add estimate_background option

USEPA · Nov 15, 2024 · 79f4f37 · 79f4f37
1 parent 1c3eaf9
commit 79f4f37
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Showing 8 changed files with 23 additions and 6 deletions.
diff --git a/bmds_ui/analysis/validators/options.py b/bmds_ui/analysis/validators/options.py
@@ -36,6 +36,7 @@ class NestedDichotomousOption(BaseModel):
     litter_specific_covariate: LitterSpecificCovariate
     bootstrap_iterations: int
     bootstrap_seed: int
+    estimate_background: bool
 
 
 class DichotomousOptions(BaseModel):

diff --git a/frontend/src/components/IndividualModel/ModelOptionsTable.js b/frontend/src/components/IndividualModel/ModelOptionsTable.js
@@ -2,7 +2,7 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
-import {getLabel} from "@/common";
+import {checkOrEmpty, getLabel} from "@/common";
 import TwoColumnTable from "@/components/common/TwoColumnTable";
 import {Dtype} from "@/constants/dataConstants";
 import {hasDegrees} from "@/constants/modelConstants";
@@ -70,8 +70,6 @@ class ModelOptionsTable extends Component {
                 ["BMR Type", getLabel(model.settings.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(model.settings.bmr)],
                 ["Confidence Level (one sided)", ff(1 - model.settings.alpha)],
-                ["Bootstrap Seed", model.settings.bootstrap_seed],
-                ["Bootstrap Iterations", model.settings.bootstrap_iterations],
                 [
                     "Litter Specific Covariate",
                     getLabel(
@@ -83,6 +81,9 @@ class ModelOptionsTable extends Component {
                     "Intralitter Correlation",
                     getLabel(model.settings.intralitter_correlation, intralitterCorrelation),
                 ],
+                ["Estimate Background", checkOrEmpty(model.settings.estimate_background)],
+                ["Bootstrap Iterations", model.settings.bootstrap_iterations],
+                ["Bootstrap Seed", model.settings.bootstrap_seed],
             ];
         } else {
             throw "Unknown dtype";

diff --git a/frontend/src/components/Main/OptionsForm/OptionsForm.js b/frontend/src/components/Main/OptionsForm/OptionsForm.js
@@ -10,6 +10,7 @@ import {
 } from "@/constants/optionsConstants";
 
 import Button from "../../common/Button";
+import CheckboxInput from "../../common/CheckboxInput";
 import FloatInput from "../../common/FloatInput";
 import IntegerInput from "../../common/IntegerInput";
 import SelectInput from "../../common/SelectInput";
@@ -99,6 +100,14 @@ const OptionsForm = props => {
                                 })}
                         />
                     </td>
+                    <td>
+                        <CheckboxInput
+                            checked={props.options.estimate_background}
+                            onChange={value =>
+                                props.saveOptions("estimate_background", value, props.idx)
+                            }
+                        />
+                    </td>
                     <td>
                         <IntegerInput
                             value={props.options.bootstrap_iterations}

diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -69,6 +69,7 @@ class OptionsFormList extends Component {
                                                 <br />
                                                 Covariate
                                             </th>
+                                            <th>Estimate Background</th>
                                             <th>
                                                 Bootstrap
                                                 <br />

diff --git a/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js b/frontend/src/components/Main/OptionsForm/OptionsReadOnly.js
@@ -2,6 +2,7 @@ import PropTypes from "prop-types";
 import React from "react";
 
 import {getLabel} from "@/common";
+import {checkOrEmpty} from "@/common";
 import {
     MODEL_CONTINUOUS,
     MODEL_DICHOTOMOUS,
@@ -48,6 +49,7 @@ const OptionsReadOnly = props => {
                             litterSpecificCovariateOptions
                         )}
                     </td>
+                    <td>{checkOrEmpty(options.estimate_background)}</td>
                     <td>{options.bootstrap_iterations}</td>
                     <td>{options.bootstrap_seed}</td>
                 </>

diff --git a/frontend/src/components/Output/OptionSetTable.js b/frontend/src/components/Output/OptionSetTable.js
@@ -3,7 +3,7 @@ import {inject, observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
-import {getLabel} from "@/common";
+import {checkOrEmpty, getLabel} from "@/common";
 import {adverseDirectionOptions, allDegreeOptions} from "@/constants/dataConstants";
 import {MODEL_CONTINUOUS, MODEL_DICHOTOMOUS} from "@/constants/mainConstants";
 import {
@@ -56,15 +56,16 @@ class OptionSetTable extends Component {
                 ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(selectedModelOptions.bmr_value)],
                 ["Confidence Level (one sided)", ff(selectedModelOptions.confidence_level)],
-                ["Bootstrap Seed", selectedModelOptions.bootstrap_seed],
-                ["Bootstrap Iterations", selectedModelOptions.bootstrap_iterations],
                 [
                     "Litter Specific Covariate",
                     getLabel(
                         selectedModelOptions.litter_specific_covariate,
                         litterSpecificCovariateOptions
                     ),
                 ],
+                ["Estimate Background", checkOrEmpty(selectedModelOptions.estimate_background)],
+                ["Bootstrap Seed", selectedModelOptions.bootstrap_seed],
+                ["Bootstrap Iterations", selectedModelOptions.bootstrap_iterations],
             ];
         } else if (outputStore.isMultiTumor) {
             rows = [

diff --git a/frontend/src/constants/optionsConstants.js b/frontend/src/constants/optionsConstants.js
@@ -25,6 +25,7 @@ export const options = {
             litter_specific_covariate: 1,
             bootstrap_iterations: 1000,
             bootstrap_seed: 0,
+            estimate_background: true,
         },
         [MODEL_MULTI_TUMOR]: {
             bmr_type: 1,

diff --git a/tests/analysis/test_validators.py b/tests/analysis/test_validators.py
@@ -127,6 +127,7 @@ def test_nested_dichotomous(self, nested_dichotomous_datasets):
                 "litter_specific_covariate": 1,
                 "bootstrap_iterations": 1000,
                 "bootstrap_seed": 0,
+                "estimate_background": True,
             }
         ]
         assert validators.validate_input(data, partial=True) is None