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New version of WFMM released (25 April 2008)
A new version of
WFMM
(Wavelet-based Functional Mixed Models) is now available for download.
This version minimizes the amount of RAM required to process large data sets
which reduces the chance that the application will run out of memory.
This version also fixes a problem in wfmm3 that caused an exception to be thrown.
Updated version of predictive probability design for phase II studies (14 January 2008)
A new version of the software for
Predictive probability design for phase II studies
was posted yesterday. The user's guide was also updated.
Adaptive Randomization and Population Drift (18 December 2007)
Adaptively randomized trials attempt to treat
more patients effectively than equally randomized
trials by tilting the randomization probabilities in favor of what appears to be the best treatment
as each patient arrives. But what happens if the population changes during the course of the trial
so that what used to be the best treatment is no longer the best? Will adaptive randomization
learn that things have changed and still treat patients more effectively,
or will it persist in assigning what used to be the best treatment?
How will operating characteristics compare to adaptive randomization with fixed response
probabilities?
A new paper explores these questions.
The Effect of Population Drift on Adaptively Randomized Trials.
Adaptive Randomization 4.1 released (12 November 2007)
This latest version of
Adaptive Randomization primarily fixes a number of
minor problems in the user interface.
TTEDesigner 1.2 released (4 October 2007)
This evening we released
TTEDesigner, software for designing
single-arm safety monitoring trials with time-to-event endpoints.
This software is the design counterpart to TTEConduct.
TTEDesigner aims to eliminate the typical simulate-and-tweak cycle.
Instead of specifying scenarios and tweaking parameters until you get
the desired operating characteristics, you can specify the desired
operating characteristics and the software will attempt to satisfy these.
CONFINT 1.1 released (3 October 2007)
We released a new version of CONFINT this morning adding
calculations for exponential survival. Includes Windows
and Mac OSX (Intel and PowerPC) executables.
STPLAN Macintosh Intel executable (2 October 2007)
The distribution file for STPLAN 4.3 now includes Intel and PowerPC executables for Macintosh OSX. The source code has not changed.
Minor changes to Predictive Probabilities, other applications (9 August 2007)
We made a couple changes to
Predictive Probabilities. We gave it a new
icon more suggestive of what the software does: a crystal ball. Also,
we swapped a couple Greek letters in the interface, changing lambda to mu
where the former had caused some confusion.
We also updated the icon for Inequality Calculator and slightly changed
the wording for part of
CRMSimulator.
New biostatistics book (2 August 2007)
Lyle Broemeling's new book
Bayesian Biostatistics and Diagnostic Medicine
was published recently. A part of this book gives an introduction to some of the clinical trial
software available on this site.
Confidence Interval of Interaction Index update (2 July 2007)
A new version of the Confidence Interval of Interaction Index software by
Jack Lee and Maiying Kong was posted today.
Why most phase III oncology trials fail (19 May 2007)
A new paper has been posted online that explores some of the reasons
why typical phase II oncology trials do such a poor job of predicting which
treatments will succeed in phase III. See
A Review of Phase 2-3 Clinical Trial Designs
by Peter Thall.
Predictive Probabilities 1.4 second release (30 April 2007)
We have released a new build of
Predictive Probabilities
version 1.4. The new build opens the most commonly used dialog, interim analysis for binary endpoints, automatically
when the program opens. Also, the User's Guide has been updated; some errors were corrected and some unclear areas expanded.
If you would like the new User's Guide without re-installing the software, the file is available
online.
Multc Lean 1.2 released (27 April 2007)
A new version of
Multc Lean
was released today that adds the option to specify a minimum number of patients to treat before evaluating the stopping rules.
This option is not generally recommended though
it is occasionally necessary.
Dose-finding software released (11 April 2007)
Toxicity Probability Intervals, software for implementing the method described in "Dose-finding in oncology clinical trials based on toxicity probability intervals" by Yuan Ji, Yisheng Li, and Nebiyou Bekele,
was posted today. This software uses Microsoft Excel to produce a table that can be used to conduct the trial. Simulation software, written in R, is also provided.
Phase II predictive probability design software released (6 April 2007)
Today we released Phase II PP,
Source code (R and S-PLUS) is provided to accompany the paper
"A predictive probability design for phase II cancer clinical trials"
by J. Jack Lee and Diane D. Liu. The method provides a flexible alternative to frequentist
two- or three-state designs for phase II trials based on Bayesian predictive probability.
WFMM released (4 April 2007)
WFMM is a Windows command-line application
that implements a Bayesian wavelet-based
functional mixed model methodology for
functional data analysis developed by Jeffrey Morris and Raymond Carroll.
PRT releaased (3 April 2007)
The
PRT software implements the statistical method described in the paper
"Monitoring Late Onset Toxicities in Phase I Trials Using Predicted Risks"
by Bekele, Ji, Shen, and Thall.
ANOVA DDP released (2 April 2007)
This software implements Bayesian inference for the ANOVA DDP model
described in De Iorio, M., Mueller, P., Rosner, G., and MacEachern, S.
An ANOVA Model for Dependent Random Measures,
Journal of the American Statistical Association, 99(465), 205–215 (2004). The ANOVA DDP model is a model for repeated measurements data.
The random effects distribution includes a regression on subject-specific covariates.
New Predictive Probabilities user's guide (16 January 2007)
There is a new version of the Predictive Probabilities user's guide
posted on the product's
download page. The new version corrects
errors in two equations, one on page 4 and one on page 5.
Comparing ways of controlling Adaptive Randomization (9 January 2007)
The
Adaptive Randomization software distributed
by our department supports three ways to control
how the randomization probabilities change in
response to incoming data. One way is to begin
the trial with a burn-in period of equal
randomization. Another is to set a lower bound
on the randomization probabilities. A third way
is to use a power transformation of the
inequality probability.
This raises several interesting questions. How
does each method impact the statistical power of
the design? How does each impact the treatment
of the patients in the trial? Which approach
should one take? A technical report released today,
Comparing methods of tuning adaptively randomized trials,
addresses these questions in the context of a
two-arm trial with a binary endpoint.
Adaptive Randomization working paper released (21 December 2006)
A new working paper,
Practical Bayesian Adaptive Randomization in
Clinical Trials by Peter F. Thall and J. Kyle Wathen
was released recently. The abstract follows.
While randomization is the
established method for obtaining
scientifically valid treatment
comparisons in clinical trials,
it sometimes is at odds with
what physicians feel is good
medical practice. If a physician
favors one treatment over
another based on personal
experience or published data, it
may be more appropriate
ethically for that physician to
use the favored treatment,
rather than enrolling patients
on a randomized trial. Still,
the randomized trial may later
show the physician's favored
treatment to be inferior. This
paper reviews a statistical
method, Bayesian adaptive
randomization, that provides a
practical compromise between the
scientific ideal of conventional
randomization and choosing each
patient's treatment based on a
personal preference that may
prove to be incorrect. The
method will first be illustrated
by a simple hypothetical
example, then by a recent trial
in which patients with
unresectable soft tissue sarcoma
were adaptively randomized
between two chemotherapy
regimens.
Adaptive Randomization tuning parameter technical report released (14 December 2006)
The Adaptive Randomization software distributed by our department allows the user
to specify a tuning parameter λ. A recent
technical report explains the motivation
for this parameter and how it effects a trial
design's operating characteristics. The report
concludes with some suggestions for
determining the value to use when designing a clinical trial.
TTEConduct 2.0 Released (6 November 2006)
The latest version of TTEConduct now has a Windows user interface for ease of use.
The statistical functionality is the same as in the earlier commandline version.
Self-extracting product files (18 October 2006)
A number of our users have had trouble extracting zip files.
(See the first two questions on our
FAQ page
for details.) We released EffTox 2.10 as a
self-extracting file a couple months ago, and
the feedback has been positive. This week we
converted a few more of our download products
from .zip
format to self-extracting .exe
format. If the new format
causes you difficulty, please
let us know.
EffTox version 2.10 released (15 August 2006)
Several changes were made
in this version of EffTox.
- Numeric inputs now work correctly with
non-English versions of Windows. The
software asks the operating system for the
local convention for decimal separators.
- The tutorial has been expanded and
converted to PDF format.
- Documentation for the new Lp contours
has been added.
- Error handling has been improved.
Also, beginning with this release we are
making products available as self-extracting zip
files. We believe users will find this more
convenient than customary zip files. If this
causes a problem, please
let us know.
Bayesian Chi-square TTE fit released (15 August 2006)
Today we released BCSTTE, Bayesian Chi-square TTE fit software.
This software uses the Bayesian chi square test of Valen Johnson
to assess goodness-of-fit for several parametric models to
right-censored time-to-event data. The following distribution families are supported:
exponential, gamma, inverse gamma, Weibull, log normal, log logistic, and log odds rate.
Predictive Probabilities 1.4 released (27 July 2006)
Version 1.4 of Predictive Probabilities has several improvements over
the previous version:
- The binary outcome model has been
generalized. Where the model previous used
P(X > Y) it now uses P(X > Y + delta). The
delta term can represent a required level of
improvement or an allowable slippage.
- The
user's guide has been completely
rewritten.
- A few changes in the user interface make
the software easier to use.
- An incompatibility with non-English
versions of Windows has been fixed. The
software now queries the operating system
for the correct local decimal separator
character.
Multc Lean with cohorts released (20 July 2006)
Multc Lean version 1.1 was released today. This version
allows the user to specify the cohort size used for trial monitoring.
Previous versions only supported continuous monitoring, i.e.,
cohorts of size 1. Now the cohort size can be any number that
evenly divides the maximum number of patients.
This version also fixes a problem with running the software
on non-English versions of Windows. (Earlier versions assumed that the
decimal separator was always a period rather than asking the operating
system for the local convention.) The input validation has also been
improved.
Inequality Calculator 2.3 released (20 July 2006)
This version of Inequality Calculator fixes a problem with running the software
on non-English versions of Windows. (Earlier versions assumed that the
decimal separator was always a period rather than asking the operating
system for the local convention.) The input validation has also been
improved.
This version also fixes an error in previous versions that occurred when an
inverse gamma distribution had shape parameter equal to exactly 1 or 2.
Parameter Solver 2.3 released (20 July 2006)
This version of Parameter Solver fixes a problem with running the software
on non-English versions of Windows. (Earlier versions assumed that the
decimal separator was always a period rather than asking the operating
system for the local convention.) The input validation has also been
improved.
This version also fixes an error in previous versions that occurred when an
inverse gamma distribution had shape parameter equal to exactly 1 or 2.
CRMSimulator 5.3 released (20 July 2006)
This version of CRMSimulator fixes a problem with running the software
on non-English versions of Windows. (Earlier versions assumed that the
decimal separator was always a period rather than asking the operating
system for the local convention.) The input validation has also been
improved.
Smaller downloads (20 July 2006)
Several of our software products require the Microsoft .NET framework.
We have been including the framework as part of our zip files for
distribution in case users do not have the framework installed.
We continue to do this, but now we are adding the option of
downloading a smaller file that does not contain the framework
for the convenience of those who already have the necessary version of the framework installed.
The download site will suggest the smaller download file
if it determines that the necessary version of the
.NET framework is installed and will suggest the larger version otherwise.
EffTox User's Guide updated (18 July 2006)
The EffTox
User's Guide posted
on the
EffTox download page has been extended
to include more guidelines for selecting the program inputs.
The new guide gives advice for choosing cohort size, starting
dose, outcome model, etc.
ARAND tuning parameter explanation (4 July 2006)
The download page for Adaptive Randomization added a
link to a
short paper explaining the design tuning parameter in detail.
Call for beta testers and user feedback (27 June 2006)
If you would be interested in volunteering as a beta tester for some of our software applications,
please
send us a note. Also, if you have any comments on released software (bug reports,
suggestions for new features, suggestions for clarifying documentation, etc.) please
let us know.
CI of Interaction Index released (21 June 2006)
This S-PLUS software estimates interaction indices and their confidence intervals for assessing multiple drug interactions.
CONFINT released (21 June 2006)
This commandline software calculates requisite sample size to achieve a specified probability
of a confidence interval of at most a specified size. Windows and Macintosh OSX executables and source code included.
STATTAB Updated (21 June 2006)
The Windows and Macintosh OSX executables have been recompiled and the documentation was converted to LaTeX.
Predictive Probabilities 1.3.1 released (6 June 2006)
Today we released an update to Predictive Probabilties.
The previous version had a bug that effected time-to-event interim analysis
if the exponential distribution were parameterized in terms of rate.
Since most users parameterize the exponential in terms of its mean,
we simply removed the rate parameterization option and now require the mean parameterization.
CRMSimulator 5.04 released (2 June 2006)
CRMSimulator version 5.04 was released today.
This minor release fixes a bug in the user interface of the previous version.
EffTox 2.9 released (31 May 2006)
EffTox 2.9 was released today. This version uses
a new method for specifying efficacy-toxicity
trade-offs, described detail in this
technical report. The new trade-off functions are simpler and more flexible
than their counterparts in previous versions.
Color coding was added to the efficacy and
toxicity input labels to reduce the chance that
the user might accidentally reverse these
inputs.
Book featuring MDACC software published (31 May 2006)
Wiley has
just published
Statistical Method for
Dose-Finding experiments, edited by Sylvie
Chevret, a book which features several software
applications available on this download site.
Chapter 13, "A two-stage design for dose-finding
with two agents", is about the statistical
method implemented in the
ToxFinder software. Chapter 14, "Using both
efficacy and toxicity for dose-finding",
describes the method used in the
EffTox software. Chapter 15 also mentions our
CRM and
CRMSimulator software.
STPLAN 4.3 released (24 May 2006)
A new version of STPLAN was released today.
A summary of the changes follows. For details, see the
"news" file included in the distribution.
- In previous versions, there was an error
in the significance calculations for the
two-sided test for one-sample randomized
clinical trials. This has been corrected.
- The algorithm for computing the
two-sample Poisson test has changed.
- The information time method for
randomized clinical trials with an
exponential distribution of time to event
has been added.
- In the one-sample binomial test, the
code now picks the smallest sample if
several samples have the same power.
- The documentation was rewritten as PDF
(from LaTeX) with bookmarks.
Upcoming software releases (1 May 2006)
We plan to release new versions of STPLAN, EffTox, and Multc Lean
over the next several weeks.
The coming version of STPLAN changes the way the two-sample Poisson test
is calculated. Also, the information time method for randomized clinical trials with an
exponential distribution of time to event has been added. Finally, the documentation
has been revised.
The coming version of EffTox will introduce the
new Lp contours and will resolve a problem with dependent scenarios.
The new release may also modify the algorithm used to solve for hyperparameters
based on elicted probabilities.
The coming version of Multc Lean will add an option for monitoring in cohorts;
the current version supports only continuous monitoring, that is, cohorts of size 1.
TTEConduct version 1.2 released (26 April 2006)
TTEConduct version 1.2 was released this afternoon. The new version has three changes:
- The previous version had assumed an
upper limit of 100 years for the total time
on test. This limit was too restrictive for
large trials. The new limit is trial size
times 10 years.
- The new user's guide includes an example at the end.
- The new software runs several times faster than the previous version.
EffTox technical report posted (14 April 2006)
This
report describes the a method of computing efficacy-toxicity trade-offs
in the EffTox dose-finding method. This method will be used in a new
version of the EffTox software to be released in a few weeks.
Multc Lean version 1.0.3 Released (7 April 2006)
We recently discovered a sequence of events that could prevent Multc Lean version 1.0.0
from displaying help files. This bug is fixed in version 1.0.3.
As part of the same release, we also revised the statistical tutorial.
TTEConduct user's guide updated (4 April 2006)
TTEConduct was re-released today with an updated ReadMe file.
The new documentation gives recommendations for how one may
select the design parameters. The new ReadMe file is posted
on the
TTEConduct page on the software download site as well
as being bundled with the TTEConduct download distribution.
Note that TTEConduct trial designs need to be simulated
in order to understand their operating characteristics.
We currently have internal software for simulating such trials
but do not have anything ready to release to the public yet.
We hope to release such software in the future, perhaps
this summer.
Adaptive Randomization 3.2.2 released (30 March 2006)
The latest version of Adaptive Randomization, version 3.2.2, contains a bug fix, and optimization, and a more convenient installer.
(You can tell what version of Adaptive Randomization you are running by looking at Help -> About ARand.)
We discovered recently that previous versions of Adaptive Randomization would occasionally stop a trial early even if the early stopping rules were effectively turned off by setting impossibly high stopping boundaries. This has been corrected.
In addition, the procedure used to calculate the randomization probabilities has been made more efficient, speeding up simulation.
The new installer will automatically remove the previous version before installing the latest version; there is no need to manually remove the previous version from the control panel.
Adaptive Randomization 3.2 released (21 March 2006)
There were a few changes to the User's Guide and the code to bring it up.
A few typos in the user interface were corrected.
Predictive probability interim analysis software
released (20 March 2006)
Today we released a new version of our software for predictive probability
interim analysis of clinical trials. The changes
in version 1.3 are as follows.
- Online documentation has been revised
- Broken dialogs have been fixed
- Menus have been simplified
- User interface text has been revised
The numerical output of the software has not changed.
Adaptive Randomization technical report posted (8 March 2006)
A new technical report entitled Power and Bias in Adaptively Randomized Clinical Trials
was published today. The abstract from the report follows.
"This report examines the operating characteristics of adaptively
randomized trials relative to equally randomized trials in regard to
power and bias. We also examine the number of patients in the trial
assigned to the superior treatment.
The effects of prior selection, sample size, and
patient prognostic factors are investigated for both binary and
time-to-event outcomes."
Resources page added (11 February 2006)
We've added a resources page, listing some of the software, books,
and web sites we've found useful in development the software on this site.
We intend to add more to this page over time.
Adaptive Randomization 3.1.1 User's Guide (2 February 2006)
A new release of Adaptive Randomization 3.1.1 has been posted to
our department's software download site. This release adds the User's Guide
to the help menu, but otherwise does not change the program's functionality.
The new release is available here.
The User's Guide is also available as a stand-alone document from the same page.
Time-to-event trial conduct software (26 January 2006)
Software for generating the tables described in
Continuous safety monitoring in single-arm, time-to-event trials without software
was added to the download site today. This is the software that makes it possible
to run the trial without software! That is, this software can be run at design
time to produce a table containing stopping boundaries, eliminating the need for
software to evaluate the stopping rules repeatedly during the course of the trial.
Time-to-event algorithm technical report (2 January 2006)
A new technical report entitled
Numerical Evaluation of Gamma Inequalities
was posted today. This report describes the algorithm used in
Adaptive Randomization 3.1.1
to calculate the randomization probabilities for two- and three-arm time-to-event trials.
Time-to-event non-software (16 December 2005)
A new technical report entitled
Continuous safety monitoring in single-arm, time-to-event trials without software
has recently been posted. At first it appears that one needs special software to monitor
time-to-event trials using the simple exponential/inverse gamma Bayesian model, but
in fact one can determine the stopping conditions before the trial begins and carry them
around on an index card.
Adaptive Randomization 3.1.1 (17 November 2005)
Adaptive Randomization 3.1.1 was released this morning.
This version corrects a problem with the previous version which
prevented the installation program from working on some computers.
Also, version 3.1.1 uses
a new numerical algorithm for computing randomization probabilities for 3-arm
time-to-event trials which in testing has shown to be faster and more robust.
Adaptive Randomization update (11 November 2005)
Adaptive Randomization 3.1.0 was released this morning. The new version fixes a bug in version 3.0.0
that prevented the user from being able to simulate a 3-arm time-to-event trial.
In addition, minor typos in the output were corrected.
New STPLAN user's guide available (7 November 2005)
A new STPLAN user's guide
is available. This new version has the same content as the April 2000 version, aside
from updated contact information.
However, this version has been typeset in LaTeX, making the 199-page document easier to read.
Exact Calculation of Beta Inequalities (3 November 2005)
A technical report Exact Calculation of Beta Inequalities
was published today which explains how to find P(X > Y) in closed form where
X and Y are beta random variables with some restrictions on the parameters.
This technical report may be of interest to users of Adaptive Randomization,
Inequality Calculator, and Multc Lean.
Adaptive Randomization 3.0 Released (31 Oct 2005)
This software simulates randomized trials in which the randomization probabilities
adapt in response to the outcome data. More patients are treated with the better treatment
while retaining the benefits of randomization. The software supports both binary and time-to-event
outcomes. Numerous design options are supported.
Adaptive Randomization software coming soon (26 Oct 2005)
Software for simulating a wide variety of adaptively randomized clinical trials
is in its final stages of testing and should be available for download early in November.
The software supports up to 10 arms. Stopping rules may be based on a maximum patient
accrual or maximum trial length. Optionally one may specify a minimum number of patients in the trial.
Also, one may specify the number of patients to randomize fairly before adaptive randomization begins.
Stopping rules are based on posterior probabilities.
FAQ added (21 Oct 2005)
A frequently asked questions
list has been added to the software download site.
New Software Download Site (17 Oct 2005)
The Department of Biostatistics and Applied Mathematics has just deployed a new
software download site.
Content from two previous sites has been merged. More information is available for each product,
and search functionality has been added.
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