R Markdown Reports
Created by Chia, Jonathan, last modified on Apr 09, 2022
Introduction
Refer to this article when you want to organize a report that includes code
Table of Contents
Why Use R Markdown?
Helps to keep your code organized
Create clean reports where you can hide/show code when needed
Can export as pdf, word, presentation, html, markdown, website, and dashboards
Can create automated reports that get emailed to people
Template for HTML report
Below is the code from an R Markdown file that includes a table of contents (toc), adds code hide/show buttons (code_folding), and outputs as a html document
---
title: 'Title'
author: 'Name'
date: 'Jan 20, 2021'
output:
html_document:
toc: yes
number_sections: no
code_folding: hide
theme: cosmo
highlight: tango
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
# load other libraries here
```
# This is the first header
Datatable
```{r}
mtcars %>% filter(mpg < 21) %>% head(6)
```
## This is the second header
Histogram of mpg
```{r}
hist(mtcars$mpg)
```
### This is the third header
_italics_
**bold**
- bullet
1. numberOutput
Below is the output of the above code
Outputting to Word
Key packages:
Officedown
Officer
Flextable
htmlwidgets
pagedown
Officedown
Lets you adjust page margins, landscape, columns, and other Word specific options
Example:
Insert this code block below your outputs that you want to be in landscape mode
block_section(
prop_section(
type = "continuous",
page_size = page_size(orient = "landscape", width = 14, height = 8.5),
page_margins = page_mar(
bottom = .75,
top = .75,
right = .75,
left = .75,
header = 0.1,
footer = 0.1,
gutter = 0.1
)
))Officer
Officer has to be loaded to pair with officedown and flextable
Flextable
This package is so much better than DT package (unless you need DT for interactivity and filters)
Example:
params$customer_counts %>% mutate(Line = seq(1,nrow(.))) %>%
select(ncol(.), 1:ncol(.)-1) %>%
flextable() %>%
style(part = 'body', pr_t = fp_text(font.size = 6), pr_c = cell_style) %>%
add_header_row(values = c('Customer Counts',
paste0("Week of ",
format(as.Date(params$customer_counts_date1[1]), '%m/%d')),
paste0("Week of ",
format(as.Date(params$customer_counts_date2[1]), '%m/%d')),
paste0("Week of ",
format(as.Date(params$customer_counts_date3[1]), '%m/%d'))
),
colwidths = c(3,3,3,3)) %>%
align(align = 'center', part = 'header') %>%
theme_box() %>%
merge_v(j = 2) %>%
merge_at(i = c(1), j = c(2,3)) %>%
merge_at(i = c(2), j = c(2,3)) %>%
bg(part = 'header', i = 2, bg = '#d3d3d3') %>%
# this next part copies the conditional formatting from excel
bg(j = c(6,9,12), bg = function(x) {
out <- rep('transparent', length(x))
quantile <- quantile(x, prob = seq(0,1, by = 1/21))
out[x >= quantile[1] & x < quantile[2]] <- '#f8696b'
out[x >= quantile[2] & x < quantile[3]] <- '#f87779'
out[x >= quantile[3] & x < quantile[4]] <- '#f88688'
out[x >= quantile[4] & x < quantile[5]] <- '#f99597'
out[x >= quantile[5] & x < quantile[6]] <- '#f9a3a6'
out[x >= quantile[6] & x < quantile[7]] <- '#fab2b5'
out[x >= quantile[7] & x < quantile[8]] <- '#fac1c3'
out[x >= quantile[8] & x < quantile[9]] <- '#facfd2'
out[x >= quantile[9] & x <= quantile[10]] <- '#fbdee1'
out[x >= quantile[10] & x <= quantile[11]] <- '#fbedf0'
out[x >= quantile[11] & x <= quantile[12]] <- '#FFFFFF'
out[x >= quantile[12] & x <= quantile[13]] <- '#edf6f2'
out[x >= quantile[13] & x <= quantile[14]] <- '#def0e5'
out[x >= quantile[14] & x <= quantile[15]] <- '#cfead8'
out[x >= quantile[15] & x <= quantile[16]] <- '#bfe4cb'
out[x >= quantile[16] & x <= quantile[17]] <- '#b0ddbd'
out[x >= quantile[17] & x <= quantile[18]] <- '#a1d7b0'
out[x >= quantile[18] & x <= quantile[19]] <- '#91d1a3'
out[x >= quantile[19] & x <= quantile[20]] <- '#82cb96'
out[x >= quantile[20] & x <= quantile[21]] <- '#73c589'
out[x >= quantile[21] & x <= quantile[22]] <- '#63be7b'
out
}) %>%
vline(j = c(3,12), border = border_style) %>%
hline(i = c(2,8,14,20,26,31), border = border_style) %>%
set_formatter(
`Date 1 YOY Diff` = function(x) format_percent_integer(x),
`Date 2 YOY Diff` = function(x) format_percent_integer(x),
`Date 3 YOY Diff` = function(x) format_percent_integer(x)
) %>%
fontsize(part = 'header', size = 6) %>%
height(part = 'body', height = .2) %>%
hrule(rule = 'exact') %>%
valign(part = 'body', valign = 'top') %>%
valign(part = 'body', j = 2, valign = 'center') %>%
# line_spacing(part = 'body', space = .5) %>%
align(part = 'body', i = c(1,2), j = 2, align = 'center') %>%
set_table_properties(layout = "autofit") %>%
fit_to_width(12)Output:
HTML widgets and Pagedown to save HTML as picture
I use these two packages to save highcharter, ggplot, or plotly html charts as png files. Then I display the png in Word using include_graphics().
Example:
highchart() %>%
hchart() %>%
htmlwidgets::saveWidget(file = 'highchart1.html')
pagedown::chrome_print(input = 'highchart1.html',
output = 'highchart1.png',
wait = 3, format = 'png')
knitr::include_graphics('highchart1.png')Other Useful Links
https://rmarkdown.rstudio.com/authoring_basics.html
https://bookdhttps://bookdown.org/yihui/rmarkdown/r-code.html own.org/yihui/rmarkdown/r-code.html
https://rmarkdown.rstudio.com/gallery.html
Random Useful Code
Widen the margins of the html output - really useful when you can't fit all your columns in your tables
Put this right after the yaml section:
<style type="text/css">
.main-container {
max-width: 1800px;
margin-left: auto;
margin-right: auto;
}
</style>Document generated by Confluence on Apr 09, 2022 02:02
Last updated