BMDS Release History

Learn about the various Benchmark Dose Software (BMDS) version updates which include fixes and enhancements from BMDS 3.0 to version 3.3.

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3.3.2
3.3.1
3.3
3.2.0.1
3.2
3.1.2
3.1.1
3.1
3.0

3.3.2

Released March 2023

Fixed bug in dichotomous scaled residual calculations that occurred when estimated probability equals one.

3.3.1

Released March 2023

Fixed bug in dichotomous scaled residual calculations. These calculations also affect the reported chi² and overall p-value reported.
Fixed bug in reduced model deviance calculations. These calculations also affect the reduced model p-value reported.

3.3

Released October 26, 2022

BMDS 3.3 includes significant “under-the-hood” improvements to the BMDS model code library. These improvements provide better overall performance, consistent results with previous BMDS releases, and better error management support.

The updated model code library lays the foundation for future enhancements and additions to the BMDS Model Suite, most notably the capability to run BMDS models, potentially, on multiple operating systems.

An important enhancement for EPA users is support for OneDrive, EPA’s current Cloud storage solution. EPA's recent expansion of OneDrive backup for EPA computers highlighted the need for BMDS to support OneDrive-synced network directories.

BMDS 3.3 includes the following fixes to the existing models:

Fixed issue where the A2 log-likelihood for the Power model returned an infinity value for specific datasets.
Fixed issues observed with the continuous models when using log-normal distributions, where BMDS reported log-scale SD for the estimated SD, but normal SD for the observed.
Fixed issue with some continuous models where they did not return maximum-likelihood estimation (MLE) values and did not provide a warning when this happened.
Fixed an issue where some polynomial models returned erroneous BMDL and BMDU values.
Fixed issue related to developmental nested model scaled residual summary.

BMDS 3.3 includes the following user interface enhancements:

A Reset to Default Models button is available on each model group worksheet (Continuous, Dichotomous, Dichotomous-Nested) to reset the model selections to the BMDS default recommended models.
Users can now specify the maximum number of degrees to use in Multistage and Polynomial model runs. The default value for number of degrees to run will be the lesser of n-1 or 3, but the user can change this to a higher number of degrees up to the lesser of n-1 or 8.
The user-entered text in the [Dose] and [Incidence] fields are now used as labels for the plots on the dataset modeling results.
Dichotomous Model Averaging Cumulative Distributive Function (CDF) values are now included in the Results Workbook model averaging output.
The “MS_Combo” label has been changed to "Multistage Cancer/Multitumor,” which can be used for individual as well as multitumor cancer dataset modeling. The Multistage Cancer/Multitumor model auto-applies EPA’s Multistage Cancer model degree selection criteria, but also shows individual dataset results for degrees not selected. When multiple datasets are analyzed, a warning is given regarding the combined Multitumor results; the warning text advises users to ignore Multitumor results for datasets that are not independent and from the same experiment.
Several popup messages and warnings have been added to the interface:
- Users are now warned via popup message when they select polynomial degrees higher than 3. The warning also appears in the Results Workbook’s summary table. The warning message is “Studies have indicated that higher degree polynomial models are not warranted in that they generally do not sufficiently improve fit over simpler models (Nitcheva et al., 2007). Complex models also increase processing time and the chance of model failure.”
- A popup warning appears when a dataset has missing values.
Plots are now included for model-averaged results.
An indication of model restriction (either "Restricted" or "Unrestricted") has been added to the results workbook for each frequentist model results worksheet.
Confidence intervals are now included for parameter estimates.
Analysis workbooks now can be stored in a network/OneDrive path; earlier versions of BMDS could not be run from a network drive.

BMDS 3.3 includes the following fixes and feature enhancements:

Fixed issue where deleting a dataset from the MS_Combo model type view did not delete the background column.
Fixed issue where CDF tabular results would jump to and cutoff at plateaus of 65535.
Fixed issue where rounding off returned negative values in log-likelihood ratios.
Fixed plot title for frequentist nested models where the wrong options were included.
Fixed summary reporting of the scaled residuals (min, max, avg of scaled residuals, and absolute values of scaled residuals).
Fixed issue with running multiple option sets for continuous models within the same analysis.

3.2.0.1

Released March 15, 2022

BMDS 3.2.0.1 removed the preview Bayesian continuous models from the application. No other changes or enhancements were made.

3.2

Released August 20, 2020

The most significant enhancement is the addition to the BMDS model suite of preview versions of Bayesian continuous models. Users can set up individual Bayesian model runs as Normal, Lognormal, or combined Normal and Lognormal.

BMDS 3.2 includes the following enhancements and fixes to the existing continuous models:

Rescaled the v parameter for the Hill model to agree with BMDS 2.7 results.
Rescaled model parameters during the optimization process to improve robustness and efficiency of optimization routines.
Devised a new maximum for the beta term in the Exponential 5 model (frequentist and Bayesian) for compatibility with the BMDS optimizers.
In some cases, some continuous models may not return values for the maximum-likelihood estimation (MLE). For these cases, BMDS will display an appropriate warning on the results summary tab for that model; the individual model result tab will not be created. This issue will be corrected in a future release.
For continuous models, when the degrees of freedom value is less than or equal to zero, BMDS now reports “NA.”
Fixed a bug with the continuous Bayesian check-all (“Enable”) button on the Main tab.

The BMDS 3.2 interface disables controls for continuous model averaging, which was originally slated to be included in this release. Continuous model averaging will appear in a future release.

BMDS 3.2 includes the following user interface enhancements

BMDS graphs now extend the plots to zero dose for all models. All plots will begin at dose=0, even if the data has a lowest dose greater than 0.
Added a hover tip to the “Select Output Directory” box that displays the full path name on the Analysis Workbook’s Main and Report Options tabs; the path is updated when a previous analysis is loaded, and when a user changes the specified output directory.
The first five rows of the Analysis Workbook’s Data tab are frozen to keep the Insert New Dataset and Import Dataset buttons visible as new datasets are entered.
On the Results Workbook’s Abbreviations tab, added the abbreviations list for all models (previously, only the dichotomous model abbreviations were listed).
On the Data tab, clarified custom header cells for datasets by 1) changing the custom header columns to “[Custom]”, and 2) adding informational text to the right of the Insert and Import buttons.
Added “Distribution” information for the continuous models on the ModelParms tab.
Improved error messaging for easier bug reporting when models fail while retrieving results from the dynamic link library (DLL).
The Results Workbook entry for Litter Specific Covariate (LSC) (under User Input > Model Options) now reports the fixed LSC value in output for nested models.

BMDS 3.2 includes the following fixes and feature enhancements:

Fixed a bug that caused dichotomous multi-tumor analysis (MS_Combo) to crash 64-bit Excel.
Fixed an MS_Combo bug that allowed multiple runs to be set as selected when searching for lowest Akaike Information Criterion (AIC) when no model parameters hit a boundary.
Corrected the equation used to plot the Dichotomous Hill dose-response curve.
When importing BMDS 2.7 .dax files that contain disallowed characters in the column headers, BMDS 3.2 will remove the disallowed characters.
Fixed an issue that caused “delete” buttons to render inaccurately when deleting option sets.
Fixed a bug in the model code that caused some model parameters to be incorrectly classified as bound.

3.1.2

Released November 8, 2019

BMDS 3.1.2 includes the following fixes, changes, and enhancements:

Fixed issue with unrestricted frequentist LogProbit model fitting for specific datasets.
Fixed issue with Weibull model crashes for specific datasets.
Fixed issue with dichotomous model crashes for some combinations of datasets and option sets.
Resolved continuous and dichotomous model convergence issues that caused result discrepancies between BMDS 2.7 and 3.1.1 in some cases.
Consistent with BMDS 2.x versions, 3.1.2 now defaults to the restricted version of the dichotomous Hill model.
The model weight column heading on the main tab of BMDS3.x was changed from "Model Weight" to "Prior Weights”, and added hover text to clarify intent of model weights.

3.1.1

Released July 31, 2019

BMDS 3.1.1 includes the following enhancements and changes:

Added Cumulative Distributive Function (CDF) table to BMDS results.
Users can now save datasets as .dax files to use later in another analysis.
A new Import Dataset button on the Data worksheet enables you to import .dax datasets created in BMDS 2.x or BMDS 3.x (starting with BMDS 3.1.1).
Data points have been added to summary plots for continuous, dichotomous, and nested model types.
Confidence interval error bars have been implemented for continuous and dichotomous model plots. Error bars for lognormal models will be implemented in a future release.
On the Main tab’s Datasets table, click the Enable checkbox in the header to toggle selection/deselection of all loaded datasets.
The following modifications were made to the MS_Combo (Multitumor) model
- The decision logic for the MS_Combo recommendations now employs the user-defined test thresholds from the logic worksheet for the following criteria:
  - Goodness of fit p-test (cancer)
  - Ratio of BMD/BMDL (caution)
  - Abs(Residual of interest) too large
  - Abs(Residual at control) too large
- If the analysis results do not meet the “Test Threshold” value set in the “Ratio of BMD/BMDL (Caution)” on the “Logic” tab, BMDS displays a pop-up message to the user that “BMD/BMDL ratio > [value]; consider consulting a statistician.” The model is not removed from the MS_Combo results.
- In the Model column, hover the cursor over a cell to see hover text containing the name of the dataset for each multistage run.
- Results for all multistage model degrees analyzed are presented on individual model result tabs. Only user-selected models are presented on the Summary tab.
- For the MS_Combo summary plot, individual tumors are now named according to the dataset (endpoint) name.
The “Test Threshold” default value for “Ratio of BMD/BMDL (Caution)” in the “Logic” tab was changed from 5 to 3 to be consistent with the BMDS Technical Guidance on Choosing Appropriate Stage of a Multistage Model for Cancer Modeling.
- Be careful when loading a previously saved analysis. Loading a previously saved analysis will also load the settings that were used for that analysis, which may be different from the new default test threshold settings.
To improve performance of creating Result workbooks, BMDS performs the following steps when processing continuous, dichotomous, and nested dichotomous datasets:
- Turn off screen updating.
- Close dataset files after they are generated (unless only one dataset is being analyzed).
- After all dataset files are created, inform user that “Result Workbook files have been saved to …” and display a confirmation dialog asking whether BMDS should open all of the result workbook files.
- If user responds “No” or cancels the operation, nothing happens. If the user responds “Yes,” then all Result Workbook files will be opened.

BMDS 3.1.1 also includes the following fixes:

Loading an analysis now loads datasets that were selected when the analysis was run/saved.
Improved continuous model convergence.
Fixed the parameter count issue for the first-degree multistage model.
Fixed a bug where MS_Combo was not using the “Test Threshold” value for “Ratio of BMD/BMDL (Caution)” in the “Logic” tab.
Fixed a bug related to Word report generation from MS_Combo analysis.

3.1

Released February 2019

Now compatible with all 32- and 64-bit versions of Excel released since 2007.
Numerous UI improvements and enhancements:
- Moved the "Load Analysis" button from result workbooks into the main analysis workbook to provide better workflow and more robust behavior.
- When changing the output directory, BMDS will prompt whether to save the new directory as the default
- Added links to the Summary table so that clicking a model's name displays the model's individual model results tab
- Redesigned the Report Options tab to make the Export and Word Report Options boxes expandable
- Added the dose-response and variance model formulas to the individual model output pages
- Fixed issue with model selection and added a more informative message when BMDL=0
- Fixed issue where the Results Workbook summary table reported inappropriate recommendations for Bayesian models
- Fixed Multistage plots so the linear extrapolation line for the goes to estimated background response, not zero
- Fixed a missing link for Model Averaging results
- Fixed issue with running a nested analysis with empty rows
- Fixed issue with Excel auto-adding secondary axis to plots
- Minor tweaks and updates to the user interface to enhance clarity and usability
- Added model and option set information to the "Running selected models" message box:

Numerous programmatic improvements and enhancements:
- Fixed an issue with Akaike Information Criterion (AIC) derivation for continuous response models
- Fixed issue where "Added Risk" and BMRF=0.001 caused slow performance for Dichotomous Hill and Bayesian MA models
- Fixed issue with Test 3 and Individual Response Analysis for continuous models
- Fixed issue with continuous models Likelihood of Interest reporting incorrect number of parameters
- Fixed issue with continuous models Test of Interest and p-values
- Fixed a problem with running BMDS from a network drive
- Fixed the Weibull model default parameter values and priors
- Fixed miscellaneous issues with the nested logistic model
- Fixed intermittent crashes with the Polynomial, Multistage and other models
- Resolved a problem with A3 and R log-likelihood values, which are used to measure goodness-of-fit
- Minor improvements

3.0

Released September 30, 2018.

Implemented in Microsoft Excel, with modeling computations performed in custom DLLs.
Fast analysis of multiple datasets and options
Enables users to see and specify modeling options in a single worksheet
Flexible documentation and report generation
Includes auto-selection features for identifying the “best” results in accordance with EPA recommendations or user-defined logic
Documents all inputs and outputs in a single results workbook for each dataset modeled
Provides flexible print options for displaying results in Microsoft Word tables formatted in a manner suitable for presentation in a risk assessment
Backwards compatible with prior BMDS versions
Bayesian versions of all traditional frequentist dichotomous models
Bayesian model averaging using all or weighted dichotomous models
Hybrid approach added to all continuous models
Lognormal response distribution added for all continuous models
All existing models have been re-coded to facilitate their maintenance and improve their performance in terms of stability, accuracy, reliability, and speed.