The Model Averaging for Dichotomous Response Benchmark Dose (MADr-BMD) Tool
The Model Averaging for Dichotomous Response Benchmark Dose (MADr-BMD) tool is a downloadable program that implements model averaging based upon dichotomous dose-response data.
Key characteristics of the program include:
- Providing quantal response models, which are also used in the U.S. EPA benchmark dose software suite, and generates a model-averaged dose response model to generate benchmark dose and benchmark dose lower bound estimates.
- Developed by Matthew W. Wheeler (CDC/NIOSH) and A. John Bailer (Miami University and CDC/NIOSH) and is freely available.
- Descriptions of the statistical approach, use and set-up with examples are available in the manuscript by Wheeler and Bailer published in 2008 in the Journal of Statistical Software and available at https://www.jstatsoft.org/article/view/v026i05.
- Source code and example input files are available online as a supplement to the journal article. This source code compiled as an executable software program is posted below for download.
Download Model Averaging for Dichotomous Response Benchmark Dose (MADr-BMD) (EXE)(1 pg, 2 MB)
User Instructions for the Dichotomous Response Benchmark Dose (MADr-BMD)
The MADr-BMD software is a stand-alone command line program that is executable under the Microsoft Windows operating system’s shell command prompt. Once madrbmd.exe is downloaded, move the file to a new directory where you have write permission. For example open C:\ and create a new folder by right-clicking, selecting New\Folder and typing the new name such as MA. Also add the input file to be used to this new directory. An example input file is included in the supplemental information to the Wheeler and Bailer 2008 manuscript in J. Stat. Soft. available online at https://www.jstatsoft.org/article/view/v026i05. Once the zip file is downloaded open the zip file (double click) and create a copy of (by dragging) the input.txt file in the directory with the madrbmd.exe file (for example C:\MA).
To run MADr-BMD open the windows start menu and in the entry line at the bottom, type cmd and press enter to open a command prompt window. Change directory (use the cd command) to the directory where you placed the madrbmd.exe file and the input file. For example type cd C:\MA. Use the dir command to confirm that the madrbmd.exe file and an input file (e.g. input.txt) are in the current working directory.The MADr-BMD program is invoked with the command madrbmd. Given no input arguments (i.e., typing madrbmd) the program assumes an input file named input.txt is located in the current working directory.
To provide a user specified file the input filename is added after madrbmd, for example typing madrbmd 1BPinput.txt would instruct the program to use 1BPinput.txt as the input file. The input file specifies convergence criteria, model selections, the random seed, averaging criterion, statistical parameters, and data specification. A full description of the input file is in Table 1 of Wheeler and Bailer 2008 and example input files are available in the supplemental information to the manuscript as described above.
MADr-BMD, by default, outputs all calculations to the command prompt; however, output can be saved to a file using redirection at the command prompt. For example madrbmd 1BPinput.txt > 1BPoutput.txt would take data from the file 1BPinput.txt and output the data to the file 1BPoutput.txt. The output can then be viewed using any text editor.