How-to: Modeling Dichotomous Data in BMDS Online
For users new to BMDS Online, the following sections walk through the basics of creating and sharing an online analysis using dichotomous data. The steps also include tips on how to use BMDS Online effectively.
On this page:
Creating a New Analysis
- Navigate to the BMDS Online website.
- Select the Create a new BMDS analysis button (Figure 1).
BMDS Online displays a new, empty analysis page with the Settings tab selected (Figure 2). From here, you can configure an analysis, load a dataset, execute the analysis, and select results. Each BMDS Online analysis is self-contained; it includes all of the inputs and outputs for the executed analysis.
Analyses and URLs
When a new analysis is created, a unique URL is created for the analysis that can be shared with others (Figure 3).
You can create as many analyses as you want, but only the most recent execution is saved with an analysis. If you edit the data or add new data or new options, then the resulting analysis will overwrite the previous analysis.
Therefore, if you want to analyze multiple sets of data, create a new analysis instead of overwriting an existing analysis.
Configuring and Executing an Analysis
Steps Required to Run the Analysis
BMDS Online tracks the steps required to run an analysis (Figure 4). For a new analysis, the green checkmarks show that the default set of models and options have been selected for the analysis. Red x’s show that, currently, no dataset has been selected and the analysis has not been saved.
Specifying an Analysis
- On the Settings tab, specify a name and description for the analysis (Figure 5).
- Select the model type for your analysis (i.e., are you modeling dichotomous or continuous data?) (Figure 6). For this example, the dichotomous model type has been selected.
Note: An analysis can only be composed of a single model type; you cannot mix continuous and dichotomous data in single analysis. Instead, create two analyses. - Select which models will be used for the analysis. For this example, the default selection of dichotomous maximum-likelihood estimation (MLE) models will be used, plus all of the Bayesian dichotomous model averaging models. To use all the models in a column, check the Select All box (Figure 7).
- Select which option sets will be used for the analysis (maximum of six). For this example, we will create a single option set with the default benchmark response (BMR) of 10% extra risk.
You can add/delete option sets by clicking the blue plus or red trash can icons, respectively, to the right of the option set window (Figure 8).
Specifying Datasets
An analysis can have a maximum of 10 datasets.
- To add a dataset, click the Data tab to the top right of the screen (Figure 9).
- On the data tab, click the New button to add an individual dataset (Figure 10). BMDS Online can model dichotomous data (e.g., lesion incidence), summarized continuous data (e.g., data measured on a continuous scale and presented as means and standard deviations), and individual continuous data (data measured on a continuous scale presented as dose and response data for each test subject).
For this analysis, only the dichotomous option is shown for New dataset because dichotomous was chosen as the model type on the Settings tab. - After a new empty dataset has been added, you can specify the dataset name, dose name and units, and response name and units. BMDS Online will use this information to identify the dataset in results and reports.
For this example, the incidence of hepatocellular hyperplasia will be modeled with dose units of mg/kg-day, as noted in Figure 11. - You can add datasets to BMDS Online in two ways:
- Manually enter dose, N, and Incidence data by typing the data into the table. BMDS Online automatically adds five rows of data when adding new datasets. New rows can be added by clicking the blue plus icon; unneeded rows can be deleted by clicking the red trash can icon (Figure 12).
- Paste data directly from Excel into the table.
- Enter the data in Excel.
- Select and copy the Excel cells (numbers only; do not include column titles or header text) (Figure 13).
- In BMDS Online, select the aqua Excel icon in the dataset table header (Figure 14a). A Paste from Excel window displays.
Click the mouse inside the Paste from Excel window's text box, paste the data, and select the Load icon (Figure 14b). The dataset is then fully entered in BMDS Online.
Note that the plot to the right of the dataset table updates as data is entered (Figure 15).
Executing an Analysis and Viewing Results
- After all datasets are loaded, return to the Settings tab to run the analysis (Figure 16).
- On the Settings tab, a green checkmark now appears next to At least one dataset is selected (Figure 17).
- For dichotomous data, BMDS Online automatically selects the Maximum multistage degree to be 3. However, you may manually select a range of options from the drop-down menu (Figure 18). For this analysis, the default setting is used.
- Select the Save Analysis button to complete all the steps required to run analysis button. Notice that all steps now have a green checkmark next to them (Figure 19).
- Select the Run Analysis button to execute the analysis. A running analysis can be stopped by selecting the Cancel execution button (Figure 20).
- After successful execution, the modeling results are displayed on the Output tab (Figure 21).
- Numerical results are displayed in a summary table for all models. Select the Show icon in the Recommendation and Notes column header to display a full set of model notes and warnings (Figure 22). Select the Hide icon to hide the model notes (Figure 23).
- As users hover the cursor over rows within the Model Results table, individual model curves will display in the plot to the right (Figure 24).
- To investigate an individual model's results, select that model's name in the Model column. Doing so will display a window showing all of the numerical and graphical model outputs for that model (Figure 25).
- For the frequentist models, BMDS Online applies a set of model selection logic criteria to recommend a best fitting model (the blue row in Figure 24). The logic criteria used to make the recommendations are located on the Logic tab (Figure 26).
- On the Logic tab, you can investigate the criteria BMDS Online used to recommend the best fitting model. Users can change any of the criteria for model selection based on the needs of their analysis or to comport with the modeling guidance of their organizations. However, it is highly recommended that new users leave the logic settings as-is; logic settings should only be changed under the guidance of experienced modelers. For more information, refer to the BMDS User Guide, section 15.0, "BMDS Recommendations and Decision Logic."
- If any logic setting changes, the default logic settings can be reapplied by selecting the Reset to Default Logic button
- After you have confirmed the recommended model, or selected an alternative one, you can choose that model from the Selected best-fitting model picklist (Figure 27).
- Enter notes on model selection in the Selection notes window (Figure 28).
- Use the Save model selection button to finalize model selection. BMDS Online displays the selected model row in green, and any selection notes will be displayed in a footnote at the bottom of the table (Figure 29).
- Individual model and model averaging results can also be investigated by clicking on the desired row in the results table. In Figure 30, the Model Average link was selected to display the Model Average results graph. Hover the mouse across the curves to investigate results in more detail.
Analysis Downloading and Sharing
After an analysis has been configured and successfully executed, it can be downloaded or shared with others. The Share and Actions menus in the top-right corner of the analysis page include options for other ways to interact with the analysis.
Actions Menu
- Load analysis: load a previously downloaded analysis (using the Download analysis option described below).
- Extend deletion date: BMDS Online will store analyses for 180 days after the date of creation. Selecting Extend deletion date will extend deletion to 180 days from the time this button was clicked.
- Delete analysis: completely delete the current analysis. If an analysis is deleted, it cannot be restored.
- Download data: download the analysis data as an Excel file.
- Download report: download the analysis results as a Word file (options for the Word report include only the user-selected model, all models, and all models with the BMD Cumulative Data Function (CDF) table). Note that the Word report contains the analysis URL, and users can access their analyses via generated reports.
- Download analysis: download the analysis as a JSON file. This is a machine-readable file format that can be saved or shared, and uploaded via selecting Load Analysis for use in a subsequent analysis.
Share Menu
- Read-only links: users can use the link to view the current analysis and download reports, but cannot edit or execute the analysis.
- Edit link: users can use the link to edit the settings, change input data, and re-execute the analysis.
Only the Most Recent Analysis is Available
Note: When a link is shared, only the most recent execution of an analysis is preserved and would be available to others. Therefore, we recommend creating a new analysis whenever you want to perform a different analysis after sharing an analysis link.