A state-of-the-art way to make reproducible reports is to use a statistical computing language such as R and its knitr package in conjunction with either RMarkdown or Quarto, with the latter likely to replace the former. Both of the report-making systems allow one to produce reports in a variety of formats including html, pdf, and Word. Html is recommended because pages can be automatically resized to allow optimum viewing on devices of most sizes, and because html allows for interactive graphics and other interactive components. Pdf is produced by converting RMarkdown or Quarto-produced markdown elements to $$\LaTeX$$.

Report formatting is very much enhanced by using variable attributes such as labels and units of measurement that are not considered in base R. Methods for better annotating output using labels and units are given below.

This document can serve as a template for using R with Quarto; one can see the raw script by clicking on Code at the top right of the report. When one has only one output format target, things are fairly straightforward except some situations where mixed formats are rendered in the same code chunk. Click below for details.

To make use of specialized functions that produce html or $$\LaTeX$$ markup, one often has to put results='asis' in the code chunk header to keep the system from disturbing the generated html or $$\LaTeX$$ markup so that it will be typeset correctly in the final document. This process works smoothly but creates one complication: if you print an object that produces plain text in the same code chunk, the system will try to typeset it in html or $$\LaTeX$$. To prevent this from happening you either need to split the chunks into multiple chunks (some with results='asis' and some not) or you need to make it clear that parts of the output are to be typeset verbatim. To do that a simple function pr can sense if results='asis' is in effect for the current chunk. If so, the object is surrounded by the markdown verbatim indicator—three consecutive back ticks. If not the object is left alone. pr is defined in the marksupSpecs$markdown$pr object, so you can bring it to your session by copying into a local function pr as shown below, which has a chunk option results='asis' to show that verbatim output appears anyway. If the argument obj to pr is a data frame or data table, variables will be rounded to the value given in the argument dec (default dec=3) before printing. If you specify inline=x the object x is printed with cat() instead of print(). inline is more for printing character strings.

An example of something that may not render correctly due to results='asis' being in the chunk header (needed for html(...)):

options(prType='html')
f <- ols(y ~ rcs(x1, 5))
f    # prints model summary in html format
m <- matrix((1:10)/3, ncol=2)
m
# use pr(obj=m) to fix

Here are examples of pr usage.

require(Hmisc)
pr <- markupSpecs$markdown$pr
x <- (1:5)/7
pr('x:', x)

x:

[1] 0.1428571 0.2857143 0.4285714 0.5714286 0.7142857
pr(obj=x)
[1] 0.1428571 0.2857143 0.4285714 0.5714286 0.7142857
pr(inline=paste(round(x,3), collapse=', '))

0.143, 0.286, 0.429, 0.571, 0.714


Instead of working to keep certain outputs verbatim you can use knitr::kable() to convert verbatim output to markdown.

## 3.1Quarto Syntax for Figures

One can specify sizes, layouts, captions, and more using Quarto markup. Captions are ignored unless a figure is given a label. Figure labels must begin with fig-. The figure can be cross-referenced elsewhere in the document using for example See \@fig-scatterplot. Figure will be placed in front of the figure number automatically. Here is example syntax.

{r}
#| label: fig-myplot
#| fig-cap: “An example caption (use one long line for caption)”
#| fig-height: 3
#| fig-width: 4
plot(1:7, abs(-3 : 3))


If the code produces multiple plots you can combine them into one with a single overall caption and include subcaptions for the individual panels:

{r}
#| label: fig-myplot
#| fig-cap: “Overall caption …”
#| fig-height: 3
#| fig-width: 4
#| layout-ncol: 2
#| fig-subcap:
#| - “Subcaption for panel (a)”
#| - “Subcaption for panel (b)”
plot(1:7, abs(-3 : 3))
hist(x)


To include an existing image while making use of Quarto for sizing and captioning etc. use this example.

{r out.width=“600px”}
#| label: fig-mylabel
#| fig-cap: “…”
knitr::include_graphics(‘my.png’)


If you don’t need to caption or cross-reference the figure use e.g.

Other examples are in the next section.

The reptools repository has helper functions for building a table of figures. To use those, put addCap() or addCap(scap="short caption for figure") as the first line of code in the chunk. The full caption is taken as the fig-cap: markup. If you don’t specify scap too addCap the short caption will be taken as the fig-scap: markup, or if that is missing, the full caption. At the end of the report you can print the table of figures using the following syntax (but surround the last line with back ticks).

# Figures

r printCap()

For chunks having #| label: fig- you can automatically have knitr call addCap at the start of a chunk, extracting the needed information, if you run the reptools function hookaddcap() in a chunk before the first chunk that produced a graph. This procedure is used through this book. addCap makes use of fig-scap: for short captions.

## 3.2Quarto Built-in Syntax for Enhancing R Output

Helper functions described below allow one to enhance graphical and tabular R output by taking advantage of Quarto formatting features. These functions allow one to produce different formats within one code chunk, e.g., a plot in the margin and a table in a collapsible note appearing after the code chunk. But if you need only one output format within a chunk you can make use of built-in syntax as described here. The yaml-like syntax also allows you to specify heights and widths for figures, plus multi-figure layouts.

Here is some example code with all the markup shown.

{r}
#| column: margin
#| fig-height: 1
#| fig-width: 3
par(mar=c(2, 2, 0, 0), mgp=c(2, .5, 0))
set.seed(1)
x <- rnorm(1000)
hist(x, nclass=40, main=’’)
x[1:3] # ordinary output stays put
knitr::kable(x[1:3]) # html output put in margin
hist(x, main=’’)


This results follow.

par(mar=c(2, 2, 0, 0), mgp=c(2, .5, 0))
set.seed(1)
x <- rnorm(1000)
hist(x, nclass=40, main='')

x[1:3]               # ordinary output stays put
[1] -0.6264538  0.1836433 -0.8356286
knitr::kable(x[1:3]) # html output put in margin
x
-0.6264538
0.1836433
-0.8356286
hist(x, main='')

Here are a few markups for figure layout inside R chunks.

Wide page (takes over the margins) and put multiple plots in 1 row:

#| column: screen-inset
#| layout-nrow: 1

When plotting 3 figures put the first 2 in one row and the third in the second row and make it wide.

#| layout: [[1,1], [1]]

Make the top left panel be wider than the top right one.

#| layout: [[70,30], [100]]

Top left and top right panels have equal widths but devote 0.1 of the total width to an empty region between the two top panels.

#| layout: [[45, -10, 45], [100]]

See here for details about figure specifications inside code chunks.

## 3.3Quarto Report Writing Helper Functions

Helper functions are defined when you run the Hmisc function getRs to retrieve them from Github, i.e., getRs('reptools.r'). You can get help on these functions by running rsHelp(functionname). Several of the functions construct Quarto callouts which are fenced-off sections of markup that trigger special formatting, especially when producing html. The special formatting includes collapsible sections and marginal notes. Here is a summary of some of the reptools helper functions.

Function Purpose
dataChk run a series of logical expressions for checking data consistency, put results in separate tabs using maketabs, and optionally create two summary tabs
dataOverview runs a data overview report
missChk creates a series of analyses of the extent and patterns of missing values in a data table or data frame, and puts graphical summaries in tabs
hookaddcap makes knitr automatically extract figure labels, captions, short captions for use in list of figures
htmlList print a named list using the names as headers
kabl front-end to knitr::kable and kables. If you run kabl on more than one object it will automatically call kables.
makecallout generic Quarto callout maker used by makecnote, makecolmarg
makecnote print objects or run code and place output in an initially collapsed callout note
makecolmarg print objects or run code and place output in a marginal note
maketabs print objects or run code placing output in separate tabs
makemermaid makes a mermaid diagram with R variable values included in the diagram
varType classify variables in a data table/frame or a vector as continuous, discrete, or non-numeric non-discrete
conVars use varType to extract list of continuous variables
disVars use varType to extract list of discrete variables
vClus run Hmisc::varclus on a dataset after reducing it

The input to maketabs, as will be demonstrated later, may be a named list, or more commonly, a series of formulas whose right-hand sides are executed and the result of each formula is placed in a separate tab. The left side of the formula becomes the tab label. For makecolmarg there should be no left side of the formula as marginal notes are not labeled. For the named list option the list names become the tab names. Examples of both approaches appear later in this report. In formulas, a left side label must be enclosed in back ticks and not quotes if it is a multi-word string. A wide argument is used to expand the width of the output outside the usual margins. An initblank argument creates a first tab that is empty. This allows one to show nothing until one of the other tabs is clicked. Alternately you can specify as the first formula   ~  .

The two approaches to using maketabs also apply to makecnote and makecolmarg. Examples of the “print an object and place it inside a callout” are given later in the report for makecnote and makecolmarg. Here is an example of the more general formula method that can render any object, including html widgets as produced by plotly graphics. An interactive plotly graphic appears at the bottom of the plots in the right margin. You can single click on elements in the legend to turn them off and on, and double click within the legend to restore to default values.

require(Hmisc)
options(plotlyauto=TRUE)  # makes Hmisc use plotly's auto size option
# rather than computing height, width
getRs('reptools.r', put='source')
set.seed(1)
x <- round(rnorm(100, 100, 15))
makecolmarg(~ table(x) + raw + hist(x) + plot(ecdf(x)) + histboxp(x=x))
x
67  70  73  77  78  79  81  82  83  84  86  87  88  89  90  91  92  93  94  95
1   1   1   1   1   1   2   1   1   1   1   1   1   3   1   6   1   3   3   2
96  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 116 117
1   6   5   3   2   1   2   2   4   5   2   2   6   2   3   3   1   2   1   3
118 120 121 122 123 124 130 133 136
2   1   1   1   1   2   1   1   1 

# or try makecnote(makecnote example ~ kabl(table(x)) + hist(x) + ...
# Avoid raw by using kabl(table(x)) instead of table(x)

Adding + raw to a formula in makecnote, makecolmarg, or maketabs forces printed results to be treated as raw verbatim R output.

makecallout is a general Quarto callout maker that implements different combinations of the following: list or formula, print or run code, defer executing and only produce the code to execute vs. running the code now, and close the callout or leave it open for more calls.

reptools also has helper functions for interactively accessing information to help in report and analysis building:

Function Purpose
htmlView view html-converted objects in RStudio View pane
htmlViewx view html-converted objects in external browser

## 3.4 Multi-Output Format Reports

To allow one report to be used to render multiple output formats, especially html and pdf, it is helpful to be able to sense which output format is currently in play, and to use different functions or options to render output explicitly for the current format. Here is how to create variables that can be referenced simply in code throughout the report, and to invoke the plotly graphics package if output is in html to allow interactivity. A small function ggp is defined so that if you run any ggplot2 output through it, the result will be automatically converted to plotly using the ggplotly function, otherwise it is left at standard static ggplot2 output if html is not the output target.

See this for examples of articles rendered in both html and PDF from the same script.
outfmt <- if(knitr::is_html_output ()) 'html'  else 'pdf'
markup <- if(knitr::is_latex_output()) 'latex' else 'html'
ishtml <- outfmt == 'html'
if(ishtml) require(plotly)
ggp <- if(ishtml) ggplotlyr else function(ggobject, ...) ggobject
# See below for more about ggplotlyr (a front end for ggplotly that can
# correct a formatting issue with hover text)

Quarto has a excellent facility for conditionally including document sections depending on the currently chosen output format.

The Hmisc, rms, and rmsb packages have a good deal of support for creating $$\LaTeX$$ output in addition to html. They require some special $$\LaTeX$$ packages to be accessed. In addition, if using any of Quarto’s nice features for making marginal notes, there is another $$\LaTeX$$ package to attach. Below you’ll find what needs to be added to the yaml prologue at the top of your script if using Quarto. You have to modify pdf-engine to suit your needs. I use luatex because it handles special unicode characters. In the future (approximately July 2022) a bug in Pandoc will be fixed and you can put links-as-notes: true in the yaml header instead of redefining href and linking in hyperref.

format:
html:
self-contained: true
. . .
pdf:
pdf-engine: lualatex
toc: false
number-sections: true
number-depth: 2
top-level-division: section
reference-location: document
listings: false
\usepackage{marginnote, here, relsize, needspace, setspace, hyperref}
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}

The href redefinition above turns URLs into footnotes if running $$\LaTeX$$.

There is one output element provided by Quarto that will not render correctly to $$\LaTeX$$: a marginal note using the markup .column-margin. To automatically use an alternate in-body format, define a function that can be used for both typesetting formats.

mNote <- if(ishtml) '.column-margin'
else
'.callout-note appearance="minimal"'

Then use r mNote enclosed in back ticks in place of the .column-margin callout for generality.

Even when producing only html, one may wish to save individual graphics for manuscript writing. For non-interactive graphics you can right click on the image and download the .png file. For interactive plots, plotly shows a “take a snapshot” icon when you hover over the image. Clicking this icon will produce a static .png snapshot of the graph. Some graphs are not appropriate for static documents, and the variables created in the code above can be checked so that, for example, an alternative graph can be produced when making a .pdf file. But in other cases one just produces an additional static plot that is not shown in the html report. See the margin note near Figure 14.18 for an example.

As done with various Hmisc and rms package functions, one can capitalize on Hmisc’s special formatting of variable labels and units when constructing tables in $$\LaTeX$$ or html. The basic constructs are shown in the code below.

# Retrieve a set of markup functions depending on typesetting format
# See below for definition of ishtml
specs    <- markupSpecs[[if(ishtml) 'html' else 'latex']]
# Hmisc markupSpecs functions create plain text, html, latex,
# markdown, or plotmath code
varlabel <- specs\$varlabel  # retrieve an individual function
# Format text describing variable named x
# hfill=TRUE typesets units to be right-justified in label
# Use the following character string as a row label
# Default specifies the string to use if there is not label
# (usually taken as the variable name)
varlabel(label(x, default='x'), units(x), hfill=TRUE)

As exemplified in Chapter 7, Mermaid provides an easy way to make many types of diagrams. Diagrams are more valuable when they are dynamic. Mermaid provides an easy way to include pop-up tooltips in diagram nodes, to provide deeper information about the node. When the tooltips contain tables whose columns need to line up, you need to put the following in your document so that tooltips will used a fixed-width font and preserve white space. The best way to include this is to put it in a .css file that is reference in the report’s yaml, or to surround the four lines with <style></style>.

mermaidTooltip {
font-family: courier;
white-space: pre;
}