Week9_practical
Daniel Dowd
27/04/2023
This is document refreshing your knowledge of R Markdown and introducing a few new functions necessary to publish the data analysis results as HTML documents.
Install the packages first:
library("knitr")
library("rmarkdown")
library("summarytools")## Warning: package 'summarytools' was built under R version 4.2.3R 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 new document will be generated that includes both content as well as the output of any embedded R code chunks within the document. This will be saved as a HTML fail in your project folder. Press the Knit button now to see if it works.
R chunks and in-line r code
A code chunk starts with three back ticks followed by curly brackets
{} where r code goes in, and ends with three back
ticks.
Figure 1. Screenshot of R chunk
Explore the cog icon on the right side to see how you can quickly change settings of the r chunk.
And as a code and an output it will look like this:
summary(cars)## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00Cars is a demo data for R. Note that after ‘r’ in the chunk I added a chunk name. This is useful, as chunk names are used as output names when saved.
You can write as much code as you want in a r chunk, but it is better not to embed to many operations in one chunk as it is more difficult to find a problem.
Inline R code is embedded in the narratives of the document using one
back tick on each side of a code r.
Plots
You can embed any outputs, such as graphs, for example:
Note that the echo = FALSE parameter was added to the
code chunk to prevent printing of the R code that generated the
plot.
Tables
kable function from “knitr” package produces good
looking tables in HTML format. This
section of an R Markdown book provides more examples on how to use
it.
Let’s display the same first 5 rows of our data using kable function.
kable(cars[1:5, ], caption = "Table 1. Overview of first 5 rows in data")| speed | dist |
|---|---|
| 4 | 2 |
| 4 | 10 |
| 7 | 4 |
| 7 | 22 |
| 8 | 16 |
A more informative table would be some summary statistics of
variables in the dataset. Note that for functions from the
“summarytools” package we had to add plain.ascii = FALSE,
style = 'rmarkdown' in the table options and set the knitr
chunk option results="asis" so they work in RMarkdown.
descr(cars, plain.ascii = FALSE, style = 'rmarkdown')Descriptive Statistics
cars
N: 50
| dist | speed | |
|---|---|---|
| Mean | 42.98 | 15.40 |
| Std.Dev | 25.77 | 5.29 |
| Min | 2.00 | 4.00 |
| Q1 | 26.00 | 12.00 |
| Median | 36.00 | 15.00 |
| Q3 | 56.00 | 19.00 |
| Max | 120.00 | 25.00 |
| MAD | 23.72 | 5.93 |
| IQR | 30.00 | 7.00 |
| CV | 0.60 | 0.34 |
| Skewness | 0.76 | -0.11 |
| SE.Skewness | 0.34 | 0.34 |
| Kurtosis | 0.12 | -0.67 |
| N.Valid | 50.00 | 50.00 |
| Pct.Valid | 100.00 | 100.00 |
Now let’s improve the table by tidying it up a little.
descr(cars, stats = c("mean", "sd", "min", "max"), transpose = TRUE, headings = FALSE, caption="Table 1. Descriptive statistics for key variables")| Mean | Std.Dev | Min | Max | |
|---|---|---|---|---|
| dist | 42.98 | 25.77 | 2.00 | 120.00 |
| speed | 15.40 | 5.29 | 4.00 | 25.00 |
Read more on the descr fucntion in “summarytools”
package here.
Excercises
Excercise 1: Practice R Markdown formatting
Look into basic formatting options of R Markdown and play with the text below: https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf
Make this word bold
Make this word italics
###Make this line a 3-level header
1.Create two level list:
- Level 1
- Level 2
- Level 1
- Level 2
This a quote, so use formatting to create a block quote.
Add a hyperlink to this word to the SMI website.
Copy the r chunk with the plot twice and change the r chunk options so:
- code and graph is displayed
plot(pressure)
- only code is displayed
plot(pressure)Embed a picture - e.g. SMI logo below
Picture of SMI Logo
Excercise 2: Good looking data summary
Improve the below table so it is displayed in R Markdown friendly format (not with ASCII language). Decide what descriptive statistics should be displayed. Add table number and title.
descr(cars)## Descriptive Statistics
## cars
## N: 50
##
## dist speed
## ----------------- -------- --------
## Mean 42.98 15.40
## Std.Dev 25.77 5.29
## Min 2.00 4.00
## Q1 26.00 12.00
## Median 36.00 15.00
## Q3 56.00 19.00
## Max 120.00 25.00
## MAD 23.72 5.93
## IQR 30.00 7.00
## CV 0.60 0.34
## Skewness 0.76 -0.11
## SE.Skewness 0.34 0.34
## Kurtosis 0.12 -0.67
## N.Valid 50.00 50.00
## Pct.Valid 100.00 100.00Look into the package summarytools here: https://cran.r-project.org/web/packages/summarytools/vignettes/introduction.html
and use freq function to create another table for the same
data.
freq(cars)## Frequencies
## cars$speed
## Type: Numeric
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- ------ --------- -------------- --------- --------------
## 4 2 4.00 4.00 4.00 4.00
## 7 2 4.00 8.00 4.00 8.00
## 8 1 2.00 10.00 2.00 10.00
## 9 1 2.00 12.00 2.00 12.00
## 10 3 6.00 18.00 6.00 18.00
## 11 2 4.00 22.00 4.00 22.00
## 12 4 8.00 30.00 8.00 30.00
## 13 4 8.00 38.00 8.00 38.00
## 14 4 8.00 46.00 8.00 46.00
## 15 3 6.00 52.00 6.00 52.00
## 16 2 4.00 56.00 4.00 56.00
## 17 3 6.00 62.00 6.00 62.00
## 18 4 8.00 70.00 8.00 70.00
## 19 3 6.00 76.00 6.00 76.00
## 20 5 10.00 86.00 10.00 86.00
## 22 1 2.00 88.00 2.00 88.00
## 23 1 2.00 90.00 2.00 90.00
## 24 4 8.00 98.00 8.00 98.00
## 25 1 2.00 100.00 2.00 100.00
## <NA> 0 0.00 100.00
## Total 50 100.00 100.00 100.00 100.00Excervise 3: Edit YAML metadata
Add table of content option in the YAML settings at the top of the document.
Change date and your name as the author.
Knit as a HTML page, click the publish button on the right top, and publish on your Rpubs account. Send the link to Aneta for feedback when all is done.
Session info
sessionInfo()## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 22621)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United Kingdom.utf8
## [2] LC_CTYPE=English_United Kingdom.utf8
## [3] LC_MONETARY=English_United Kingdom.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United Kingdom.utf8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] summarytools_1.0.1 rmarkdown_2.20 knitr_1.42
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 highr_0.10 plyr_1.8.8 bslib_0.4.2
## [5] compiler_4.2.2 pillar_1.8.1 pryr_0.1.6 jquerylib_0.1.4
## [9] base64enc_0.1-3 tools_4.2.2 digest_0.6.31 jsonlite_1.8.4
## [13] lubridate_1.9.2 evaluate_0.20 lifecycle_1.0.3 tibble_3.1.8
## [17] checkmate_2.1.0 timechange_0.2.0 pkgconfig_2.0.3 rlang_1.0.6
## [21] cli_3.6.0 rstudioapi_0.14 magick_2.7.4 yaml_2.3.7
## [25] xfun_0.37 fastmap_1.1.0 withr_2.5.0 stringr_1.5.0
## [29] dplyr_1.1.0 generics_0.1.3 vctrs_0.5.2 sass_0.4.5
## [33] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
## [37] tcltk_4.2.2 purrr_1.0.1 tidyr_1.3.0 reshape2_1.4.4
## [41] pander_0.6.5 magrittr_2.0.3 MASS_7.3-58.1 rapportools_1.1
## [45] backports_1.4.1 codetools_0.2-18 htmltools_0.5.4 matrixStats_0.63.0
## [49] utf8_1.2.3 stringi_1.7.12 cachem_1.0.6