88 lines
3.0 KiB
Plaintext
88 lines
3.0 KiB
Plaintext
% Usage: knitr an
|
|
\documentclass{article}
|
|
\usepackage{relsize,setspace} % used by latex(describe( ))
|
|
\usepackage{needspace}
|
|
\usepackage{longtable,epic} % used by print(..., latex=TRUE)
|
|
\usepackage{url} % used in bibliography
|
|
\usepackage[superscript,nomove]{cite} % use if \cite is used and superscripts wanted
|
|
% Remove nomove if you want superscripts after punctuation in citations
|
|
\usepackage{lscape} % for landscape mode tables
|
|
\textwidth 6.75in % set dimensions before fancyhdr
|
|
\textheight 9.25in
|
|
\topmargin -.875in
|
|
\oddsidemargin -.125in
|
|
\evensidemargin -.125in
|
|
\usepackage{fancyhdr} % this and next line are for fancy headers/footers
|
|
\pagestyle{fancy}
|
|
\newcommand{\bc}{\begin{center}} % abbreviate
|
|
\newcommand{\ec}{\end{center}}
|
|
\newcommand{\code}[1]{{\smaller\texttt{#1}}}
|
|
\newcommand{\R}{{\normalfont\textsf{R}}{}}
|
|
\newcommand{\vr}[1]{\texttt{#1}}
|
|
\newcommand{\mc}[2]{\multicolumn{#1}{c}{#2}}
|
|
\title{Analysis of Race and Severe Aortic Stenosis}
|
|
\author{Frank Harrell\\\smaller Department of Biostatistics\\\smaller Vanderbilt University School of Medicine}
|
|
\begin{document}
|
|
\maketitle
|
|
\tableofcontents
|
|
|
|
<<echo=FALSE>>=
|
|
require(rms)
|
|
@
|
|
|
|
\section{Univariable Descriptive Statistics}
|
|
|
|
<<describe,results='asis'>>=
|
|
Load(ras)
|
|
ras <-
|
|
within(ras, {
|
|
label(age) <- 'Age'
|
|
diabetes <- ifelse(diabetes.after.review=='No', 0,
|
|
ifelse(diabetes.after.review=='Yes', 1,
|
|
ifelse(diabetes.search=='No', 0,
|
|
ifelse(diabetes.search=='Yes', 1,
|
|
NA))))
|
|
htn <- ifelse(htn.after.review=='No', 0,
|
|
ifelse(htn.after.review=='Yes', 1,
|
|
ifelse(htn.search=='No', 0,
|
|
ifelse(htn.search=='Yes', 1,
|
|
NA))))
|
|
dialysis <- ifelse(dialysis.after.review=='No', 0,
|
|
ifelse(dialysis.after.review=='Yes', 1,
|
|
ifelse(dialysis.search=='No', 0,
|
|
NA)))
|
|
cad <- ifelse(cad.after.review=='No', 0,
|
|
ifelse(cad.after.review=='Yes', 1,
|
|
ifelse(cad.search=='No', 0,
|
|
ifelse(cad.search=='Yes', 1,
|
|
NA))))
|
|
gender <- factor(ifelse(gender=='Female', 'Female',
|
|
ifelse(gender=='Male', 'Male',
|
|
NA)))
|
|
})
|
|
latex(describe(ras), file='')
|
|
@
|
|
|
|
\section{Missing Data}
|
|
Let's look at patterns of missing values, especially which variables
|
|
are missing on the same patients.
|
|
|
|
<<naclus,top=2>>=
|
|
r <- subset(ras, select=c(gender,race,age,bmi,ldl,diabetes,htn,dialysis,
|
|
cad,statin,sasr,sas.etiology,creatinine))
|
|
dd <- datadist(r)
|
|
n <- naclus(subset(r, select=-sas.etiology))
|
|
naplot(n, which='na per obs')
|
|
@
|
|
|
|
<<naplot,top=2,rt=1,ps=8>>=
|
|
options(datadist='dd')
|
|
naplot(n, which='mean na')
|
|
@
|
|
|
|
<<naplot2>>=
|
|
plot(n)
|
|
@
|
|
|
|
\end{document}
|