A guest of this TWiki web, not unlike yourself. You can leave your trace behind you, just add your name in .TWikiRegistration and create your own page. Personal Preferences ...
I am a TWiki:Main/CoreTeam member (I am guilty of the Plugins developement ; ) ) See home page at TWiki:Main/AndreaSterbini Main.AndreaSterbini 13 Dec 2001
* Name: Peter Thoeny * Email: Peter #64;Thoeny.com * Comment: Peter is the author of TWiki and therefore a TWiki:Codev/CoreTeam member. See home page at TWiki ...
* Name: Test User * Email: dale.plummer #64;vanderbilt.edu * Phone: * Comment: Personal Preferences (details in .TWikiVariables) * Horizontal size of ...
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 ...
SAS Macros for Assisting with Survival and Risk Analysis, and Some SAS Procedures Useful for Multivariable Modeling Several unsupported SAS macros written by Harrell ...
Archive from the 2 4 June 2003 Regression Modeling Strategies Short Courses * Final S Plus script * Corrected final S Plus script Main.FrankHarrell 01 Feb ...
Programming Prerequisites for Statistical Computing Courses To take a full course in statistical computing you must have learned and used a computer language such ...
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 ...
A variety of functions for correspondence analysis are available from Bernard Perbal of the Centre de Recherche Public Centre Universitaire, Luxenbourg (E mail: ...
Thanks to Stephen Smith, James B. Ramsey, Frank e Harrell, F. Tusell, Renaud Lancelot, Nick Ellis and Pat Burns for their helpful and quick replies. The summary of ...
Other S Functions A variety of functions for correspondence analysis are available from Bernard Perbal of the Centre de Recherche Public Centre Universitaire, Luxenbourg ...
Exporting Microsoft Outlook Email Folders and Contacts into .mbox and .vcard Format Below are step by step instructions you can follow to reliably export specific ...
* Name: LAC Linux * Email: support #64;laclinux.com * Phone Number: * Comment: Personal Preferences (details in .TWikiVariables) * Horizontal size of ...
Statistical Computing and Graphics Concepts to Master 1 Difference between a functional language with live access to data and a procedural or macro language ...
options(digits=3) # Generate 10 random normal observations with mean 80, s.d. 15 rnorm(10, 80, 15) # Re issue this command multiple times to see new sets of random ...
General Modeling Issues Discussion Board What to Do with a Dataset that is Too Small? John Fieberg (John.Fieberg #64;dnr.state.mn.us) asked the following on 2 Mar ...
title; option pageno=1; libname d "c:\data\preavg"; libname da "c:\data\avg"; *Merge all the data together. New and old data. So that we will have a complete data ...
A Mockup of an R (or S Plus) Script for Specifying a Research Database # Institutional variable definitions used as defaults for all projects # Will usually be in ...
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 ...
Summary of Research Findings An important finding of our studies concerns the relationship between proliferative breast disease and breast cancer. (New England Journal ...
* Name: Osman Al Radi * Email: osman.al.radi #64;utoronto.ca * Phone Number: 416 920 9505 * Comment: Personal Preferences (details in .TWikiVariables) ...
Note: This documentation comes from the PCL CVS source distribution. I've rearranged the chapters in order of importance. Main.JeffreyHorner 4. Getting started This ...
This is a 2U rack mount server. It would have 160GB of SATA disk consisting of two mirrored drives. The drives are swappable from the front of the case but the system ...
* Microarray or mass spec? * Average by sample location? * Do PROC MEANS on each patient to verify normalization * Create/verify peak definition file ...
Notes on trouble shooting Twiki problems 20 Apr 2004 a user recently got this error message when trying to save a change. Biostatistics TWiki . Main . ReduceDMC ...
Information on Xforms See http://www.w3schools.com/xml/default.asp for a nice tutorial on xforms. This is (finally) something I can understand without having to plow ...
A Quick Howto for Konqueror/Cervisia/CVS This brief tutoiral will teach you how to check out the rreport module from the Biostat server. You must have installed Cervisia ...
Demonstration and Review of PercipEnz Oncore System Interspersed are some responses (marked DM) from David DeMets, and Sorena Nadaf (marked SN), key personnel involved ...
Demonstration and Review of Metaclinic System Basis Software Oracle, Apache, mod_perl (increases speed by maintaining Perl and metadata in memory), Javascript Features ...
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 ...
This is your own TWiki User page. Edit the template as you see fit. Wendy Reid, CCRPComputer Systems Analyst E mail: wendy.reid@vanderbilt.edu Phone ...
Review of Paul Harris' System Goal Be able to implement data management tools for a wide variety of studies, and to build a toolset that uses best security practices ...
Preface The purpose of this text is to enable biomedical researchers to use a number of advanced statistical methods that have proven valuable in medical research ...
Ideas for Seminar and Workshop Topics * Formulating a model * Measuring predictive performance * Seminar or discussion of mixed models helpful, in either ...
* Download this folder from the template account on the biostat server * .sylpheed/* * Run sylpheed to configure the account, specifying their own ID in place ...
Public Domain Software Available for Download from Vanderbilt Biostatistics * Power and Sample Size Estimation Software * Software for Converting Relative Risks ...
PhOSCo PhOSCo is a complete electronic data capture system for multi site clinical trials that has been in use for seven years. It is written in object oriented Java ...
Please put your feedback on this system. I think that this will work, but I am open to better solutions. Jeremy. At this point in time, use the console tester to write ...
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 ...
Prediction Error in Cox Models Varying Number of Predictors This program runs Cox fits of simulated data with exponential survival and 1 30 covariables. Each covariable ...
Miscellaneous S Examples * Graphical Demo of Numerical Differentiation * Simulate Difference in Life Expectancy for Mixed Exponential/Weibull Distribution ...
Windows Utility Software * wget program for Windows, a command line utility for downloading files from the WWW * Exporting Microsoft Outlook mailboxes * GnuPG ...
GnuPG Privacy Guard Instructions These instructions tell you how to install and configure the high security free and open source encryption/decryption software called ...
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 ...
Commenting Guidelines * Add class/function header at time of creation * Use summary to describe a function/class. * Use value to describe a property ...
* Copy and Paste will work * WfccmExceptionCodes Creation error "\n Failure when trying to create " this.GetType().ToString() " `" this.name "'!" Add row ...
Binary Response, Three Potential Predictors, Independent Observations In a hypothetical study, a sample of 500 subjects had three potential predictors measured: age ...
Don Hong, Ph.D. (CV) Visiting Professor of Biostatistics, VUProfessor of Mathematics, ETSU Email: don.hong@vanderbilt.edu Phone: 615.936.1415 Fax: 615.936 ...
MySQL tools * mysqlnavigator use apt get install mysql navigator Using OpenOffice as a front end to MySQL database using ODBC OpenOffice is running on user's ...
Some Issues and Current Recommendations Regarding Research Data Management, for Principal Investigators There are many approaches to implementing a data management ...
Requirements Statement The software to be designed will control the generation of scores to be used is the distance analysis of genes and proteins via WFCCM. The program ...
* Name: Mike Calder * Email: ceo at phosco.com * Phone Number: * Comment: Personal Preferences (details in .TWikiVariables) * Horizontal size of text ...
Section 1: Introduction to Statistical Concepts Instructor: Frank Harrell Statistical inference is the process of drawing general conclusions from specific studies ...
Needed Changes in Medical School and Pre Med Curricula Quoted from Santana S: Educators seek curriculum revision to reflect changes in sciences, Reporter 13 No. 11 ...
The following are the guidelines for submitting data for analysis. These guidelines are established to make the process better for both sides. Following the guidelines ...
K3B will complain about not having any SCSI devices if the cdwriter is using ATAPI. It also may give errors about some of the packages it uses, including problems ...
Questions for Discussion From FrankHarrell 1 Methods based on filtering out "winners" result in effect estimates that are biased high. Likewise, stepwise variable ...
Survival Design 1 create timediff variable from date of diagnosis to date of death in days. 1 Clean the data by changing the log 10 data from continous data ...
The Department of Biostatistics Vanderbilt University School of Medicine Statistical Thinking in Biomedical Research October 7, 14, 21, 28, November 4, 11, 18 2004 ...
Database Specification The department has decided to build a database to handle tracking of personnel's professional development and percent effort. The design of ...
Checklist for Course Organizer 1 Order enough copies of Essential Medical Statistics, Second Edition by Betty R Kirkwood and Jonathan AC Sterne (Blackwell Publishing ...
Statistical Thinking in Biomedical Research Checklist for Participants * Purchase book from medical center bookstore * Check schedule; some sections are reordered ...
Policies for Participation in Abstract Submission For biostatisticians funded by a project or by the collaboration plan to work on an abstract we require a minimum ...
Notes for Instructors of Statistical Thinking in Biomedical Research The short course is designed so that the sessions are for the most part independent. This allows ...
Survival Design 1 Create timediff variable from date of diagnosis to date of death in days. 1 Create flag variable from status at event time. 1 = dead, 0 = alive ...
Example: Simulation Study of elm vs. Bootstrap ## Define elm function and its service functions f mu, 2, mean) cat('\nRight Tail Areas:\n\n') apply(cl ,,'upper' ...
Permutation TTest Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must ...
Marnett 2 Timepoint Study * Start Date: 20 October 2004 * Due Date: 25 October 2004 * Research Drive Directory: /Marnett/041005 * Data Type: MicroArray ...
Fredrik Lundgren kindly provided the following notes on updating S source code for S Plus 6.x on Windows systems. In 'Professional Edition Version 6.0.3 Release 2 ...
Section 4: Experimental Design and Analyzing Serial Measurements Instructor: This section introduces the principles of experimental design as applied to biomedical ...
Nephrology Journal Club 9 Nov 2004 Background Handout * Tepel M, van der Giet M, et al: Prevention of radiographic contrast agent induced reductions in renal ...
Statistical Software Recommendations * Unfortunately learning time is directly proportional to power and flexibility of software * Full power and flexibility ...
Statistical Thinking in Biomedical Research Schedule Note: Measuring change is currently listed as a topic in both Sections 1 and 5. It will only be briefly discussed ...
Side Effects of Merging SAE: 1 Low level term name is missing in CRF data therefore it is substituted by AEVTX variable which will appear in capital letters in ...
Review of Tepel et al, NEJM 2000;343:180 4 Biostatistical Reviewer: FrankHarrell This paper demonstrates that even in a premier journal, statistical reviews are frequently ...
Review of Bakris et al, Kidney International 2004 65:1991 2002 Biostatistical Reviewier: FrankHarrell This is a meta analysis of randomized clinical trials with at ...
* Name: Stephen Deppen * Email: steve.deppen #64;vanderbilt.edu * Phone Number: 3 6284 * Comment: Database Analyst in Department of Nursing. Working with ...
Section 5: Measuring Effects and Quantifying Evidence in Biomedical Research Instructor: This section introduces commonly used measures of frequency and effect in ...
Critique of Medical Research Council Trial of Treatment of Hypertension in Older Adults, BMJ 304:405 412, 1992 Minor Problems 1 Continuous variables were not used ...
Department of Biostatistics Seminar Individual Response to Treatment: Theranostics Between Hope and Hype Stephen Senn, Ph.D. Department of Statistics, University ...
Project Directory Structure for DMC Reporting by the Vanderbilt Statistical Analysis Center For a project named X use the following structure on workstations and the ...
MissedValues Note: This class's structure is dependent entirely on DistanceReport.WriteMissedColumn() function Public Members * highlightRuns Arraylist of highlighted ...
SummaryPanel Public Methods * SummaryPanel() Default constructor * SummaryPanel(SummaryPercentages) create a new Summary panel with the given percentages ...
ChartPanel Public Methods * saveImage(String imgName) saves image of the chart (as a PNG file) to the given image name * setDimensions(float top, bottom, ...
DataContainer Public Methods * DataContainer(DataContainer) Copy constructer. * AddColumn(string) Appends a new column of data, sets the name, and returns ...
InformationSet Parent: DataContainer Public * SetDataPoint(int, int, string) Set the data at that point. * GetDataPoint(int, int) Gets the data at that ...
FilteredScore Parent: Score Public Methods * FilteredScore(Score, CriteriaSet) Filters a score according to the criteria set. Creates the numPass column. ...
Fisher Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There ...
CutoffManager Parent: CriteriaManager Public Methods * CutoffManager(CutoffManager) The copy constructor. * Add(string, string, double) Adds a score name ...
TopNManager Parent: CriteriaManager Public Members * TopNManager(TopNManager) The copy constructor. * Add(string, string, double) Adds a score name, operator ...
CombinationManager Public Methods * SetBases(ArrayList of int) Sets the sizes of the bases. * Arraylist GetCombination(int) Returns the 0 base indices that ...
Expression Public Methods * Expression(string) Creation constructor. Sets function to the passed string, checks the validity of the function and converts to ...
DistanceResult Public Members * FilteredScores List of ids, numPass and the modifiers. * CriteriaSet criteria * DistanceOutput train * DistanceOutput ...
Summary Public Methods * ScoreSummary(ArrayList) Returns an InformationSet that summarizes all of the Scores given. * ScoreSummary(Score, ...) ScoreSummary ...
PartitionedDataSet Public Methods * PartitionedDataSet(string) Constructor that takes the path to the DataSet. * PartitionedDataSet(string, int) Constructor ...
MissedChart Public Methods * MissedChart(MissedValues) creates a new missed chart to visualize the given object (can be null) Properties * InfoSet The ...
InformationPane Public Methods * ProcessTag() Function that changes contents after a new observation has been specified (must be called separately because ...
CriteriaManagerPanel Public Methods * loadCM(CriteriaManager, ArrayList, bool) Takes the CriteriaManager to load, a list of score names, and whether or not the ...
DataGroupingPanel Public Methods * loadDG(DataSetInfo, DataGrouping, bool, bool) Takes the data information, the grouping to load, and whether the grouping is ...
Statistical Thinking in Biomedical Research Discussion Board To add new topics or modify existing ones, click on Edit at the bottom, and click on the GoodStyle link ...
Sudden Death Associated with Treatment for Hypertension Original Article Zipped SPSS Save File FrankHarrell's Critique of the Article Analyze the MRC dataset ...