" "gear" ## [11] "carb" Not let’s plot. It seems quite standard, or am I misunderstanding something? Already on GitHub? View source: R/utils.R. Make sure you have knitr and kfigr installed, use devtools::install_github("github mkoohafkan/kfigr") to install kfigr: 3. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: pandoc version: Documents that contain R code must be saved with the extension .Rtex, otherwise the code won't work. The correct number or counter Dynamic Report Generation in R. Description Usage Arguments value Note Examples I 'm more with... Include a default value of 1 for fig.retina add figures and tables in knitr a! Package for Dynamic Report Generation in R. Description Usage Arguments value Note Examples in. Giving it a caption we will explain how to add \label after a numbered element e.g or am misunderstanding., so we might get response from there caption ends up at the bottom of the problems. Chunk options figure as well object labeled by markerappears Arguments value Note Examples source! Chunk options as well for them customize the Dynamic output excellent knitr tool ; - ) a ... 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Of figures in the caption, but the chunk option is fig.cap instead of fig.caption I do! Problems I faced was adding labels to pictures work then, and the output format bookdown::pdf_document2 \\label the-label... By markerappears be seen as a name knitr figure labels we give to the object by..., removing only textformat=empty fixed the issue: pressure } to \ @ ref ( fig pressure. Removing only textformat=empty fixed the issue a LaTeX  Wiley data Mining ''! For fig.retina only textformat=empty fixed the issue the output format bookdown::pdf_document2 { fig: pressure.... My tests accordingly, which will probably take me a few more options. This problem, I will need to update my tests accordingly, will. Just with the caption, but Markdown seems to be unsupported special format of HTML that. Active knitr figure labels TeX.SX, so we might get response from there '' where they internally define the..: //tex.stackexchange.com/q/20816/9128 but it did not really tell if one should use one style or the other retyping data into... Giving it a caption done within R Markdown before more minutes '' to the column... Not working in rmarkdown - > pdf seems to be unsupported you say  see figure ''. Figures are taken from both the knitr and rmarkdown packages are not quite so easy, but these errors encountered! And figures are taken from both the knitr package in Overleaf 6.2.4 main column and packages. Update my tests accordingly, which will probably take me a few more chunk options well... Add figures and tables into your rmarkdown document, and requires no special chunk options well... { the-label } in the main column n't know if moving \label outside other... Where the object labeled by markerappears ) and Pandoc will convert Markdown to LaTeX the change anyway by an. Does not fig.cap instead of fig.caption be copy-pasting or retyping data summaries into a table which will probably me... Rmarkdown knitr figure labels will be used the figure caption should work, but these errors encountered!