1 Introduction

This is a set of reproducible examples for the R¹ Hmisc package², put together in an rmarkdown html document using RStudio and knitr. When viewing the resulting html file you can see all the code, and there exist options to download the entire rmarkdown script, which is especially helpful for seeing how knitr chunks are specified. Graphics that have a plotly method for them are rendered using plotly instead of using defaults such as base graphics, lattice, or ggplot2. That way the plots are somewhat interactive, e.g., allow for drill-down for more information without the viewer needing to install R.

Much of the tabular output produced here was created using html methods, which are especially easy to implement with rmarkdown and make for output that can be directly opened using word processors. Jump to Computing Environment for a list of packages used here, and their version numbers.

Rmarkdown themes such as bookdown and rmdformats::readthedown (the latter is used here) allow one to number figures and the symbolically reference them. The knitrSet capfile='captions.md' argument below capitalizes on this to make it easy for the user to insert a table of figures anywhere in the report. Here we place it at the end. A caption listed in the table of figures is the short caption (scap= or fig.scap in the chunk header) if there is one, otherwise the long caption is used. If neither caption is used, that figure will not appear in the table of figures.

The full script for this report may be found here.

2 Setup

require(Hmisc)

knitrSet(lang='markdown', h=4.5, fig.path='png/', fig.align='left',
         capfile='captions.md')  # + sometimes ,cache=TRUE
# knitrSet redirects all messages to messages.txt
options(grType='plotly') # for certain graphics functions
mu <- markupSpecs$html   # markupSpecs is in Hmisc
cap  <- mu$cap           # function to output html caption
lcap <- mu$lcap          # for continuation for long caption
# These last 2 functions are used by the putHfig function in Hmisc
cat('', file='captions.md')   # initialize table of short captions

The following (r mu$styles()) defines HTML styles and javascript functions, such as ffig, smg and the function for expanding and collapsing text as done by the expcoll function.

Here is an example using expcoll. Click on the down arrow to expand; it turns to an up arrow which can be clicked to contract.

3 Fetching Data, Modifying Variables, and Printing Data Dictionary

The getHdata function is used to fetch a dataset from the Vanderbilt DataSets web site hbiostat.org/data. The upData function is used to

• create a new variable from an old one
• add labels to 2 variables
• add units to the new variable
• remove the old variable
• automatically move units of measurements from parenthetical expressions in labels to separate units attributed used by Hmisc and rms functions for table making and graphics

contents is used to print a data dictionary, run through an html method for nicer output. Information about the data source may be found here. Click on the number of levels in the contents table to jump to the value labels for the variable.

getHdata(pbc)

# Have upData move units from labels to separate attribute
pbc <- upData(pbc,
              fu.yrs = fu.days / 365.25,
              labels = c(fu.yrs = 'Follow-up Time',
                         status = 'Death or Liver Transplantation'),
              units = c(fu.yrs = 'year'),
              drop  = 'fu.days',
              moveUnits=TRUE, html=TRUE)

Input object size:   80952 bytes;    19 variables    418 observations
 Label for bili changed from Serum Bilirubin (mg/dl) to Serum Bilirubin 
    units set to mg/dl 
 Label for albumin changed from Albumin (gm/dl) to Albumin 
    units set to gm/dl 
 Label for protime changed from Prothrombin Time (sec.) to Prothrombin Time 
    units set to sec. 
 Label for alk.phos changed from Alkaline Phosphatase (U/liter) to Alkaline Phosphatase 
    units set to U/liter 
 Label for sgot changed from SGOT (U/ml) to SGOT 
    units set to U/ml 
 Label for chol changed from Cholesterol (mg/dl) to Cholesterol 
    units set to mg/dl 
 Label for trig changed from Triglycerides (mg/dl) to Triglycerides 
    units set to mg/dl 
 Label for platelet changed from Platelets (per cm^3/1000) to Platelets 
    units set to per cm^3/1000 
 Label for copper changed from Urine Copper (ug/day) to Urine Copper 
    units set to ug/day 
 Added variable     fu.yrs
 Dropped variable   fu.days
 New object size:   84744 bytes;    19 variables    418 observations

# The following can also be done by running this command
# to put the results in a new browser tab:
# getHdata(pbc, 'contents')
html(contents(pbc), maxlevels=10, levelType='table')

Data frame:pbc

4 Descriptive Statistics Without Stratification

The html method is used for the describe function, and the output is put in a scrollable box. Other than for the overall title and variable names and labels, the output size used here is 80 (0.8 × the usual font size¹). But the graphical display of the descriptives statistics that follows this is probably better.

# did have results='asis' above
d <- describe(pbc)
html(d, size=80, scroll=TRUE)

pbc

19 Variables   418 Observations

---

bili: Serum Bilirubin mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
418	0	98	0.998	3.221	3.742	0.50	0.60	0.80	1.40	3.40	8.03	14.00

lowest : 0.3 0.4 0.5 0.6 0.7 , highest: 21.6 22.5 24.5 25.5 28.0

---

albumin: Albumin gm/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
418	0	154	1	3.497	0.473	2.750	2.967	3.243	3.530	3.770	4.010	4.141

lowest : 1.96 2.10 2.23 2.27 2.31 , highest: 4.30 4.38 4.40 4.52 4.64

---

stage: Histologic Stage, Ludwig Criteria

n	missing	distinct	Info	Mean	Gmd
412	6	4	0.893	3.024	0.9519

 Value          1     2     3     4
 Frequency     21    92   155   144
 Proportion 0.051 0.223 0.376 0.350
 

---

protime: Prothrombin Time sec.

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
416	2	48	0.998	10.73	1.029	9.60	9.80	10.00	10.60	11.10	12.00	12.45

lowest : 9.0 9.1 9.2 9.3 9.4 , highest: 13.8 14.1 15.2 17.1 18.0

---

sex

n	missing	distinct
418	0	2

 Value        male female
 Frequency      44    374
 Proportion  0.105  0.895
 

---

age: Age

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
418	0	345	1	50.74	11.96	33.84	36.37	42.83	51.00	58.24	64.30	67.92

lowest : 26.27789 28.88433 29.55510 30.27515 30.57358 , highest: 74.52430 75.00000 75.01164 76.70910 78.43943

---

spiders

n	missing	distinct
312	106	2

 Value       absent present
 Frequency      222      90
 Proportion   0.712   0.288
 

---

hepatom

n	missing	distinct
312	106	2

 Value       absent present
 Frequency      152     160
 Proportion   0.487   0.513
 

---

ascites

n	missing	distinct
312	106	2

 Value       absent present
 Frequency      288      24
 Proportion   0.923   0.077
 

---

alk.phos: Alkaline Phosphatase U/liter

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
312	106	295	1	1983	1760	599.6	663.0	871.5	1259.0	1980.0	3826.4	6669.9

lowest : 289.0 310.0 369.0 377.0 414.0 , highest: 11046.6 11320.2 11552.0 12258.8 13862.4

---

sgot: SGOT U/ml

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
312	106	179	1	122.6	60.45	54.25	60.45	80.60	114.70	151.90	196.47	219.25

lowest : 26.35 28.38 41.85 43.40 45.00 , highest: 288.00 299.15 328.60 338.00 457.25

---

chol: Cholesterol mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
284	134	201	1	369.5	194.5	188.4	213.6	249.5	309.5	400.0	560.8	674.0

lowest : 120 127 132 149 151 , highest: 1336 1480 1600 1712 1775

---

trig: Triglycerides mg/dl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
282	136	146	1	124.7	64.07	56.00	63.10	84.25	108.00	151.00	195.00	230.95

lowest : 33 44 46 49 50 , highest: 319 322 382 432 598

---

platelet: Platelets per cm³/1000

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
308	110	210	1	261.9	107.8	117.7	139.7	199.8	257.0	322.5	386.5	430.6

lowest : 62 70 71 79 80 , highest: 493 514 518 539 563

---

drug

n	missing	distinct
418	0	3

 Value      D-penicillamine         placebo  not randomized
 Frequency              154             158             106
 Proportion           0.368           0.378           0.254
 

---

status: Death or Liver Transplantation

n	missing	distinct	Info	Sum	Mean	Gmd
418	0	2	0.71	161	0.3852	0.4748

---

edema

n	missing	distinct
418	0	3

 Value                            no edema     edema, no diuretic therapy
 Frequency                             354                             44
 Proportion                          0.847                          0.105
                                          
 Value      edema despite diuretic therapy
 Frequency                              20
 Proportion                          0.048
 

---

copper: Urine Copper ug/day

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
310	108	158	1	97.65	83.16	17.45	24.00	41.25	73.00	123.00	208.10	249.20

lowest : 4 9 10 11 12 , highest: 412 444 464 558 588

---

fu.yrs: Follow-up Time year

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
418	0	399	1	5.251	3.429	0.671	1.661	2.992	4.736	7.155	9.649	11.063

lowest :	0.1122519	0.1177276	0.1396304	0.1943874	0.2108145
highest:	12.3203285	12.3449692	12.3832991	12.4736482	13.1279945

---

# prList is in Hmisc; useful for plotting or printing a list of objects
# Can just use plot(d) if don't care about the mess
# If using html output these 2 images would not be rendered no matter what
p <- plot(d)
# The option htmlfig=2 causes markupSpecs$html$cap() to be used to
# HTML-typeset as a figure caption and to put the sub-sub section
# marker ### in front of the caption.  htmlfig is the only reason
# results='asis' was needed in the chunk header
# We define a long caption for one of the plots, which does not appear
# in the table of contents
# prList works for html notebooks but not html documents
# prList(p, lcap=c('', 'These are spike histograms'), htmlfig=2)

You can also re-form multiple plotly graphs into a single HTML object. If you want to have total control over long and short figure captions, use the Hmisc putHfig function to render the result, with a caption and a short caption for the table of contents. That would have fixed a problem with the chunk below: when plotly graphics are not rendered in the usual way, the figure is not numbered and no caption appears.

htmltools::tagList(p)    # lapply(p, plotly::as.widget)

You can also create figure captions outside of R code by using the smg, fcap HTML tags defined in markupSpecs. The long caption not appearing in the table of contents will be in a separate line without ###.

5 Stratified Descriptive Statistics

Produce stratified quantiles, means/SD, and proportions by treatment group. Plot the results before rendering as an advanced html table:

• categorical variables: a single dot chart
• continuous variables: a series of extended box plots

s <- summaryM(bili + albumin + stage + protime + sex + age + spiders +
              alk.phos + sgot + chol ~ drug, data=pbc,
                            overall=FALSE, test=TRUE)
plot(s, which='categorical')

To construct the caption outside of the code chunk use e.g. ### r cap(‘Proportions and’, mu$chisq(), ‘tests for categorical variables’) where a backtick is placed before r and after the last ).

plot(s, which='continuous', vars=1 : 4)

plot(s, which='continuous', vars=5 : 7)

html(s, caption='Baseline characteristics by randomized treatment',
     exclude1=TRUE, npct='both', digits=3, middle.bold=TRUE,
     prmsd=TRUE, brmsd=TRUE, msdsize=mu$smaller2)

with(pbc, histboxp(x=sgot, group=drug, sd=TRUE))

The following is a better way to display proportions, for categorical variables. If computing marginal statistics by running the dataset through the Hmisc addMarginal function, the plot method with options(grType='plotly') is especially useful.

pbcm <- addMarginal(pbc, drug)
s <- summaryP(stage + sex + spiders ~ drug, data=pbc)
# putHcap('Proportions stratified by treatment')
plot(s, groups='drug')

s <- summaryP(stage + sex + spiders ~ drug, data=pbcm)
plot(s, marginVal='All', marginLabel='All Treatment Groups')

6 Better Demonstration of Boxplot Replacement

getHdata(support2)
with(support2, histboxp(x=meanbp, group=dzgroup, sd=TRUE, bins=200))

7 Changing Size of Figure Captions

As explained here, one can place captions under figures using ordinary knitr capabilities, and one can change the size of captions. The following example defines a CSS style to make captions small (here 0.6em), and produces a plot with a caption. Unlike using putHfig captions given in knitr chunks do not also appear in the table of contents.

# Note: in the chunk header cap is an alias for fig.cap defined by knitrSet
plot(runif(10))

Figure 7.1: This is a simple figure caption

8 Computing Environment²

 R version 4.0.0 (2020-04-24)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Pop!_OS 20.04 LTS
 
 Matrix products: default
 BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
 
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
 [1] Hmisc_4.4-1     ggplot2_3.3.0   Formula_1.2-3   survival_3.1-12
 [5] lattice_0.20-41
 

R Core Team (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.

9 Bibliographic File Managament

# Note: mu was defined in an earlier code chunk
# Only need to install .csl file once.
mu$installcsl(rec=TRUE)   # get list of recommended styles
mu$installcsl()     # web search of styles meeting your criteria
# Install a .csl file to your project directory:
mu$installcsl('american-medical-association')

10 Table of Figures

Note: the hidden R command that rendered the table of figures (including short captions) was markupSpecs$markdown$tof().