Code Chunks

This lesson is called Code Chunks, part of the R in 3 Months (Fall 2022) course. This lesson is called Code Chunks, part of the R in 3 Months (Fall 2022) course.

Transcript

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Your Turn

Solution

wp:coblocks/gist {"url":"
          ---
          title: "My Super Fancy Report"
          author: "David Keyes"
          output: html_document
          ---

          ```{r setup, include=FALSE}
          knitr::opts_chunk$set(echo = FALSE)
          ```
          # Introduction
          This report is the best report ever. Pretty much the **bees' knees**. Can't say that I've *ever* seen a better report.
          ## Reasons Why This Report is the Best
     
          - It's amazing
          - It's quite amazing
          - It's seriously amazing

          ## R Markdown
          This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
          When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
          ```{r cars, include = FALSE}
          summary(cars)
          ```
          ## Including Plots
          You can also embed plots, for example:
          ```{r pressure, echo=FALSE}
          plot(pressure)
          ```
          Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
          ```{r warning = FALSE, message = FALSE}
			
          library(skimr)
          skim(cars)
          ```

        ","file":"","meta":false,"caption":""} /--></div>
</details>
</div>
<p>

Change the default chunk options in the setup code chunk so that echo = FALSE. Knit your report and notice what is different.
Change the chunk options in the cars code chunk so that include = FALSE. Knit your report and notice what is different.
Add a new code chunk (don’t worry about naming it). In it, load the package skimr(hint: use the library function). Then, use the skim function that you learned about in the Getting Started course (see the Examine our Data lesson in particular) to skim the cars data frame. Knit your report to see the output.

Learn More

Many people print out the RMarkdown cheatsheet and keep it as a reference. It’s got a lot of information on YAML, Markdown text, and code chunks.

Interested in why you might considering naming code chunks? Maëlle Salmon wrote an article on this topic. Note that for most beginners, naming code chunks isn’t necessary. It’s only when you’re doing more complicated things with RMarkdown that it makes a difference.

Have any questions? Put them below and we will help you out!

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Lucilla Piccari • March 21, 2021

When knitting the added code chunk (the one where we used the skim() function) I got a different-looking result as the one demonstrated on the solution video, more "polished" looking, and I'm not sure why.

Atlang Mompe • March 21, 2021

Hi David,

The links for both these sections don't work: On another note, if you have issues getting the histograms to display properly and you’re using Windows, there is a known issue. Please see the skimr documentation for potential solutions.

Thanks, Atty

Jody Oconnor • March 24, 2021

My html output (after checking that my code is exactly the same as the example solution), also looks more 'polished'... there are no hash tags and the font is the report font, not the code font, and a few other differences. The warnings are not shown in the report, even before adding 'warning = FALSE, message = FALSE' Not sure what I would need to do to make the warnings/messages appear in the report.

Odile DOREUS • August 8, 2021

Hello, I did the steps but having error messages. So I went ahead and install tydiverse still not work.

My codes install.packages("tidyverse")

library(skimr)
skim(cars)

ERROR messages received for tidiverse and library(skimr) Warning in install.packages : 'lib = "/usr/local/lib/R/site-library"' is not writable Would you like to use a personal library instead? (yes/No/cancel) yes trying URL 'https://mran.microsoft.com/snapshot/2020-03-19/src/contrib/tidyverse_1.3.0.tar.gz' Content type 'application/octet-stream' length 712837 bytes (696 KB) ================================================== downloaded 696 KB

Error: ERROR: no permission to install to directory ‘/usr/local/lib/R/site-library’ Warning in install.packages : installation of package ‘tidyverse’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpGXw6hh/downloaded_packages’ > install.packages("skimr") Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning in install.packages : 'lib = "/usr/local/lib/R/site-library"' is not writable Would you like to use a personal library instead? (yes/No/cancel)

Lina Khan • September 19, 2021

Hi David, similar to notes below, the report looks more polished, no ## and stuff.

https://imgur.com/369hjiU

Payal Mulchandani • September 20, 2021

Getting this error when I try to due Include=False: > ```{r cars, include=FALSE} Error: attempt to use zero-length variable name

Lindsay Quarles • October 18, 2021

Everything worked for me except the include = FALSE. The output never went away. I did not get any error message, the output just remained.

Sara Cifuentes • March 24, 2022

Is there a video in this section?

Sara Cifuentes • March 24, 2022

Yesterday something happened with videos, but now it is working!

Zaynaib Giwa • March 29, 2022

Hello everyone! I know that we don't go super in-depth with R-Markdown in this class but I was wondering what would be a scenario for giving a code chunk a name? Is it for reusability purposes if you need the same graph multiple times in a report?

Josh Gutwill • September 26, 2022

Where do the data for cars and for pressure come from? I don't see them in the getting-started-master folder, nor in the faketucky dataset. summary(cars) is clearly calling that data, but I don't see how. :-) Thanks!

Matt Kropp • September 28, 2022

Is there a way to knit code automatically every time it is run?

Ellen Wilson • October 5, 2022

Similar to what others have commented, I get a more polished looking result from the cars skim. No warnings or messages, no hashtags, and it has a data summary at the top (telling the number of columns and rows). I'm using a Mac. It doesn't seem like there was ever a definitive answer to what others said about this, and maybe it doesn't matter, but it is a bit puzzling.