My R Functions Create time intervals data for time varying covariates in survival analysis When several time varying covariates present in survival analysis, creating ...
Changes to document since 1 August 1997 1997 Added section 3.1.1 Adjustments to Variables after Input 15 Aug 97: Added section 4.1.7 Accessing Data Frames in ...
Analysis Of Observer Variability See https://github.com/harrelfe/rscripts files named observerVariability* To load the function definitions into an RStudio session ...
A back to back barplot from scratch This example is shown in Figure 3.30 in Paul Murrell's R Graphics book. Also, be aware of the Hmisc package's histbackback() function ...
General Handouts and Reference Material on Biostatistical Modeling * Syllabus from a course on Biostatistical Modeling (updated 9Jan03; click here for a pdf file ...
Bios 311 Syllabus The syllabus will be updated weekly. Thursday, August 21 Learning Objectives (LOs) * Get a sense of the class; determine if it is a good fit ...
BIOS 330 Assignment Zero Your assignment is to install and configure R and RStudio to produce an html file from the reproducible knitr document below. 1 Install ...
Biostatistician Responsibilities Requirements for Statistical Reports All statistical reports produced by biostatisticians must be reproducible in that the report ...
On September 22, we will have a class discussing data visualization in biomedical research with guest lecturer, Meridith Blevins. We will review a basic recipe for ...
Software and Example Code for Bootstrap Confidence Intervals for Means and Differences in Means The following uses the simple nonparametric bootstrap percentile approach ...
Adding a 'broken axis' to a plot We've all seen a plot with a 'broken axis' e.g., the axis goes from 0 to 9 in units of 1, then shows a 'break' (//) and then continues ...
A plot that illustrates the effect of categorizing continuous covariates in a logistic regression model The idea behind this problem is the fact that fitting a categorized ...
Main.JoAnnAlvarez 09 Nov 2012 Vanderbilt Center for Surgical Quality Outcomes Research Projects on their own page * CeasarData * CeasarProjTxVars * CeasarProject ...
Department of Biostatistics Seminar/Workshop Series Maintaining R Cole Beck Computer Systems Analyst III, Department of Biostatistics Vanderbilt University School ...
Possible Collaborative Editing Workflows 1 Statistician puts document template online and shares with collaborators 1 Statistical analysis plan put in a special ...
Journal Club for Analysis of Complex Datasets Sebastiani et al, Nature Genetics 37:435;2005: Genetic dissection and prognostic modeling of overt stroke in sickle ...
Completed IT Tasks As the ComputingTodo list gets too long we will move some of the completed tasks here. * Develop plan to bring up new server * Bring up new ...
*NOTE*: This page is superseded by https://hbiostat.org/rms/full BIOS 330: Regression Modeling Strategies Frank E. Harrell, Jr. f.harrell@vanderbilt.edu Professor ...
Preparing data for survival analysis Our original data file, temp.csv, has repeated glucose values for each subject (DeID) at various times points (Time) from both ...
Rafe's Dataset Reshape Problem Rafe posed the following problem. The original data set had three measurements for each 'specimen' (spec). The goal was was to turn ...
Procedures for Preparing Datasets for Analysis and for Transmission to the Department of Biostatistics Data Sharing Data must be in a rectangular format with one ...
The generic datadensity() function The datadensity() function is a generic functions used to show data densities in more complex situations. There are two class specific ...
The Design Package The Design package is now obsolete. R users must use the rms package instead * Overview of the Design Library * Online Help Documentation ...
Survival analysis with the survival and Design packages The following are some examples of how to perform survival analysis using the survival and Design packages ...
A function that returns the desired output from another function Often, you do not want to return all of the default output from a specific function. The following ...
General Information about LaTeX and other Document Processing Tools * Comprehensive TeX Archive Network * Online LaTeX Documentation FAQ Schneider's Resources ...
Useful Stuff in R: Inserting Latex Tables into Microsoft Word Theresa A Scott, M.S. Biostatistician II, Department of Biostatistics Vanderbilt University School ...
Presentations by Frank E Harrell Jr Note: Slides from more recent talks are contained in the Biostatistics for Biomedical Research handouts available at ClinStat The ...
Generating multiple regression models in a for loop Often, we wish to generate multiple regression models that are all similar, but all different. For example, all ...
Frank E Harrell Jr, PhDProfessor of BiostatisticsFounding Chair E mail: f.harrell@vumc.org Phone: 615.322.2001 Fax: 615.343.4924 Vanderbilt University ...
Department of Biostatistics Seminar/Workshop Series Using R, Rmarkdown, RStudio, knitr, and HTML for the Next Generation of Reproducible Statistical Reports Frank ...
Department of Biostatistics Seminar/Workshop Series A New Model for Reproducible Clinical Trial Statistical Reporting Frank Harrell, PhD Professor and Chair, Department ...
Department of Biostatistics Seminar/Workshop Series Teaching R to Non Statisticians Frank E. Harrell, Jr., Ph.D Professor and Chairman, Department of Biostatistics ...
Recommendations, Analyses, and Data for Health Services Research, Diagnosis, and Prognosis Clinic Archive Current Notes 23Dec13 Heidi Silver, Director, Vanderbilt ...
German Breast Cancer Dataset This dataset is courtesy of Patrick Royston and Willi Saurbrei. It is the official version of a dataset from the website for their book ...
Statistical Graphics for Exploring Data, Presenting Information, and Understanding Statistical Models Scripts Graphical methods are being increasingly used for exploratory ...
New Functions in the R Hmisc Package summaryM In place of summary(group ~ a b c, method='reverse') (which calls summary.formula) use summaryM(a b c ~ group ...
Using the Hmisc package's summary.formula() function This following is an illustration of the many uses of the Hmisc package's summary.formula() function. The sample ...
Hmisc Todo List Unimplemented featuredone Split summary.formula into three functions summary.formula.response, summary.formula.cross, and summary.formula.reverse ...
Department of Biostatistics IT Team Skills and Experience The Department of Biostatistics boasts a strong IT support team consisting of 7 programmers and analysts ...
Statistics for Biomedical Research Discussion Board Go to WelcomeGuest to learn about twiki. You will see a place to click to go to the TWikiRegistration page to ...
JoAnn Alvarez, MA Biostatistician III E mail: joannmalvarez #64;gmail.com Office: 490 Preston Research Building My CV and resume (word file) Interests ...
Welcome to the Department of Biostatistics! Here are some useful resources for you to learn about R, Sweave/LaTeX, longitudinal data analysis, survival analysis and ...
How to use knitr knitr html report Template Introduction knitr is a newer way to create reproducible documents with R and LaTeX. It has several advantages over ...
knitr HTML Template Example html Document Reproducible Research Using knitr in conjunction with Rmarkdown and RStudio one can produce nice html reports and material ...
How to Obtain Updates to Individual Functions in R Packages Between Releases This page shows you how to read in source code to override functions in a package. The ...
Using the layout() function to generate multiple plots The par() function's mfrow= argument is often used to generate multiple plots on one page. However, as you ...
Software in the Hmisc and Design libraries is Copyright (C) 1991 2004 by Frank E Harrell Jr This is free software; you can redistribute it and/or modify it under ...
Examples of Dealing with Multiple Data Frames Stored in a List Common Application: Used sasxport.get to import multiple SAS datasets into one S list object a a ...
Reweighted Mahalanobis Distance Matching in Observational Studies and Randomized Trials Matched Randomization R Package nbpMatching The current version of the R package ...
Using the fill.missing() function The function fill.missing() is automatically called by gendistance(), so the user will often be able to skip calling it directly ...
Miscellaneous Examples of S Code for Spline Fits Note: These examples assume that the Hmisc and Design packages are attached. * Linear Spline Basis Functions and ...
Final Project Analysis File By now you must have completed importing, annotating, and recoding the data you will use in your final project, and turn in an html report ...
MSCI Biostatistics II Course Schedule February 2024 ul{ margin: 0; } Key: A = Whitlock and Schluter (text) B = Biostatistics for Biomedical Research (handout) ...
Plot the Kaplan Meier (K M) curves from two different K M calculations on the same plot The motivating data set for this example is the Rtestdata.sav SPSS data set ...
Converting dates of the form 'mddyy', 'mddyyyy', 'mmddyy', or 'mmddyyyy' to the form 'YYYY MM DD' Problem: A data file contains multiple date columns, whose format ...
Omics Data Clinic Notes and Analyses 2023 December 12 Nicole Malofsky, Biomedical Engineering Determining TB bacteria drug susceptibility is essential to match TB ...
psfrag: Inserting LaTeX Code Inside Graphics There are many approaches for inserting LaTeX equations, symbols, tables, and other output inside postscript and pdf graphics ...
Binary Response, Random Sample of 1000 Patients from the SUPPORT Study, Missing Data Analyze the support dataset available at http://biostat.mc.vanderbilt.edu/twiki ...
Sudden Death Associated with Treatment for Hypertension Original Article Zipped SPSS Save File FrankHarrell's Critique of the Article Analyze the MRC dataset ...
Graphics for Clinical Trials Frank E Harrell JrVanderbilt Department of BiostatisticsOffice of Biostatistics FDA CDER DIA/FDA Statistics Forum, North Bethesda MD ...
The R Clinic The R Clinic is a monthly clinic to assist with learning R and troubleshooting difficult programming questions. You might also be interested in the ...
Configuring R Using html Help Facility Linux users of R version 2.10 and later may want to take advantage of the new dynamic html rendering of help pages. The konqueror ...
Making Dot Charts in R Rachel Hayes brought a problem to R Clinic on 23Oct08. The Hmisc Dotplot function can produce multi panel dot charts with error bars while ...
Using the Hmisc plsmo Function for Plotting Nonparametric loess Trend lines R Clinic 23Oct08 The following examples use a new Titanic passenger and group survival ...
Methods of Retrieving Datasets Most of the datasets on this site are in the S dumpdata format (file suffix of .sdd) and R compressed save() file format (suffix of ...
An R function for redcap exports through the API Here is an R function that exports data from redcap through the API within R. This function, along with new options ...
Steps for Creating Analysis Files Importing SAS Data Library 1 Store SAS macro exportlib.sas in ~/sas/exportlib.sas 1 In the project area for the current report ...
Methods of Retrieving Datasets Most of the datasets on this site are in the S dumpdata format (file suffix of .sdd) and R compressed save() file format (suffix of ...
Converting dates of the form 'mddyy' or 'mddyyyy' or 'mmddyy' or 'mmddyyyy' to the form 'YYYY MM DD' Theresa A Scott, M.S. Biostatistician II, Department of Biostatistics ...
*NOTE*: This page has been replaced by more up to date material at https://hbiostat.org/rms REGRESSION MODELING STRATEGIES Semester Course Short Course Software ...
Regression Modeling Strategies With Applications to Linear Models, Logistic and Ordinal Regression, and Survival Analysis Major Changes Since The First Edition ...
Predictive Accuracy and Model Validation Discussion Board How to validate the predictive accuracy of an ordinal logistic regrsesion model? Colin Robertson (colinr23 ...
rreport Package rreport is an R package that produces statistical reports in LaTeX for clinical trials. It is especially useful for producing interim reports for ...
Overall Miscellaneous Usage Instructions for Our R packages To load the packages, use one of these commands: library(Hmisc) # if using Hmisc without using Design ...
How to export data from SAS and import to R Here are a few ways to get data from SAS to R with a focus on preserving metadata (labels and formats/factor levels). ...
This should be merged with the existing wiki page SASexportHowto. A Way to Import SAS Data to R With All the Formats and Labels If you have a SAS .sas7bdat file with ...
Conversion of SAS Code to Compute Multiple Stratified Statistics on More than One Analysis Variable Greg Adkison gadkison #64;email.wcu.edu writes: Say for example ...
S Graphics Hints and Tricks * Graphics Setup Templates * Adding panel numbers in margins of multi panel graphs * Embedding fonts for certain journal submissions ...
Software Mirrors Ubuntu To use our Ubuntu repository, add the following to (or replace) your /etc/apt/sources.list as root: deb http://debian.mc.vanderbilt.edu/ubuntu ...
Plot the odds ratios (ORs) for a specific covariate from different logistic regression models Perhaps you are interested in the effect of a specific covariate from ...
cp up ~/S/Hmisc/S.dll Hmisc.windows.dll cp up ~/S/Design/S.dll Design.windows.dll cd /usr/local/splus/library rm f ~/biostat/s/library/splus6/*intel* zip r ~/biostat ...
R Code and Examples from Class Introduction R is an powerful statistics package that is also capable of creating publication quality graphics. The experienced user ...
Statistical Computing and Graphics Concepts to Master 1 Difference between a functional language with live access to data and a procedural or macro language ...
S for Statistical Data Analysis and Graphics Frank E. Harrell, Jr. (f.harrell@vanderbilt.edu) Professor of Biostatistics and Statistics Chair, Department of Biostatistics ...
Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data Reproducible Research ...
The Statistical Computing Series The Statistical Computing Series is a monthly event for learning various aspects of modern statistical computing from practitioners ...
Converting Documents Produced by Sweave and knitr Converting from LaTeX to html The recommended format for statistical reports to send to collaborators is pdf produced ...
Main.JoAnnAlvarez 20 May 2010 Suppose you are using R to conduct your analysis in conjunction with Sweave to get a nice looking report. Suppose further that you are ...
Sweave and knitr Templates NOTE: SUPERCEDED by knitr and LaTeX Styles knitrl and spaper; See GitHub rlatex Project Using LaTeX Style Sweavel /template3.pdf ...
Incorporate the third contrast of a three level categorical predictor into the odds ratio summary plot of a logistic regression model In any regression model, by default ...
Data and Analysis for Clinical and Health Research Clinic Notes (2021) 2021 December 09 Marianna LaNoue, VUSN * I have been wrestling with the issue of statistical ...
1 Upgrade to R 1.9 (FH and SE) 1 Convert all R functions in Hmisc and rreport to use new R date class instead of POSIXct for pure date variables (FH) 1 Copy ...
1 Change import.s to get all SAS CRF files from data/rda/*.rda (FH has probably done all this, just check) (SE) 1 Change report.s to remove sas from rdaInFiles ...
Omics Data Clinic Notes and Analyses 2024 March 26 Neil Dani, Cell and Developmental Biology We are interested in characterizing the neurodegenerative processes ...
Using Subversion * Subversion is a version control system that allows users to keep track of changes made over time to any type of electronic data * See Subversion ...
R Packages To Install When Updating R install.packages("Design") # rms should be used over Design install.packages("rms") install.packages("MASS") install.packages ...
Generating a variable that correctly labels each subject's records as their first, second, etc. visit according to a visit date The idea behind this problem is that ...
Web Application Registry Members of the Department of Biostatistics and the Center for Quantitative Sciences have developed or participated in the development of web ...
Biostatistics applications in surgery, anesthesiology, and emergency and critical care medicine Clinic Notes (2015) 2015 December 16 Jason Singer, Medical student ...
Biostatistics applications in surgery, anesthesiology, and emergency and critical care medicine Clinic Notes (2016) 2016 December 28 canceled due to holiday 2016 ...
Biostatistics applications in surgery, anesthesiology, and emergency and critical care medicine Clinic Notes (2017) 2017 December 20 Rachel Labianca, Pharmacy resident ...
Notes for Wednesday Biostatistics Clinic Archive Current Notes 2013 December 11 Catherine Bulka, Anesthesiology * Wants to demonstrate/examine group balance ...
R and RStudio Workshop About the Course One day course by Cole Beck , Senior Applications Developer, Department of Biostatistics, Vanderbilt University School ...