Tables of Descriptive Statistics in HTML

Create HTML tables of descriptive statistics, as one would expect to see as the first table (i.e. "Table 1") in a medical/epidemiological journal article.

An R package for generating tables of descriptive statistics in HTML.

Installation

To install from CRAN:

install.packages("table1")

To install the latest development version directly from GitHub:

require(devtools)
devtools::install_github("benjaminrich/table1")

Getting Started

An introduction to the package with examples is provided in the vignette.

Example

For this example, we will use data from the Mayo Clinic trial in primary biliary cirrhosis (PBC) of the liver found in the survival package.

require(table1)
require(survival)
 
dat <- subset(survival::pbc, !is.na(trt))  # Exclude subjects not randomized
 
dat$trt     <- factor(dat$trt, levels=1:2, labels=c("D-penicillamine", "Placebo"))
dat$sex     <- factor(dat$sex, levels=c("m", "f"), labels=c("Male", "Female"))
dat$stage   <- factor(dat$stage, levels=1:4, labels=paste("Stage", 1:4))
dat$edema   <- factor(dat$edema, levels=c(0, 0.5, 1),
                      labels=c("No edema",
                               "Untreated or successfully treated",
                               "Edema despite diuretic therapy"))
dat$spiders <- as.logical(dat$spiders)
dat$hepato  <- as.logical(dat$hepato)
dat$ascites <- as.logical(dat$ascites)
 
label(dat$age)      <- "Age (y)"
label(dat$sex)      <- "Sex"
label(dat$stage)    <- "Histologic stage of disease"
label(dat$edema)    <- "Edema status"
label(dat$spiders)  <- "Blood vessel malformations in the skin"
label(dat$hepato)   <- "Presence of hepatomegaly or enlarged liver"
label(dat$ascites)  <- "Presence of ascites"
label(dat$platelet) <- "Platelet count (&times; 10<sup>9</sup> per liter)"
label(dat$protime)  <- "Standardised blood clotting time"
label(dat$albumin)  <- "Serum albumin (g/dL)"
label(dat$alk.phos) <- "Alkaline phosphotase (U/L)"
label(dat$ast)      <- "Aspartate aminotransferase (U/mL)"
label(dat$bili)     <- "Serum bilirubin (mg/dL)"
label(dat$chol)     <- "Serum cholesterol (mg/dL)"
label(dat$copper)   <- "Urine copper (&mu;g/day)"
label(dat$trig)     <- "Triglycerides (mg/dL)"
 
table1(~ age + sex + stage + edema + spiders + hepato + ascites +
         platelet + protime + albumin + alk.phos + ast + bili + chol +
         copper + trig | trt, data=dat)