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Transcript

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Your Turn

  1. Change the default chunk options in the setup code chunk so that echo = FALSE. Knit your report and notice what is different.

  2. Change the chunk options in the cars code chunk so that include = FALSE. Knit your report and notice what is different.

  3. 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

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.

David Keyes

David Keyes

March 21, 2021

Is your result more polished or is the one in the video more polished? Do you mind posting a screenshot of what yours looks like? You can use imgur or something similar to do so.

Atlang Mompe

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

David Keyes

David Keyes

March 23, 2021

Thanks, Atty! I updated the links so they work now.

Jody Oconnor

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.

David Keyes

David Keyes

March 24, 2021

What format did you knit to?

Odile DOREUS

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)

David Keyes

David Keyes

August 9, 2021

What operating system are you working with? And are you working on a computer with a network drive by chance?

Odile DOREUS

Odile DOREUS

August 9, 2021

Hi, my operating system is Windows 10 Pro and I am not working with a network drive.

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

https://imgur.com/369hjiU

This is likely just a difference in how things print on a Mac (which I use) versus Windows (which I'm guessing you use). Since this isn't something you'd likely print in a report for a client (I use skim() to just get a sense of my data before doing analysis), let's not worry too much about it!

Payal Mulchandani

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

Can you post your full RMarkdown code as a GitHub gist so I can see what you have? I can't tell if something weird is happening with the text formatting when you post a comment here on the website.

Lindsay Quarles

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.

David Keyes

David Keyes

October 18, 2021

The output will remain until you clear it (though because you added include = FALSE it won't reappear in the future). To remove the output, click Edit > Clear All Output. See https://show.rfor.us/JKdfOx

Sara Cifuentes

Sara Cifuentes

March 24, 2022

Is there a video in this section?

Sara Cifuentes

Sara Cifuentes

March 24, 2022

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

Charlie Hadley

Charlie Hadley

March 24, 2022

I'm glad it's working now!

Sara Cifuentes

Sara Cifuentes

March 24, 2022

Thank you Charlie!

Zaynaib Giwa

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?

Charlie Hadley

Charlie Hadley

March 29, 2022

Hello Zaynaib! This is a good question! There are two reasons that naming code chunks can be useful:

Make sure your code chunks only contain letters, numbers or dashes. Any other characters can break internal cross referencing.

This article gives some more information about the use of code chunk names.

Cheers,

Charlie

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!

Charlie Hadley

Charlie Hadley

September 27, 2022

Great question, Josh!

When we first load up RStudio it loads "base R" which is a collection of many packages, including the {datasets} package which contains the cars and pressure data.

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

Charlie Hadley

Charlie Hadley

September 28, 2022

Hi Matt! When we knit an .Rmd document all of the code chunks get run (from top to bottom). Could you help me understand your question a little bit more? Thanks - Charlie

Now I understand. I didn't realize when you knit it runs the whole code. Can you put a timestamp in the header or footer?

Ellen Wilson

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.

David Keyes

David Keyes

October 6, 2022

I'm guessing this is just from a new version of the skimr package, but it's hard to know for sure. If you post a screenshot to imgur.com and share a link here I can take a look.

Julieth Silao

Julieth Silao

October 31, 2022

https://juliethsilao.imgur.com/all/?third_party=1

link to imgur.com to see my output

David Keyes

David Keyes

November 1, 2022

Unfortunately, that link doesn't work.

Caitlin Tracey-Miller

Caitlin Tracey-Miller

October 12, 2022

I kept getting errors until I put my library request on the same line as the R code line. Is that strange?

Julieth Silao

Julieth Silao

October 31, 2022

Hello David. when i install new chuck and run skimr, i didnt get the summary report as in solution you provide

Dimeji Olawuyi

Dimeji Olawuyi

December 23, 2022

The warning message about the version disappeared when I uninstalled the version I was using and installed a recent version.

Glad you got it figured out! The error looks an extra close parentheses to me for what it's worth.