I am using knitr for a report wherein I have a lot of inline output text, mostly numeric values, using \Sexpr{}. I want to highlight All these inline outputs in my generated pdf.
Example code:
\documentclass[12pt]{article}
\begin{document}
<<echo=FALSE, include=FALSE>>=
N <- 100 # Total
N_f <- 60 # Women
#
There were \Sexpr{N} people in the company, \Sexpr{N_f} women and \Sexpr{N - N_f} men.
\end{document}
Hence, in the output all the number should be highlighted, i.e. with a shaded background (similar to using with \hl{} with the \usepackage{soul}).
It seems to me that the solution would use one of the inline output hooks. Another possibility might be to write a LaTeX function which search all the \Sexpr{...} expressions in the entire document and highlights them in the generated pdf. I am still learning and can not figure out how to implement these.
Thanks for any help or hints.
Note: The knitr page by yihui talks about manipulation of the numeric value (scientific notation, digits after decimal points) which I have got covered.
The output hook inline can be used to style output from \Sexpr{}. This is as simple as
knit_hooks$set(inline = function(x) { sprintf("\\textbf{%s}", x)})
Just define an arbitrary function that takes an argument x and returns the string to be printed. In this example I used \textbf to make the output bold, but this can be extended to any LaTeX commands.
In this answer, Yihui suggests an improvement that still takes the default inline hook into account. This ensures rounding as usually performed by the default hook:
hook_inline <- knit_hooks$get('inline')
knit_hooks$set(inline = function(x) { sprintf("\\textbf{%s}", hook_inline(x))})
Related
I have an RMarkdown document where I use data.tree and DiagrammeR to generate models. I then display these using a set-up similar to the one used in How to include DiagrammeR/mermaid flowchart in a Rmarkdown file
For example:
```{r fig.cap="Structureel model bij enkelvoudige regressie.", fig.with=4, fig.height=1}
drawStructuralModel <- function(covariates, criterion) {
### Create tree
res <- Node$new(criterion);
for (covariate in covariates) {
res$AddChild(covariate);
}
### Set display settings
SetEdgeStyle(res, dir='back');
res <- ToDiagrammeRGraph(res, direction = "descend");
res <- add_global_graph_attrs(res, "layout", "dot", "graph");
res <- add_global_graph_attrs(res, "rankdir", "RL", "graph");
### Draw and return tree
render_graph(res);
}
drawStructuralModel("X", "Y");
```
So far so good. The caption text is added, which is what you'd expect.
Except :-)
Above, in the 'setup' knitr chunk, I used setFigCapNumbering from userfriendlyscience (see https://github.com/Matherion/userfriendlyscience/blob/master/R/setFigCapNumbering.R). This function uses knit_hooks$set to set a hook for plots, so that the captions are automatically numbered.
But this numbering isn't applied to the DiagrammeR output.
I guess that makes sense, since it's not actually a plot, rather an HTML widget or some SVG or so. I would still like it to be numbered as a figure, though.
But how do I find out which hook knitr invokes when DiagrammeR output is generated?
I could always resort to using the more generic 'automatic caption' function setCaptionNumbering (https://github.com/Matherion/userfriendlyscience/blob/master/R/setCaptionNumbering.R), and tell it to use the same counter option as the figure caption thingy uses. That would sidestep the issue, but I'd prefer to modify the appropriate knitr hook.
And since this problem (figuring out which hook knitr uses for output produced by a given function) probably occurs more often, I thought it would be worth opening an SA question.
Does anybody know how you can find this out?
knitr calls knit_print on the output produced by a given chunk. This then calls the appropriate method based on the class of the output. You can find out what methods are available by running methods("knit_print"), then see if any of those match the class of the output from DiagrammeR.
Looking at your example, I'm guessing the class of your output is "DiagrammeR" "htmlwidget", so knitr is calling knit_print.htmlwidget.
Digging into that source code, it calls htmltools::knit_print.html, which wraps the tags and then outputs asis. So to answer your question, it uses the default hooks for asis output in whatever output format you're using.
I'd like to print a few sentences in a knitr LaTeX doc (.Rnw), but only if some data exists. Those sentences are mostly text, but with some R.
Example:
A chi-squared test of your observed sizes has a p-value of
\Sexpr{format(calculated_chisq$p.value,digits=3,scientific=F)}.
A p-value below 0.05 means you should be concerned that your
groups are broken. The lower the p-value, the more worried you
should be.
I tried a chunk with results='asis', but I think the chunk is interpreted as R.
I tried print() and paste() with R. It's ugly, but it works. However, it puts extra text in that seems to correspond to the R prompt.
Is there a nice way to do this?
This is related, but different. This is the same, but unanswered.
This question is closely related to that question, but not duplicate I think: The accepted answer there translates into an ugly \Sexp monster with a condition inside. The code will be neither nice to read nor to write.
My own answer there is also not applicable because 1) the asis engine does not allow for dynamic elements in the text and 2) because output from the asis gets a gray background color in RNW documents.
I suggest the following solution:
\documentclass{article}
\begin{document}
<<>>=
x <- rnorm(1)
#
The value of $x$ is \Sexpr{x}.
<<echo=FALSE, results = "asis">>=
pattern <- "This will only be displayed if $x$ is positive. The value of $x$ is %.2f."
if (x > 0) cat(sprintf(pattern, x))
#
\end{document}
The conditional output is easy to read and write (pattern) and the dynamic elements are inserted via sprintf.
I have a long .Rnw document which consists mostly of text (typeset in LaTeX) with a few chunks here and there. I have also written a chunk which outputs a specific figure. The figure contains a plot, the values for the plot are currently read from a .csv file and some parameters like colors defined manually within the chunk.
Now I want to have the same figure in a different place in the document, but with different values for the plot and a few other parameters different. Ideally, I would like to include the chunk as a child twice, and pass parameters to it somehow, including the name of the .csv to be used for the plot values. I would hate to copy paste the chunk code with hardcoded parameters, as it is complex enough that potential changes will be difficult to synchronize.
How can I do such "parameterized reuse" of chunks?
update
As requested, a small example
This is saved as include-chunk-reuse.Rnw
<<toReuse, echo=FALSE, result='asis'>>=
l <- 25
#
\newlength{\mylength}
\setlength{\mylength}{\Sexpr{l}pt}
%Omitted: a lot of complicated LaTeX commands
\rule{\mylength}{1pt}
This is the document which is supposed to reuse the chunk. It doesn't even compile, as it complains that the same label is used twice: Error in parse_block(g[-1], g[1], params.src) : duplicate label 'toReuse'
\documentclass{article}
\begin{document}
This is some text. And now comes a 25 pt wide line.
<<first-figure, child='include-chunk-reuse.Rnw'>>=
#
This is some text. The next line is also 25 pt wide. But I would like to call the chunk in a way which makes it 50 pt wide instead.
<<second-figure, child='include-chunk-reuse.Rnw'>>=
#
\end{document}
For the knitr part to work simply leave out the chunk-name in the child document, then you don't have the duplicated label and the knitr part works.
Passing Parameters does not really work as far as I know, but you can just set a global variable before including the child. (For example \Sexpr{l <- 200}
You are still redefining \mylength which is why LaTeX will throw an error, so move the first definition of \mylength from the child to the main document.
The example below demonstrates two ways to reuse and parametrize a chunk.
Reusing Chunks
The mechanism is explained here. Basically, the simplest way to reuse a chunk is to add another empty chunk with the same label. Alternatively, the chunk option ref.label lets a chunk inherit another chunks code.
Both approaches of reusing chunks are largely equivalent – with one exception: figures generated in chunks are saved as chunklabel-i.pdf, where i is the figure index counted by chunk. Therefore, if a chunk is reused by repeating its label, figure i from the second use will overwrite figure i from the first use. This is the reason why I use ref.label (and thus distinct chunk labels) in the example below (otherwise, the points on both plots would be green).
In the example below, I used eval = FALSE in order to prevent evaluation of the masterchunk where it is defined. An alternative would be to externalize the chunk and read it by read_chunk().
Parameterizing Chunks
The two most straightforward options to "pass" parameters to a chunk are
chunk options and
global variables
Also when reusing chunks, each use can set different chunk options. The example below exploits this to set different captions.
As all chunks run in the same environment, setting a variable in an early chunk affects subsequent chunks accessing this variable. In the example below, mycolor is modified this way.
\documentclass{article}
\begin{document}
<<masterchunk, eval = FALSE>>=
plot(1:10, col = mycolor)
#
<<config1>>=
mycolor <- "red"
#
<<use1, ref.label = "masterchunk", fig.cap = "Red dots">>=
#
<<config2>>=
mycolor <- "green"
#
<<use2, ref.label = "masterchunk", fig.cap = "Green dots">>=
#
\end{document}
I am looking for a way to put inline latex code into a R code chunk in Knitr.
Here is my example code from the knitr example site :
\documentclass{article}
\begin{document}
Example text outside R code here; we know the value of pi is \Sexpr{pi}.
<<my-label, echo=FALSE, eval=TRUE>>=
set.seed(1213) # for reproducibility
x = cumsum(rnorm(100))
m <- mean(x) # mean of x
print(m)
cat(m)
plot(x, type = 'l') # Brownian motion
#
\textit{Mean is :} \textbf{\Sexpr{m}}
\end{document}
For something simple like this is I could use result='asis' but for a more complicated piece of code, where you want to periodically write the result out to the document, (especially you have complex ggplot graphs), that solution does not work very well.
In the given example, I have 3 queries :
How would I use inline latex code for the output from line 8, in case I wanted to color, bold etc. that text.
Can one eliminate the grey box that appears when we use the cat or print command.
Can the numbering which appears with the print command, which is eliminated with the cat command be eliminated for the print command as well, since print has many variants in many packages for data frames data tables etc. and might be more commonly used to print a portion of data.
In summary, I am mainly looking for the inverse of line 12 in the code.
I have also unsuccessfully tried knit_print with printr, and asis_output, in lieu of print. Although I may have been incorrectly using them.
Thanks!
In the knitr package I like the kable function. It gives a nice layout of tables and data frame like objects even as it is called from within an R code chunk. Now I want to do the same thing with a character value. Is there a function that gives a kable-like output ("kprint") that can be formated?
knitr::kable() # exists for tables
knitr::kprint() # does a function like this exists for character values?
This is what I get now:
print("character value") # within the R Chunk
Output in generated report:
## [1] "character value"
And this is what I want, just:
character value
EDIT cat("character value") is not the solution I am looking for because I don't want an R output anymore, but just a plain text.
There are two things to do to get a "raw" character string (without any formatting or additional output like [1]) from R to TEX:
Use the chunk option results = "asis" to instruct knitr not to modify the output.
Use cat instead of print because print adds the lenght of the vector and quotes to the output.
In this context, inline output using \Sexpr{} might be useful because values in \Sexpr{} are by default printed "as they are": \Sexpr{myoutput}.
As there was the question of how to format the output in the comments, here some options:
Add LaTeX to the text you pass to cat: cat("\\emph{foo}"). Don't forget to escape \ by an additional \.
Do the same thing as above, but use a function to do the "dirty work":
makeItNiceR <- function(x) {
return(paste("\\fbox{\\texttt{", x, "}}"))
}
cat(makeItNiceR("foo bar is nice"))
(Note that we could use cat inside makeItNiceR to save some typing, but this makes the function less flexible and we cannot use it in combination with \Sexpr{} anymore.)
Manually add LaTeX formatting commands around \Sexpr{}:
Add formatting to \emph{\Sexpr{myoutput}} directly in LaTeX.
Combine makeItNiceR and \Sexpr{} to get nicely formatted output from \Sexpr{}:
\Sexpr{makeItNiceR(paste(myoutput, "is nice"))}
The following minimal examples demonstrates the usage of all code snippets from above:
\documentclass{article}
\begin{document}
<<results = "asis">>=
makeItNiceR <- function(x) {
return(paste("\\fbox{\\texttt{", x, "}}"))
}
myoutput <- "slim"
cat("foo")
cat("\\emph{foo}")
cat(makeItNiceR("foo bar is nice"))
#
\paragraph{Outside of chunk:} ~\\
\Sexpr{myoutput} \\
Add formatting to \emph{\Sexpr{myoutput}} directly in LaTeX. \\
\Sexpr{makeItNiceR(paste(myoutput, "is nice"))}
\end{document}