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AlexFun
My R Functions Create time intervals data for time varying covariates in survival analysis When several time varying covariates present in survival analysis, creating ...
AlzolaHarrellChangeLog
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 ...
AmericanAccentTrainingNextMeetingSampling
library(Hmisc) s sample(s, replace=F)
AnalysisOfObserverVariability
Analysis Of Observer Variability See https://github.com/harrelfe/rscripts files named observerVariability* To load the function definitions into an RStudio session ...
BackToBackBarplot
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 ...
BioMod
General Handouts and Reference Material on Biostatistical Modeling * Syllabus from a course on Biostatistical Modeling (updated 9Jan03; click here for a pdf file ...
Bios311Syllabus2014
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 ...
Bios330Assign0
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 ...
BiostatisticianResponsibilities
Biostatistician Responsibilities Requirements for Statistical Reports All statistical reports produced by biostatisticians must be reproducible in that the report ...
BlevinsMSCI
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 ...
BootstrapMeansSoftware
Software and Example Code for Bootstrap Confidence Intervals for Means and Differences in Means The following uses the simple nonparametric bootstrap percentile approach ...
BrokenAxisExample
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 ...
CTSAbMeetings
VICTR CTSA Biostatistics Group Meetings 2015 Jan 14 Attending: * VICTR biostat support guideline: http://biostat.mc.vanderbilt.edu/VICTRBiostatPolicies * Annual ...
CatContinuous
Problems Caused by Categorizing Continuous Variables References Key Reference Key Reference for Response Variables More References Myths About Risk Thresholds ...
CategorizingContinuousCovariates
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 ...
CenterForSurgQualOutcomes
Main.JoAnnAlvarez 09 Nov 2012 Vanderbilt Center for Surgical Quality Outcomes Research Projects on their own page * CeasarData * CeasarProjTxVars * CeasarProject ...
ChangelogDesign
Design Package Change Log This change log is now handled by CVS. See it here. 1996 1997 1998 1999 2000 2001 2002 2003 2004 #LoG96 1996 Submitted ...
ChangelogHmisc
Hmisc Package Change Log This change log is now handled by CVS. See it here. 1996 1997 1998 1999 2000 2001 2002 2003 2004 #LoG96 1996 Submitted ...
CharlesDupontStuff
/Sandbox/' method='post' * New example topic: "}% This is a Change This is a Change THis is another change Why wont you change ...
ColeBeckNov112015
Department of Biostatistics Seminar/Workshop Series Maintaining R Cole Beck Computer Systems Analyst III, Department of Biostatistics Vanderbilt University School ...
CollabFlow
Possible Collaborative Editing Workflows 1 Statistician puts document template online and shares with collaborators 1 Statistical analysis plan put in a special ...
ComplexDataJournalClub
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 ...
ComputingDone
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 ...
CourseBios330
*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 ...
DMEx3
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 ...
DMEx4
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 ...
DataSets
NOTE This page is obsolete. Instead use https://hbiostat.org/data Datasets Most of the datasets on this page are in the S dumpdata and R compressed save() file ...
DataTransmissionProcedures
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 ...
DatadensityFunction
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 ...
Design
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 ...
DesignSurvivalAnalysis
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 ...
DesiredOutputFn
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 ...
DocProcess
General Information about LaTeX and other Document Processing Tools * Comprehensive TeX Archive Network * Online LaTeX Documentation FAQ Schneider's Resources ...
EPSLatexTables
Useful Stuff in R: Inserting Latex Tables into Microsoft Word Theresa A Scott, M.S. Biostatistician II, Department of Biostatistics Vanderbilt University School ...
FHHandouts
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 ...
ForLoopRegression
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 ...
FrankHarrell
Frank E Harrell Jr, PhDProfessor of BiostatisticsFounding Chair E mail: f.harrell@vumc.org Phone: 615.322.2001 Fax: 615.343.4924Assistant: Tawanna ...
FrankHarrell083116
Department of Biostatistics Seminar/Workshop Series Using R, Rmarkdown, RStudio, knitr, and HTML for the Next Generation of Reproducible Statistical Reports Frank ...
FrankHarrellApril092014
Department of Biostatistics Seminar/Workshop Series A New Model for Reproducible Clinical Trial Statistical Reporting Frank Harrell, PhD Professor and Chair, Department ...
FrankHarrellSept22015
Department of Biostatistics Seminar/Workshop Series Teaching R to Non Statisticians Frank E. Harrell, Jr., Ph.D Professor and Chairman, Department of Biostatistics ...
GenClinicAnalysisArchive
Recommendations, Analyses, and Data for Health Services Research, Diagnosis, and Prognosis Clinic Archive Current Notes 23Dec13 Heidi Silver, Director, Vanderbilt ...
GermanBreastCa
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 ...
GraphExplorePresent
Statistical Graphics for Exploring Data, Presenting Information, and Understanding Statistical Models Scripts Graphical methods are being increasingly used for exploratory ...
Greport
greport Package: Graphical Reporting for Clinical Trials * Presentation * How to videos * Github repository * CRAN * Changelog Viewing Reports You ...
HmiscMultivar
Hmisc Functions Related to Multivariate Analysis Function Purpose aregImpute Multiple imputation using generalized additive models dataRep Representativeness ...
HmiscNew
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 ...
HmiscSummaryFormulaFunction
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 ...
HmiscTodoList
Hmisc Todo List Unimplemented feature done Split summary.formula into three functions summary.formula.response, summary.formula.cross, and summary.formula.reverse ...
ITTeamSkills
Department of Biostatistics IT Team Skills and Experience The Department of Biostatistics boasts a strong IT support team consisting of 7 programmers and analysts ...
IntroBiostatDisc
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 ...
JoAnnAlvarez
JoAnn Alvarez, MA Biostatistician III E mail: joannmalvarez #64;gmail.com Office: 490 Preston Research Building My CV and resume (word file) Interests ...
JumpStartForNewBiostatisticians
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 ...
KnitrHowto
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 ...
KnitrHtmlTemplate
knitr HTML Template Example html Document Reproducible Research Using knitr in conjunction with Rmarkdown and RStudio one can produce nice html reports and material ...
LatestRFunctions
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 ...
LayoutFnExample
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 ...
LicenseAck
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 ...
ManyDataFrames
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 ...
MatchedRandomization
Reweighted Mahalanobis Distance Matching in Observational Studies and Randomized Trials Matched Randomization R Package nbpMatching The current version of the R package ...
MatchingWithMissingData
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 ...
MiscSplineEx
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 ...
MsciBiostatIISchedule
MSCI Biostatistics II Course Schedule February 2021 ul{ margin: 0; } Key: A = Whitlock and Schluter (text) B = Biostatistics for Biomedical Research (handout) H ...
MultipleKMCurves
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 ...
OddDateManipulation
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 ...
OmicsClinicAnalyses
Omics Data Clinic Notes and Analyses 23 January, 2018 (Attending statisticians: Chang Yu, Hakmook Kang, Li Wang) Joshua David Chew, Pediatric Cardiology Fellow ...
PsFrag
psfrag: Inserting LaTeX Code Inside Graphics There are many approaches for inserting LaTeX equations, symbols, tables, and other output inside postscript and pdf graphics ...
Puzzler2
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 ...
Puzzler3
Sudden Death Associated with Treatment for Hypertension Original Article Zipped SPSS Save File FrankHarrell's Critique of the Article Analyze the MRC dataset ...
RCTGraphics
Graphics for Clinical Trials Frank E Harrell JrVanderbilt Department of BiostatisticsOffice of Biostatistics FDA CDER DIA/FDA Statistics Forum, North Bethesda MD ...
RClinic
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 ...
RConfiguration
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 ...
RGraphicsDotplot
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 ...
RGraphicsplsmo
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 ...
RS
R Packages, Functions, and Documentation * R home R reference card R Programming Help files with output R Tutorials Videos R site search R seek ...
RSDatasetRetrieval
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 ...
RedcapApiExportR
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 ...
ReduceImport
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 ...
RetrievalDatasets
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 ...
RichardUrbanoDateProblem
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 ...
RmS
*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 ...
Rms2ndChanges
Regression Modeling Strategies With Applications to Linear Models, Logistic and Ordinal Regression, and Survival Analysis Major Changes Since The First Edition ...
RmsAccDisc
Predictive Accuracy and Model Validation Discussion Board How to validate the predictive accuracy of an ordinal logistic regrsesion model? Colin Robertson (colinr23 ...
Rreport
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 ...
RreportTodo
rreport To Do List 1 TERRI accrualReport: * Have made several improvements: 1 Modified order of generated plots and tables. 1 'Subjects ...
RusageInstruct
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 ...
SASexportHowto
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). ...
SAStoR
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 ...
SasByMeansExample
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 ...
SgraphicsHints
S Graphics Hints and Tricks * Graphics Setup Templates * Adding panel numbers in margins of multi panel graphs * Embedding fonts for certain journal submissions ...
SoftwareMirrors
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 ...
SpecificCovariateORsFromDifferentLRMs
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 ...
Splus6HmiscDesign
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 ...
StatBiomedResRNotes
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 ...
StatCompConcepts
Statistical Computing and Graphics Concepts to Master 1 Difference between a functional language with live access to data and a procedural or macro language ...
StatCompGraphShortCourse
S for Statistical Data Analysis and Graphics Frank E. Harrell, Jr. (f.harrell@vanderbilt.edu) Professor of Biostatistics and Statistics Chair, Department of Biostatistics ...
StatGraphCourse
Statistical Graphics Course Short Course * Graphics for Clinical Trials * Statistical Graphics for Exploring Data, Presenting Information, and Understanding ...
StatReport
Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data Reproducible Research ...
StatisticalComputingSeries
The Statistical Computing Series The Statistical Computing Series is a monthly event for learning various aspects of modern statistical computing from practitioners ...
SweaveConvert
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 ...
SweaveHighlightRow
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 ...
SweaveTemplate
Sweave and knitr Templates NOTE: SUPERCEDED by knitr and LaTeX Styles knitrl and spaper; See GitHub rlatex Project Using LaTeX Style Sweavel /template3.pdf ...
ThirdContrast
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 ...
ToDoAfterMay2004
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 ...
ToDoBeforeMay2004
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 ...
UnixPre5HmiscDesign
cd /tmp rm rf Hmisc Design Hmisc.zip Design.zip mkdir Hmisc cd ~/S/Hmisc cp p *.r *.f *.c /tmp/Hmisc cp p readme.txt /tmp/Hmisc/README cd /tmp/Hmisc mkdir .Data ...
UsingSubversion
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 ...
VaRPackagesToInstall
R Packages To Install When Updating R install.packages("Design") # rms should be used over Design install.packages("rms") install.packages("MASS") install.packages ...
VisitCountVariable
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 ...
WebAppRegistry
Web Application Registry Members of the Department of Biostatistics and the Center for Quantitative Sciences have developed or participated in the development of web ...
WebStatistics2004
Statistics for Main Web in 2004 Current Web Statistics Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors ...
WebStatistics2005
Statistics for Main Web in 2005 Current Web Statistics Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors ...
WednesdayClinicNotes2015
Biostatistics applications in surgery, anesthesiology, and emergency and critical care medicine Clinic Notes (2015) 2015 December 16 Jason Singer, Medical student ...
WednesdayClinicNotes2016
Biostatistics applications in surgery, anesthesiology, and emergency and critical care medicine Clinic Notes (2016) 2016 December 28 canceled due to holiday 2016 ...
WednesdayClinicNotes2017
Biostatistics applications in surgery, anesthesiology, and emergency and critical care medicine Clinic Notes (2017) 2017 December 20 Rachel Labianca, Pharmacy resident ...
WednesdayClinicNotesArchive
Notes for Wednesday Biostatistics Clinic Archive Current Notes 2013 December 11 Catherine Bulka, Anesthesiology * Wants to demonstrate/examine group balance ...
WorkshopR
R and RStudio Workshop About the Course One day course by Cole Beck , Senior Applications Developer, Department of Biostatistics, Vanderbilt University School ...
Number of topics: 116
 
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