Clustered Binary Risk Assessment 

A developmental toxicology study looked at 1142 individual live fetuses born to 102 pregnant mice
exposed to 0, 0.25, 0.5, or 1 unit of a chemical. The output for the logit model shows summary data, and indicates death rates increasing from 4.77% in the control group to 20.96% in the highest dose group.
Note that the fetal death outcomes are clustered due to the "litter effect"; live fetuses (individuals) constitute a cluster. Switching from unclustered to clustered analysis is as easy as checking one box in ToxTools. 

To model fetal death, we choose a logit model using dose as the predictor variable.
Note the model dialog option for adding a cluster variable; here, the cluster variable is ID.

Model Dialog for a Logit Fit 

For fitted plots, simply choose the Fitted Plot option from the ToxTools Plot menu. The "Clusterwise" option allows a plot with observed cluster proportions and the fitted model. A clusterwise fitted plot for the Logit model is shown below.
Parameter estimates and other summary information for the clustered Logit model is also shown below.

The results indicate a highly significant dose effect.

ToxTools provides flexibility for presenting results. Plots can be saved in the output panels along with the text and tabular output. For example, the clusterwise fitted plot may be saved with the output results above by selecting the "Paste Graph" option as seen below. 

Clusterwise Fitted Plot for Logit Model and Output for Logit Model

Parameter estimates and other summary information for the clustered Logit model is shown below. The results indicate a highly significant dose effect.

Output for Logit Model

ToxTools provides flexibility for presenting results. Plots can be saved in the output panels along with the text and tabular output. For example, the clusterwise fitted plot may be saved with the output results above by selecting the "Paste Graph" option as seen below. 

Graph Output Menu

The window shown below displays the final result.

Plot saved in output panel along with text and tabular output.