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Boomer Non-Linear Regression Program
Consider JGuiB a GUI for Boomer
This program and more is now available on CD.
For details
Download Section
Macintosh/UNIX Mac OS X Terminal versions - the latest version usually works best :-)
Double clicking on the package file after it has been downloaded will install boomer and a required library file. For the Macintosh/UNIX versions below you will need to 'install' boomer manually if you want it to be available from any folder. As an administrator user you can move boomer to your PATH and thereby invoke the program globally (from any folder such as a data containing folder). Open the Terminal program and change directory (cd) to the folder containing boomer. This will be your download folder. The downloaded file is zip archive which will usually be expanded automatically.
Issue the command
sudo cp boomer /usr/bin/boomer
Enter password
this will put boomer in a directory usually included in your PATH variable. You should now be able to run the program by typing boomer from any directory.
Linux/Fedora 2 versions - the latest version usually works best :-)
- Linux/Fedora 5 version Version 3.3.2 [17 Apr 2006]
- added include files for better cross platform development
- eOUT v1.0.2
- Transition to gfortran (please report problems to david@boomer.org)
- Untar the downloaded file with
tar -xvzf fboomer331.tar.gz
As an administrator user you can move boomer to your PATH and thereby invoke the program globally. The command:
sudo cp boomer /usr/bin/boomer
Enter password
from your download folder (where the new version of boomer resides) will put boomer in a directory usually included in your PATH variable. This can be checked with the command:
echo $PATH
- Linux/Fedora 5 version Version 3.3.1 [11 Apr 2006]
- Transition to gfortran (use earlier versions if you have problems with this version - please report problems to david@boomer.org)
- with cDAT and eOUT (see above for other changes)
- Untar the downloaded file with
tar -xvzf fboomer331.tar.gz
As an administrator user you can move boomer to your PATH and thereby invoke the program globally. The command:
sudo cp boomer /usr/bin/boomer
Enter password
from your download folder (where the new version of boomer resides) will put boomer in a directory usually included in your PATH variable. This can be checked with the command:
echo $PATH
- Linux/Fedora 2 version Version 3.1.2 [1 Dec 2004]
- Added wt to xxx.csv and xxx.html files
- Untar the downloaded file with
tar -xvzf fboomer312a.tar.gz
As an administrator user you can move boomer to your PATH and thereby invoke the program globally. The command:
sudo cp boomer /usr/bin/boomer
Enter password
from your download folder (where the new version of boomer resides) will put boomer in a directory usually included in your PATH variable. This can be checked with the command:
echo $PATH
I haven't checked this with Linux/Fedora yet but something similar should work. I only get limited time on my younger son's game machine:-)
- Linux/Fedora 2 version Version 3.1.1 ALPHA! [16 Nov 2004]
- The first version for Linux, Fedora Core 2 - features should match Mac OS X and Windows version 3.1.1 unless there is a bug ;-) Please let me know if you try this and find a problem. The xxx.htm files produced as output can be imported into Open Office.
Windows/DOS versions which run under Windows in a DOS/Command window
Windows users may find it easier to right click on the required link below, Save Target as ..., and unzip or unstuff it with Stuffit Expander (see below or Winzip or similar)
- Windows version Version 3.3.3 [22 Dec 2006]
- added eBEST v1.0
- updated eOUT v1.0.2
- Windows version Version 3.3.2 [17 Apr 2006]
- added include files for better cross platform development
- eOUT v1.0.2
- gfortran version (please let me know if you have any problems with these files - david@boomer.org)
- Windows version Version 3.3.1 [13 Apr 2006]
- gfortran version (second try - please let me know if you have any problems with these files - david@boomer.org)
- with cDAT and eOUT
- Windows version Version 3.3.1 [30 Mar 2006]
- still g77 version updated to v3.3.1
- Windows version Version 3.2.0 [25 Feb 2006]
- added Exponentially random to uniform, normal and log normal random error for data or parameters
- Windows version Version 3.1.9 [16 Feb 2006]
- fixed a bug that caused a segmentation error with more than 30 adjustable parameters ;-)
- added form feed to output
- Windows version Version 3.1.8 [24 Dec 2005]
- added Four parameter logistic model
- added AICc to the output table
- Windows version Version 3.1.7 [30 Oct 2005]
- added output of sensitivity or optimal sampling analysis
- made output of xxx.htm,xxx.csv, and xxx.mdl optional
- still under development - watch the release date
- Windows version Version 3.1.6 [27 Sep 2005]
- Added ME, MAE, RMSE and RMSE% to the output tables
- Windows/DOS version Version 3.1.5 [10 Jul 2005]
- Added ability to read and write model data
- Windows/DOS version Version 3.1.4 [6 Feb 2005]
- Fixed a few bugs related to writing *.htm and *.csv files
- Windows/DOS version Version 3.1.3 [16 Dec 2004]
- Added x ** y to double dependence for parameters
- Windows/DOS version Version 3.1.2 [1 Dec 2004]
- Added wt to xxx.csv and xxx.html files
- Windows/DOS version Version 3.1.1 [26 Oct 2004]
- Ask to overwrite xxx.csv or xxx.html files
- Windows/DOS version Version 3.1 [23 Oct 2004]
- Added data output as data.csv table file for Excel
- Added data output as data.html table file for Open Office rather rough for now
- Added Johannes Proost's equations for r and r^2 (both versions)
- Removed formfeed from print output
- Now using g77 to compile the program which is now comparable to Mac/Unix version re number of data, parameters and constants. See notes above for extra capability with this version
- Removed formfeed from print output
- Fix problem with quiet mode via web. That is, output goes to console unless to out file even in quiet mode
- Added entry of -5 for Monte Carlo number, restrict mc to < 100000
- Changed formulas for R^2, SC and LL
- Added entry of -4 and bat file name from keyboard
- Third argument is the number of runs - multi run with same bat file name
- Added call system to run gnuplot automatically after grid run
- Added command line argument for bat file, first argument is the name of the bat file and the second argument is '3' if quiet mode
- Added command line argument for bat and out file
- Allowed user to include extension during filename input
- Added () around c(calc(1)) when c(obs(1)) = 0 in AUC table
- Fix bug with WResid plot - oops - thanks Yung-jin
- Changed WResid plot versus Cp to WResid plot versus ln (Cp)
- Added log likelihood and Schwarz Criterion to the output
- Added the ability to clone components - useful for Sheiner PK/PD models
Aladdin Systems Stuffit Expander Information
Windows/DOS users may want to download Stuffit Expander to unzip some of the files on this page. This is available from Aladdin Systems for free.
Macintosh versions - the latest version usually works best :-)
- PowerMac/Fat version Shareware - full version 3.0.10 [26 Sep 2003]
- Allowed user to include extension during filename input
- Added () around c(calc(1)) when c(obs(1)) = 0 in AUC table
- PowerMac/Fat version Shareware - full version 3.0.9 [20 March 2003]
- Fix bug with WResid plot - oops - thanks Yung-jin
- Changed WResid plot versus Cp to WResid plot versus ln (Cp)
- PowerMac/Fat version Shareware - full version 3.0.8 [5 January 2003]
- Changed WResid plot versus Cp to WResid plot versus ln (Cp)
- Added log likelihood and Schwarz Criterion to the output
- PowerMac/Fat version Shareware - full version 3.0 beta 7 [17 November 2002]
- Added the ability to clone components - useful for Sheiner PK/PD models
- PowerMac/Fat version Shareware - full version 3.0 beta 6 [8 October 2002]
- PowerMac/Fat version Shareware - full version 3.0 beta 5 [4 February 2002]
- Added ability to randomly calculate time values during Monte Carlo simulation runs
- Added switches (type 42) based on (randomly generated) parameter values
- Adding ability to write NONMEM data files during Monte Carlo simulation runs
- Adding random switches as parameters (type 40) (might be used to develop bimodal distributions of other parameters)
- Added Effect = Slope x log10(C) + Intercept to Parameter type 11
- .DAT,.BAT, and .OUT files have file type/creator set for TextWrangler (see below)
- Y2K Compliant ;-)
- Reads up to 5000 data points
- Now remembers where data and batch files reside (but not between restarts of the program (yet!); may not - will not work with At Ease)
- Reads weight values from keyboard or disk file for individual data points
- Data files may be tab, space, or comma delimited
- PowerMac/Fat version Shareware - full version 2.7.9 [11 October 99]
- Added Effect = Slope x log10(C) + Intercept to Parameter type 11
- .DAT,.BAT, and .OUT files have file type/creator set for TextWrangler (see below)
- Y2K Compliant ;-)
- Reads up to 5000 data points
- Now remembers where data and batch files reside (but not between restarts of the program (yet!); may not - will not work with At Ease)
- Reads weight values from keyboard or disk file for individual data points
- Data files may be tab, space, or comma delimited
- PowerMac/Fat version Shareware - full version 2.7.8 [23 April 99]
- .DAT,.BAT, and .OUT files have file type/creator set for TextWrangler (see below)
- Y2K Compliant ;-)
- Reads up to 5000 data points
- Now remembers where data and batch files reside (but not between restarts of the program (yet!); may not - will not work with At Ease)
- Reads weight values from keyboard or disk file for individual data points
- Data files may be tab, space, or comma delimited
- PowerMac/Fat version Shareware - full version 2.7.5 [28 Sep 98]
- Y2K Compliant ;-)
- Reads up to 5000 data points
- Now remembers where data and batch files reside (but not between restarts of the program (yet!); may not - will not work with At Ease)
- Reads weight values from keyboard or disk file for individual data points
- Data files may be tab, space, or comma delimited
TextWrangler information
Macintosh users may want to download TextWrangler 2.0 for text editing and printing.
This is available from BareBones
at no cost as freeware.
The commercial, BBEdit, is even better!!
Boomer Manual as a pdf file or as one web page
Boomer Manual - Table of Contents
Title Page
Preface
Chapter I - Background
Chapter II - Fitting Algorithms
- A. Gauss-Newton
- B. Damping Gauss-Newton
- C. Modified Marquardt
- D. Simplex
- E. Simplex -> Damping Gauss-Newton
- F. Grid Search
Chapter III - Numerical Integration Algorithms
- A. Classical Fourth Order Runge-Kutta
- B. Runge-Kutta-Gill
- C. Fehlberg RKF45
- D. Adams Predictor-Corrector
- E. Gears with PEDERV subroutine
- F. Gears without PEDERV subroutine
Chapter IV - Instructions for MultiForte/Boomer
- A. Data Entry
- B. Method of Analysis
- C. Output Options
- D. Model Definition - Boomer
- E. Specifying Parameter Values
- F. Example Models - Boomer
- G. Model Definition - Multi-Forte Demo Version
- H. Numerical Integration Method
- I. Numerical Integration - Error Terms
- J. Fitting Algorithm
- K. Fitting Criteria
- L. Data Set Title
- M. Individual Data Value Entry
- N. Weighting Scheme
- O. Constants
- P.Entry of Parameter Estimates
- Q. Simulation with Error Input
- R. AUC, AUMC, MRT
- S. Plot and Final Result Options
- T. Notes
Chapter V - Output Information
Chapter VI - Boomer Tutorial
- A. Normal Fitting - Two Comparison I.V. Bolus Model
- B. Bayesian Analysis - I.V. Infusion with kel a Function of Creatinine Clearance
- C. Working with Batch (.BAT) Files - Simulation
- D. Simultaneous Fit to I.V. and Oral Data - IRWLS
- E. Simulation with Error and Monte-Carlo Simulations
- F. Grid Search Method
Chapter VII - Error Messages
- A. SYSTEM Bombs!!
- B. FORTRAN Error Messages
- C. MS FORTRAN Error Messages
- D. MULTI-FORTE Error Messages
- E. RKF45 Error Messages
- F. DIFSUB Error Messages
Chapter VIII - Subroutines
- A. Subroutine CP
- B. Subroutine MODEL
- C. Subroutine MODELOUT
- D. Subroutine PART
Chapter IX - Acknowledgments
Chapter X - Applications
Appendix I - Sample .BAT (Macintosh format) or Sample .BAT (Zipped) format) files
Macintosh users should be able to download the .BAT files below by clicking on the link. Windows users may need to right click on the link, Save Target as ..., and unstuff it with Stuffit Expander mentioned above.
Copyright 2001-3 David W. A. Bourne (david@boomer.org)