Introduction to Individualized Reproducible Reports with R & R Markdown
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The Problem and Possible Solutions
Problem Need to combine information from multiple data sources to create individualized reports for hundreds, or even thousands, of recipients. Further, these reports need to be created weekly.
In my version of the problem, my schools wanted weekly progress reports that included academic and behavior data. Some schools also wanted information on attendance, independent reading, and/or community service.
Mail Merge Solution Download or collect the data in a spreadsheet, and use Microsoft Word's Mail Merge functionality. The template is very easy to customize, but the data must be in wide format and data manipulation is often done by hand.
Visual Basic Solution Download or collect data in one spreadsheet. Write a VBA macro that tidies and transforms the data. This automates the process but is oftentimes very slow.
My predecessor used this solution. It took ~20 minutes to create 400 progress reports that only included academic data.
R and R Markdown Solution Write a R Markdown document that utilizes the power of R to get and clean data and the formatting options of Latex and HTML.
Depending on the report, I retrieve data from a database (RODBC), a GoogleSheet (googlesheets) , and even an Excel file in a shared folder (xlsx or openxlsx) . I replaced the VBA-generated progress report from above with a R Markdown-generated report that also included behavior information and a graph of words read, and the time to generate this report was still under a minute. Further, the entire process was automated. Rather than needing to write the results of a query to a file, then copy this data into the Excel file with the macro, I just opened the R Markdown file and clicked Knit PDF.
The YAML header includes several of the key elements of your report template. My basic header is:
header-includes: \pagestyle{empty} \usepackage{wallpaper} \LRCornerWallPaper{1}{path/to/image} \URCornerWallPaper{1}{path/to/image} \usepackage{geometry} \geometry{tmargin=1.5in} output: pdf_document
By default, R Markdown documents number their pages. \pagestyle{empty} removes page numbers from all but the first page, which I typically use as a title page with summary information.
The wallpaper Latex package allows you to add header and footer images in the upper-right (UR), lower-right (LR), upper-left (LR), and lower-left (LL). The number inside of the {} is the scaling of the image. On Windows, I experienced the problem of the image being placed directly in the corner of the page with no margin. A work-around is adding white-space to the image.
Depending on the size of your header image, you may need to adjust the margins before the content of the document starts. The geometry Latex package allows you to make these adjustments. ShareLatex provides a good overview of the available options.
I always output to PDF. In general, the formatting turns out cleaner compared to generating Word documents. The Latex used in this document will not render if the output is HTML.
Within your R code the first step is to pull or create a list of individuals who will receive the reports. I approach this problem by pulling a list of distinct ID numbers along with their name and other basic information like adviser and grade. For clarity, I isolate the getting and cleaning of data in the first code block and put the document-creating code in the second block.
For the document-creating code, block options should include at least
{r, echo = FALSE, results = 'asis'}
The asis option allows output to be formatted as normal text rather than R output.
The first line of code provides a way to iterate through your list.
for (i in seq_along(recipients)) {
Inside your for loop, include code for displaying the information in the report. For lines of text, use cat. print should only be used with tables.
library(knitr) name <- 'R Markdown' df <- head(mtcars[1:5]) cat(name, 'is the best!\n\n')
mpg cyl disp hp drat ------------------ ----- ---- ----- ---- ----- Mazda RX4 21.0 6 160 110 3.90 Mazda RX4 Wag 21.0 6 160 110 3.90 Datsun 710 22.8 4 108 93 3.85 Hornet 4 Drive 21.4 6 258 110 3.08 Hornet Sportabout 18.7 8 360 175 3.15 Valiant 18.1 6 225 105 2.76
# Using the following will throw an error # print(name, 'is the best!\n\n') print(kable(df))
mpg cyl disp hp drat Mazda RX4 21.0 6 160 110 3.90 Mazda RX4 Wag 21.0 6 160 110 3.90 Datsun 710 22.8 4 108 93 3.85 Hornet 4 Drive 21.4 6 258 110 3.08 Hornet Sportabout 18.7 8 360 175 3.15 Valiant 18.1 6 225 105 2.76
Notice that for printed lines, is it necessary to include \n\n to ensure line-breaks, just like when writing in typical Markdown.
Not all tables require print, such as pandoc.table from the pander package or xtable. pandoc.table is particularly useful if you have long text columns, because you can set the cell width.
At the bottom of your code block but inside your for loop, include the page break. cat('\n\n\\pagebreak\n')
This is the first example of needing to include \\. Like with regular expressions, without the extra \, R will think \p as an escape character.
Other Useful Code Elements
Three other building blocks I use often are the section header
cat('\\section*{Name of section}\n\n')
cat('\\centerline{Centered Text}\n\n')
If you have multiple graphs and would like to display them side-by-side, rather than the default one graph per line, I suggest grid.arrange from gridExtra. It is also possible to group more than two graphs. This allows you to set the fig.height and fig.width for the entire grouping, helpful if you need to fit all the graphs on a single page.
library(ggplot2) library(gridExtra) a <- rnorm(100, 50) b <- rpois(100, 1) x <- rbinom(100, 1, 0.5) y <- runif(100, 0, 100) p1 <- qplot(a, b) p2 <- qplot(x, y) p3 <- qplot(x, a) p4 <- qplot(b, y) grid.arrange(p1, p2, p3, p4)
// add bootstrap table styles to pandoc tables $(document).ready(function () { $('tr.header').parent('thead').parent('table').addClass('table table-condensed'); }); (function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })();
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