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index.Rmd
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---
md_document:
variant: markdown_github
title: "compareGroups"
output: md_document
always_allow_html: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning=FALSE, message=FALSE, comment="")
library(knitr)
```
# **compareGroups** <img src="man/figures/logo.png" align="right" width="120px"/>
**_package to create descriptive tables_**
[](https://cran.r-project.org/package=compareGroups)  
## Overview
**compareGroups** is an R package available on CRAN which performs descriptive tables displaying means, standard deviation, quantiles or frequencies of several variables. Also, p-value to test equality between groups is computed using the appropiate test. <br>
With a very simple code, nice, compact and ready-to-publish descriptives table are displayed on R console. They can also be exported to different formats, such as Word, Excel, PDF or inserted in a R-Sweave or R-markdown document.<br>
You will find an extensive manual describing all **compareGropus** capabilities with real examples in the [vignette](./articles/compareGroups_vignette.html).<br>
Also, **compareGroups** package has been published in Journal of Statistical Software [Subirana et al, 2014] (https://www.jstatsoft.org/v57/i12/).
*********
## Who we are
<img style="float:right; padding:10px" width="25%" src="./man/figures/prbb.jpg" />
**`compareGroups`** is developed and maintained by Isaac Subirana, Hector Sanz, Joan Vila and collaborators at the cardiovascular epidemiology research unit (URLEC), located at [Barcelona Biomedical Research Park (PRBB)](http://www.prbb.org/) .
<br><br><br><br><br>
<img style="float:left; padding:10px" width="20%" src="./man/figures/logo_regicor.jpg" />
As the driving force behind the [REGICOR study](https://www.regicor.org), URLEC has extensive experience in statistical epidemiology, and is a national reference centre for research into cardiovascular diseases and their risk factors.
<br><br>
*********
## Gets started
Install the package from CRAN
```{r, eval=FALSE}
install.packages("compareGroups")
```
or the lattest version from Github
```{r, eval=FALSE}
library(devtools)
devtools::install_github("isubirana/compareGroups")
```
### Building the descriptive table
```{r}
library(compareGroups)
data(regicor)
tab <- descrTable(year ~ . -id , regicor, hide.no = "no",
method=c(triglyc=2, tocv=2, todeath=2), sd.type = 3)
export2md(tab, header.background = "black", header.color = "white",
caption = "Summary by intervention group")
```
### Stratified table
<div class="small">
```{r,size=6}
tabstrat <- strataTable(update(tab, . ~ . -sex), "sex")
export2md(tabstrat, header.background = "black", header.color = "white", size=9)
```
</div>
### Visual exploration
```{r, echo=FALSE, fig.show="hide"}
plot(tab["sex"], "./man/figures/var1", type="png")
plot(tab["age"], "./man/figures/var1", type="png")
```
| | |
|:----------:|:------------:|
| `plot(tab["sex"])` | `plot(tab["age"])` |
|  |  |
### Computing Odds Ratios
```{r}
data(SNPs)
tabor <- descrTable(casco ~ .-id, SNPs, show.ratio=TRUE, show.p.overall=FALSE)
export2md(tabor[1:4])
```
### Computing Hazard Ratios
```{r}
library(survival)
regicor$tcv <- Surv(regicor$tocv, regicor$cv=="Yes")
tabhr <- descrTable(tcv ~ .-id-cv-tocv, regicor,
method=c(triglyc=2, tocv=2, todeath=2),
hide.no="no", ref.no="no",
show.ratio=TRUE, show.p.overall=FALSE)
export2md(tabhr[1:10], header.label=c("p.ratio"="p-value"),
caption="Descriptives by cardiovascular event")
```
### Web-based User Interface
For those not familiar to R syntax, a Web User Interface (**WUI**) has been implemented using [Shiny](https://shiny.rstudio.com/) tools, which can be used off line by typing `cGroupsWUI()` after having `compareGroups` package installed and loaded, or remotely just accessing the application hosted in a [shinyapp.io server](https://isubirana.shinyapps.io/compareGroups/).
