This program is a Monte Carlo EM (MCEM) algorithm for fitting the proportional hazards model for interval censored failure time data. The algorithm generates orderings of the failures from their probability distribution under the model. We maximize the average of the log-likelihoods from these completed data sets to obtain updated parameter estimates. As with the standard Cox (1972) model, this algorithm does not require the estimation of the baseline hazard function. The method is described in the paper Goggins W, Finkelstein DM and Zaslavsky A. Applying the Cox Proportional Hazards Model when the Change Time of a Binary Time-Varying Covariate is Interval-Censored. Biometrics 1999;55: 445-451
(the SPARC object file above means that using this software requires access to a SPARC-based Sun workstation with S installed on it.)
Gen.m is an m-file (Matlab/Octave) for for computing sequential boundaries, as descibed in the paper "A Simple Algorithm for Designing Group Sequential Clinical Trials" (Schoenfeld, Biometrics 57, 972-974; September 2001). If you have Matlab download gen.m, gen.m can also be run under Octave a public domain m-file interpreter which can be downloaded from the URL below. In addition sequential.zip contains a compiled version of gen.m which runs on the command line.
depcen.exe is a program for estimating survival probabilities and probabilities of attending visits as described in the paper "Analysis of Failure Time Data with Dependent Interval Censoring" (Finkelstein D.M., Goggins W.B, and Schoenfeld D.A., Biometrics 2002 58:298-304). The program was implemented in Matlab and runs as a batch job from a DOS command prompt. The time to blood shedding data from the paper is also included. "interval_censr_data.zip" contains the data in .dat format and the .sas file required for setup. When using this data, please reference the article cited above.
1s_logrank.xls is for computing one sample log rank test, confidence intervals for the SMR, calculating estimate for survivorship in the matched standard population and visually comparing survivorship of the sample to that of the standard population as described in the paper and instructions (both included in the zip file). The paper was published in the Journals of the National Cancer Institute, Vol. 95, No. 19, Oct 1 2003 pp. 1434–1439 as a commentary.
costart.html is a Javascipt application for searching the Coding Symbols for Thesaurus of Adverse Reaction Terms (5th Edition). The page can be saved to a local computer so that it can be accessed while that computer is not connected to the internet. To do this from the COSTART page, select Save from the File menu, and make sure to save the file as the type "Web page, complete .htm, .html" (Internet Explorer).
micaParalize is a set of functions that allow a user to easily run normal Matlab functions on a multi-processesor machine by dividing the work-load amongst the serval processors. The program is used for simulations, bootstraps and function maximization problems in biostatistics.
micaParalize has been superceeded by biopara, which is on the software page
Parallel enabled utilities for use with Mathworks' Distributed Computing Toolbox. A parallel for loop, parallel simulation and a parallel bootstrap that makes use of the DCT to speed up execution.
Biopara is a parallel framework designed to allow users of R to distribute execution of coarsely parallel problems over multiple machines for concurrent execution. Biopara is called from within an R session and results are returned to the same session as a list of native R objects that can be directly manipulated without reinterpretation.
Permutation test to compare variability within and distance between two groups of microarrays using the distance matrix. This software uses R, and is available through CRAN.
R code for implementing survival analysis of longitudinally collected gene expression data. Methods are described in the linked paper by Rajicic N, Finkelstein DM, and Schoenfeld DA, submitted to Bioinformatics, May 2006.
This application calculates the power or the sample size for the Cox and Logistic models. It is written in MatLab.
If you don't have MatLab on your computer, you will need to download and run MCRInstaller.exe first.
sterconv.html is a Javascript application which converts milligrams of various corticosteroids to the equivalent dose of Methylprednisolone. The conversion data is adapted from Goodman and Gilman's The Pharmacological Basis of Therapeutics, 9th ed. (1996); Hardman JG and Limbird LE editors; New York: McGraw-Hill Health Professions Division; page 1466.
This program calculates the power or sample size for a random slopes model. This model assumes that each patient has a linear trajectory in with a slope and intercept that have a multivariate normal distribution. The fixed effects are time and a time treatment interaction. The time treatment interaction is the treatment effect as it measures the extent to which the mean slope is different in the two treatment groups. The program requires the variance covariance matrix for the random effects and the error variance of observations arround a patients trajectory.
The program is an m-file (Matlab/Octave) and will run under Octave which is a public domain m-file interpreter.
The program has also been ported to R.
2009 Feb 24; Matlab program updated.
An excel spreadsheet that calculates the power of a sequential parallel design assuming dropouts based on the paper by Tamura and Huang, Cancer Trials 2007; 4:309-317.