Global Style for Rmd Example

Purpose

When presenting tables in an HTML Rmarkdown report, it is more common to have all tables styled in the same manner. This is an example of all tables having the same style, with a few overridden styles.

This package is meant to implement the concept of a grammar of tables. It allows for a simple formula expression and a data frame to create a rich summary table in a variety of formats. It is designed for extensibility at each step of the process, so that one is not limited by the authors choice of table statistics, output format. The grammar however is an integral part of the package, and as such is not modifiable.

Supposed that further in addition to the lancet style one really wanted a shade of cyan to make the document pop. This was added to the header of this document to make all this magic happen:

 <style type="text/css">
 \```{r, results='asis'}
 cat(custom_css("lancet.css"))
 ```
 .figbody thead
 {
   background: #aaffff !important;
 }
 .figbody tbody .odd
 {
   background: #aaffff !important;
 }
 </style>

Here’s an example similary to summaryM from Hmisc to get us started:

Table 1

html5(tangram("drug ~ bili[2] + albumin + stage::Categorical + protime + sex + age + spiders", pbc),
      fragment=TRUE, caption = "Hmisc::PBC", id="tbl2")

Hmisc::PBC

	N	D-penicillamine	placebo	not randomized	Test Statistic
		154	158	106
Serum Bilirubin	418	0.701.303.60	0.801.403.22	0.701.403.12	F2,415 = 0.03,P = 0.9721
Albumin	418	3.343.543.78	3.213.563.83	3.123.473.73	F2,415 = 2.13,P = 0.1201
Histologic Stage, Ludwig Criteria	412				χ2 6 = 5.33,P = 0.5022
1		0 . 0262.597 4154	0 . 0767.595 12158	0 . 0474.717 5106
2		0 . 20820.779 32154	0 . 22222.152 35158	0 . 23623.585 25106
3		0 . 41641.558 64154	0 . 35435.443 56158	0 . 33033.019 35106
4		0 . 35135.065 54154	0 . 34834.810 55158	0 . 33033.019 35106
Prothrombin Time	416	10.010.611.4	10.010.611.0	10.110.611.0	F2,413 = 0.23,P = 0.7951
sex : female	418	0 . 90390.260139154	0 . 86786.709137158	0 . 92592.453 98106	χ2 2 = 2.38,P = 0.3042
Age	418	41.448.155.8	42.951.959.0	46.053.061.1	F2,415 = 6.10,P = 0.0021
spiders : present	312	0 . 29229.221 45154	0 . 28528.481 45158		χ2 1 = 0.02,P = 0.8852

N is the number of non-missing value. ¹Kruskal-Wallis test. ²Pearson test

Table 2

x <- round(rnorm(375, 79, 10))
y <- round(rnorm(375, 80,  9))
y[rbinom(375, 1, prob=0.05)] <- NA
attr(x, "label") <- "Global score, 3m"
attr(y, "label") <- "Global score, 12m"
html5(tangram(1 ~ x+y,
                    data.frame(x=x, y=y),
                    after=hmisc_intercept_cleanup),
      fragment=TRUE, caption="Intercept", id="tbl5")

Intercept

	N	All
Global score, 3m	375	727986
Global score, 12m	374	748085

N is the number of non-missing value. ¹Kruskal-Wallis test. ²Pearson test