Two Birds With One Stone: Examples of RMarkdown Code and Data Importing
David L. Passmore
10 September 2018
How to use this document – and the Rmarkdown code that created it
In the Piazza posting, ALL IN ONE PLACE, is a .zip file, WFED540-10Sept18.zip, which contains a .Rproj directory with all of the code necessary for you to consider this example in detail. You will need to “unzip” WFED540-10Sept18.zip and double-click on the .Rpoj file, WFED540-10Sept18.Rproj, to begin.
If you are reading this report on the web at RPubs , also read the twoBirds.Rmd file on the WFED540-10Sept18 directory along with this Rpubs report to understand how the report was created through RMarkdown.
What is shown here
Study the RMarkdown code that I created to produce this web page, while making reference to the RMarkdown Cheat Sheet. The RMarkdown code is in a file, TwoBirds.Rmd in the pinned Piazza posting, “ALL IN ONE PLACE - Videos, files, slides, etc. from class meetings.”
Just to show how to include images in an RMarkdown report, here is a screen capture of the R Markdown Cheat Sheet:
This image is shown in and read from the “Files” pane in RStudio, but it just as well could have been on the web. In that case, the full URL would have been used instead of the file name.
Using R code chunks for calculation within RMarkdown
Display some simple arithmetic
Here is some simple arithmetic, showing the R code chunk that created the results of calculations:
2 + 3## [1] 54/2## [1] 25 - 3## [1] 2Notice that the HTML page shows the R code in a gray box, followed results of the code.
Here is the section of the RMarkdown Cheatsheet that describes R code chunks:
Suppress printing of R code
Here is some more code that suppresses the printing of the R code:
## [1] 2 3 5 6At most reports, you will want to suppress the R code because the coding most frequently is secondary to the answer. Of course, there are times that you will want to echo the code in the RMarkdown output for demonstration (as wil be the case in some parts of Data Science Challenges or in the Final Examination.)
Suppress double hashmarks (##) at the start of each line
Don’t like the ## at the beginning of each line? Do this:
[1] 2 3 5 6Importing data for use in RMarkdown
I can import and print a dataset stored on the web and show you the code and print output:
dave <- read.csv("http://www.personal.psu.edu/dlp/w540/datasets/state_indicators.csv")
dave statename population income illiteracy life_exp murder hs_grad
1 Alabama 3615 3624 2.1 69.05 15.1 41.3
2 Alaska 365 6315 1.5 69.31 11.3 66.7
3 Arizona 2212 4530 1.8 70.55 7.8 58.1
4 Arkansas 2110 3378 1.9 70.66 10.1 39.9
5 California 21198 5114 1.1 71.71 10.3 62.6
6 Colorado 2541 4884 0.7 72.06 6.8 63.9
7 Connecticut 3100 5348 1.1 72.48 3.1 56.0
8 Delaware 579 4809 0.9 70.06 6.2 54.6
9 Florida 8277 4815 1.3 70.66 10.7 52.6
10 Georgia 4931 4091 2.0 68.54 13.9 40.6
11 Hawaii 868 4963 1.9 73.60 6.2 61.9
12 Idaho 813 4119 0.6 71.87 5.3 59.5
13 Illinois 11197 5107 0.9 70.14 10.3 52.6
14 Indiana 5313 4458 0.7 70.88 7.1 52.9
15 Iowa 2861 4628 0.5 72.56 2.3 59.0
16 Kansas 2280 4669 0.6 72.58 4.5 59.9
17 Kentucky 3387 3712 1.6 70.10 10.6 38.5
18 Louisiana 3806 3545 2.8 68.76 13.2 42.2
19 Maine 1058 3694 0.7 70.39 2.7 54.7
20 Maryland 4122 5299 0.9 70.22 8.5 52.3
21 Massachusetts 5814 4755 1.1 71.83 3.3 58.5
22 Michigan 9111 4751 0.9 70.63 11.1 52.8
23 Minnesota 3921 4675 0.6 72.96 2.3 57.6
24 Mississippi 2341 3098 2.4 68.09 12.5 41.0
25 Missouri 4767 4254 0.8 70.69 9.3 48.8
26 Montana 746 4347 0.6 70.56 5.0 59.2
27 Nebraska 1544 4508 0.6 72.60 2.9 59.3
28 Nevada 590 5149 0.5 69.03 11.5 65.2
29 New Hampshire 812 4281 0.7 71.23 3.3 57.6
30 New Jersey 7333 5237 1.1 70.93 5.2 52.5
31 New Mexico 1144 3601 2.2 70.32 9.7 55.2
32 New York 18076 4903 1.4 70.55 10.9 52.7
33 North Carolina 5441 3875 1.8 69.21 11.1 38.5
34 North Dakota 637 5087 0.8 72.78 1.4 50.3
35 Ohio 10735 4561 0.8 70.82 7.4 53.2
36 Oklahoma 2715 3983 1.1 71.42 6.4 51.6
37 Oregon 2284 4660 0.6 72.13 4.2 60.0
38 Pennsylvania 11860 4449 1.0 70.43 6.1 50.2
39 Rhode Island 931 4558 1.3 71.90 2.4 46.4
40 South Carolina 2816 3635 2.3 67.96 11.6 37.8
41 South Dakota 681 4167 0.5 72.08 1.7 53.3
42 Tennessee 4173 3821 1.7 70.11 11.0 41.8
43 Texas 12237 4188 2.2 70.90 12.2 47.4
44 Utah 1203 4022 0.6 72.90 4.5 67.3
45 Vermont 472 3907 0.6 71.64 5.5 57.1
46 Virginia 4981 4701 1.4 70.08 9.5 47.8
47 Washington 3559 4864 0.6 71.72 4.3 63.5
48 West Virginia 1799 3617 1.4 69.48 6.7 41.6
49 Wisconsin 4589 4468 0.7 72.48 3.0 54.5
50 Wyoming 376 4566 0.6 70.29 6.9 62.9
area
1 50708
2 566432
3 113417
4 51945
5 156361
6 103766
7 4862
8 1982
9 54090
10 58073
11 6425
12 82677
13 55748
14 36097
15 55941
16 81787
17 39650
18 44930
19 30920
20 9891
21 7826
22 56817
23 79289
24 47296
25 68995
26 145587
27 76483
28 109889
29 9027
30 7521
31 121412
32 47831
33 48798
34 69273
35 40975
36 68782
37 96184
38 44966
39 1049
40 30225
41 75955
42 41328
43 262134
44 82096
45 9267
46 39780
47 66570
48 24070
49 54464
50 97203Notice that thise code printed the entire dataset (as a result of the dave command.) In fact, there usually is no need to print the dataset after I import it, unless I need to display it in the report. Remember, some datasets are very large, too large to print in a report. Check the RMarkdown code following this paragraph to see how to import a dataset from the Internet and suppress geeky messages, but not to print the dataset.
A few formatting hints
The Markdown codes tht yield particular RMarkdown formats is in the following section of the RMarkdown Cheatsheet:
Submitting an RMarkdown file to RPubs
Remember I wrote in Piazza that you would need an RPubs account?
Here is how you render a .Rmd file for uploading to RPubs:
More info about RMarkdown is available at http://rmarkdown.rstudio.com and at https://ismayc.github.io/rbasics-book/4-rmarkdown.html.
Movement of a rendered .Rmd file to Rpubs is demonstrated in the 10 September 2018 class meeting (video available).