Replacing the "Print" Function in Knitr Chunk Evaluation

Replacing the print function in knitr chunk evaluation

You need to selectively overrule the print method for the object class you want to print with pander. Do methods(pander) to figure out what is available. Some methods are not exported, so you will have to use ::: to access them. Here is a simple example.

TEST
====

```{r cache = F, comment = NA}
print.lm <- pander:::pander.lm
lm(mpg ~ wt, data = mtcars)
```

Output

TEST
====

```r
print.lm <- pander:::pander.lm
lm(mpg ~ wt, data = mtcars)
```

```

--------------------------------------------------------------
              Estimate   Std. Error   t value   Pr(>|t|) 
----------------- ---------- ------------ --------- ----------
  **(Intercept)**   37.29       1.878       19.86   8.242e-19 

           **wt**   -5.344      0.5591     -9.559   1.294e-10 
--------------------------------------------------------------

Table: Fitting linear model: mpg ~ wt
```

Display Block of R Code in Knitr With Evaluation Turned Off

Is this what you want to do, or have I misunderstood? The eval = FALSE is in one code chunk and the second chunk still plots.

---
title: "A Test Knit"
output: html_document
---

## Show code but don't run

```{r, eval = FALSE}
summary(cars)
```

## Run and render plot

```{r}
plot(pressure)
```

How to show code but hide output in RMarkdown?

As @ J_F answered in the comments, using {r echo = T, results = 'hide'}.

I wanted to expand on their answer - there are great resources you can access to determine all possible options for your chunk and output display - I keep a printed copy at my desk!

You can find them either on the RStudio Website under Cheatsheets (look for the R Markdown cheatsheet and R Markdown Reference Guide) or, in RStudio, navigate to the "Help" tab, choose "Cheatsheets", and look for the same documents there.

Finally to set default chunk options, you can run (in your first chunk) something like the following code if you want most chunks to have the same behavior:

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T,
                      results = "hide")
```

Later, you can modify the behavior of individual chunks like this, which will replace the default value for just the results option.

```{r analysis, results="markup"}
# code here
```

knitr::kable does not pretty print after running an R chunk

When you run that chunk, the tools:rstudio environment on the search list is changed to add a function called print.knitr_kable which is different from the internal one in the knitr package.

Here's what I see before:

> ls("tools:rstudio")
[1] "debugSource"              "knit_with_parameters"    
[3] "registerShinyDebugHook"   "RStudio.Version"         
[5] "rstudioDiagnosticsReport" "RStudioGD"               
[7] "source.with.encoding"  

and here's what I see after:

> ls("tools:rstudio")
[1] "debugSource"                 "dplyr_tibble_print_original"
[3] "knit_with_parameters"        "print.knitr_kable"          
[5] "registerShinyDebugHook"      "RStudio.Version"            
[7] "rstudioDiagnosticsReport"    "RStudioGD"                  
[9] "source.with.encoding"   

For whatever reason, the tools:rstudio function is executed instead of the original one. I can get the original behaviour back by running detach("tools:rstudio"), but that messes up Rstudio in several ways, so I don't recommend it. A less extreme way is to say

e <- as.environment("tools:rstudio")
e$print.knitr_kable <- knitr:::print.knitr_kable

but that doesn't last: RStudio apparently fixes it whenever you run a chunk in the notebook. You could also do an explicit call every time you want to print, e.g.

knitr:::print.knitr_kable(knitr::kable(head(iris, 3)))

Probably the best solution is for knitr to change so it does what RStudio wants when run in an RStudio notebook and the pretty printing otherwise, or for RStudio to change to run the knitr function when it's not in a notebook, but I imagine this isn't a huge priority: if you're running a notebook, why would you care what you see in the console?

How can I remove the prefix (index indicator) [1] in knitr output?

Nothing is impossible. Take a look at what can be done with knitr hooks.

Have fun!

_{^{Rmarkdown script gist}}

# A Prefix nulling hook.

# Make sure to keep the default for normal processing.
default_output_hook <- knitr::knit_hooks$get("output")

# Output hooks handle normal R console output.
knitr::knit_hooks$set( output = function(x, options) {

  comment <- knitr::opts_current$get("comment")
  if( is.na(comment) ) comment <- ""
  can_null <- grepl( paste0( comment, "\\s*\\[\\d?\\]" ),
                     x, perl = TRUE)
  do_null <- isTRUE( knitr::opts_current$get("null_prefix") )
  if( can_null && do_null ) {
    # By default R print output aligns at the right brace.
    align_index <- regexpr( "\\]", x )[1] - 1
    # Two cases: start or newline
    re <- paste0( "^.{", align_index, "}\\]")
    rep <- comment
    x <- gsub( re, rep,  x )
    re <- paste0( "\\\n.{", align_index, "}\\]")
    rep <- paste0( "\n", comment )
    x <- gsub( re, rep,  x )
  }

  default_output_hook( x, options )

})

knitr::opts_template$set("kill_prefix"=list(comment=NA, null_prefix=TRUE))

Normal:

```{r}
print( 1:50 )
```

##  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
## [24] 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
## [47] 47 48 49 50

Null prefix

```{r, null_prefix=TRUE}
print( 1:50 )
```

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
## 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
## 47 48 49 50

Set as default (and remove comment string):

```{r}
knitr::opts_chunk$set(opts.label="kill_prefix")
```

```{r}
print( 1:50 )
```

  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
 47 48 49 50

Ensure we aren't killing strings with [:digit:] patterns.

```{r}
print( paste0( paste0("[", 1:50), "]" ),quote = FALSE)
```

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