From 97ba90f2c7ec1e5bbdfdec4c660f415dda390781 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Thu, 14 Nov 2024 12:15:42 -0500
Subject: [PATCH 01/17] make top level headers h1 and h2 instead of h2 and h3

---
 bmds_ui/analysis/templates/analysis/desktop_home.html | 2 +-
 bmds_ui/static/css/epa/bmdsonline.css                 | 8 ++++++++
 bmds_ui/templates/includes/epa/header.html            | 2 +-
 frontend/src/App.js                                   | 4 ++--
 4 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/bmds_ui/analysis/templates/analysis/desktop_home.html b/bmds_ui/analysis/templates/analysis/desktop_home.html
index 5a342cc1..97f8cd03 100644
--- a/bmds_ui/analysis/templates/analysis/desktop_home.html
+++ b/bmds_ui/analysis/templates/analysis/desktop_home.html
@@ -7,7 +7,7 @@
   <div class="col-lg-8">
 
     <div class="d-flex">
-      <h3 class="flex-grow-1">Analyses</h3>
+      <h2 class="flex-grow-1">Analyses</h2>
 
       <div class="dropdown mr-2">
         <button class="btn btn-secondary dropdown-toggle" type="button" data-toggle="dropdown" aria-expanded="false">Collections</button>
diff --git a/bmds_ui/static/css/epa/bmdsonline.css b/bmds_ui/static/css/epa/bmdsonline.css
index 8f1d43b2..20b75e40 100644
--- a/bmds_ui/static/css/epa/bmdsonline.css
+++ b/bmds_ui/static/css/epa/bmdsonline.css
@@ -83,3 +83,11 @@ a.dropdown-toggle:not([href])::after {
 .bmds-desktop,.footer__column{
   width: 100%;
 }
+
+/* reduce font size */
+h1 {
+  font-size: 2rem;
+}
+h2 {
+  font-size: 1.7rem;
+}
diff --git a/bmds_ui/templates/includes/epa/header.html b/bmds_ui/templates/includes/epa/header.html
index 07b225cb..cccb63c6 100644
--- a/bmds_ui/templates/includes/epa/header.html
+++ b/bmds_ui/templates/includes/epa/header.html
@@ -111,7 +111,7 @@
   {% endif %}
 </header>
 <nav class="bmds-header navbar justify-content-between">
-    <h2><a href="{% url 'home' %}">{% if IS_DESKTOP %}Benchmark Dose Tools (BMDS) Desktop{% else %}Benchmark Dose Tools (BMDS) Online{% endif %}</a></h2>
+    <h1><a href="{% url 'home' %}">{% if IS_DESKTOP %}Benchmark Dose Tools (BMDS) Desktop{% else %}Benchmark Dose Tools (BMDS) Online{% endif %}</a></h1>
     <ul class="nav text-right">
         {% if user.is_staff %}
         <li class="nav-item">
diff --git a/frontend/src/App.js b/frontend/src/App.js
index 2648d305..bbc3103c 100644
--- a/frontend/src/App.js
+++ b/frontend/src/App.js
@@ -36,7 +36,7 @@ class App extends Component {
 
         return this.props.mainStore.isUpdateComplete ? (
             <HashRouter>
-                <h3>
+                <h2>
                     {getHeader()}
                     {isFuture ? (
                         <span
@@ -47,7 +47,7 @@ class App extends Component {
                             <Icon name="lightning-fill" />
                         </span>
                     ) : null}
-                </h3>
+                </h2>
                 <Navigation />
             </HashRouter>
         ) : null;

From f02553d41d6d620a3914df65de0435c392cb7767 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Thu, 14 Nov 2024 15:12:18 -0500
Subject: [PATCH 02/17] more header level fixes

---
 bmds_ui/static/css/epa/bmdsonline.css                  | 3 +++
 frontend/src/components/Logic/LogicRoot.js             | 1 +
 frontend/src/components/Logic/RuleTable.js             | 3 ---
 frontend/src/components/Output/Output.js               | 6 +++---
 frontend/src/components/transforms/polyk/AboutModal.js | 2 +-
 5 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/bmds_ui/static/css/epa/bmdsonline.css b/bmds_ui/static/css/epa/bmdsonline.css
index 20b75e40..383b44b8 100644
--- a/bmds_ui/static/css/epa/bmdsonline.css
+++ b/bmds_ui/static/css/epa/bmdsonline.css
@@ -91,3 +91,6 @@ h1 {
 h2 {
   font-size: 1.7rem;
 }
+h2 {
+  font-size: 1.5rem;
+}
diff --git a/frontend/src/components/Logic/LogicRoot.js b/frontend/src/components/Logic/LogicRoot.js
index 477b8c9b..bcfb42b8 100644
--- a/frontend/src/components/Logic/LogicRoot.js
+++ b/frontend/src/components/Logic/LogicRoot.js
@@ -23,6 +23,7 @@ class Logic extends Component {
         return (
             <div className="container-fluid">
                 <DecisionLogic />
+                <h3>Model Recommendation and Bin Placement Logic</h3>
                 <RuleTable />
             </div>
         );
diff --git a/frontend/src/components/Logic/RuleTable.js b/frontend/src/components/Logic/RuleTable.js
index 5380e3ed..c47d9128 100644
--- a/frontend/src/components/Logic/RuleTable.js
+++ b/frontend/src/components/Logic/RuleTable.js
@@ -18,9 +18,6 @@ class RuleList extends Component {
         return (
             <table id="rule-table" className="table table-sm">
                 <thead className="bg-custom">
-                    <tr>
-                        <th colSpan="5">Model Recommendation and Bin Placement Logic</th>
-                    </tr>
                     <tr>
                         <th>Test Description</th>
                         <th>Enabled</th>
diff --git a/frontend/src/components/Output/Output.js b/frontend/src/components/Output/Output.js
index ca3f3437..48453b28 100644
--- a/frontend/src/components/Output/Output.js
+++ b/frontend/src/components/Output/Output.js
@@ -120,7 +120,7 @@ class Output extends Component {
                     outputStore.isMultiTumor ? (
                         <div className="row">
                             <div className="col-lg-12">
-                                <h4>Model Results</h4>
+                                <h3>Model Results</h3>
                                 <MultitumorResultTable />
                                 <MultitumorPlot />
                             </div>
@@ -128,7 +128,7 @@ class Output extends Component {
                     ) : (
                         <div className="row py-2">
                             <div className="col-lg-8">
-                                <h4>Maximum Likelihood Approach Model Results</h4>
+                                <h3>Maximum Likelihood Approach Model Results</h3>
                                 <FrequentistResultTable />
                                 {canEdit ? <SelectModel /> : null}
                             </div>
@@ -145,7 +145,7 @@ class Output extends Component {
                 {selectedBayesian ? (
                     <div className="row py-2">
                         <div className="col-lg-12">
-                            <h4>Bayesian Model Results</h4>
+                            <h3>Bayesian Model Results</h3>
                             <BayesianResultTable />
                         </div>
                         <div className="col-lg-12">
diff --git a/frontend/src/components/transforms/polyk/AboutModal.js b/frontend/src/components/transforms/polyk/AboutModal.js
index 859ade69..45b2dea7 100644
--- a/frontend/src/components/transforms/polyk/AboutModal.js
+++ b/frontend/src/components/transforms/polyk/AboutModal.js
@@ -197,7 +197,7 @@ class AboutModal extends Component {
                             that each animal provides to the denominator
                         </li>
                     </ol>
-                    <h4>References:</h4>
+                    <h2>References:</h2>
                     <p>
                         Kissling GE, Portier CJ, Huff J. (2008) MtBE and cancer in animals:
                         statistical issues with poly-3 survival adjustments for lifetime studies.

From 7afc57b2622ef98c38addc9364f58bb5eb36e4ab Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Thu, 14 Nov 2024 15:14:52 -0500
Subject: [PATCH 03/17] add optional attrs to popover

---
 frontend/src/components/common/Popover.js | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/frontend/src/components/common/Popover.js b/frontend/src/components/common/Popover.js
index 3711d20e..7a0f1ce7 100644
--- a/frontend/src/components/common/Popover.js
+++ b/frontend/src/components/common/Popover.js
@@ -16,7 +16,7 @@ class Popover extends Component {
         $(this.domNode.current).popover("dispose");
     }
     render() {
-        const {children, content, title, element} = this.props;
+        const {children, content, title, element, attrs} = this.props;
         let props = _.fromPairs([
             ["ref", this.domNode],
             ["title", title],
@@ -25,6 +25,9 @@ class Popover extends Component {
             ["data-toggle", "popover"],
             ["data-content", content],
         ]);
+        if (attrs) {
+            _.extend(props, attrs);
+        }
         return React.createElement(element, props, children);
     }
 }
@@ -33,6 +36,7 @@ Popover.propTypes = {
     content: PropTypes.string.isRequired,
     title: PropTypes.string.isRequired,
     children: PropTypes.node.isRequired,
+    attrs: PropTypes.object,
 };
 Popover.defaultProps = {
     element: "div",

From 9d197786f7f865be247fc2804cf59b5a17003367 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Thu, 14 Nov 2024 15:15:05 -0500
Subject: [PATCH 04/17] label complex tables

---
 .../Main/ModelsForm/ModelsCheckBox.js         | 204 +++++++++++-------
 .../Main/ModelsForm/ModelsCheckBoxHeader.js   |  10 +-
 .../Output/FrequentistResultTable.js          |  54 ++---
 3 files changed, 155 insertions(+), 113 deletions(-)

diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
index 37f2546e..947a9926 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
@@ -32,34 +32,46 @@ const isModelChecked = function(models, type, model) {
     },
     PriorWeightTd = observer(props => {
         const {store, model, disabled} = props;
-        return store.canEdit ? (
-            <td>
-                <FloatInput
-                    disabled={disabled}
-                    value={getPriorWeightValue(store.models, model)}
-                    onChange={value => store.setPriorWeight(model, value)}
-                />
+        return (
+            <td headers="b-p">
+                {store.canEdit ? (
+                    <FloatInput
+                        disabled={disabled}
+                        value={getPriorWeightValue(store.models, model)}
+                        onChange={value => store.setPriorWeight(model, value)}
+                    />
+                ) : (
+                    getPriorWeightValue(store.models, model)
+                )}
             </td>
-        ) : (
-            <td>{getPriorWeightValue(store.models, model)}</td>
         );
     }),
     CheckBoxTd = observer(props => {
-        const {store, type, model, disabled} = props,
-            id = `${type}-${model}`;
-        return store.canEdit ? (
-            <td key={id}>
-                <CheckboxInput
-                    id={id}
-                    disabled={disabled}
-                    onChange={value => store.setModelSelection(type, model, value)}
-                    checked={isModelChecked(store.models, type, model)}
-                />
+        const {store, type, model, disabled, headers} = props,
+            key = `${type}-${model}`;
+        return (
+            <td key={key} headers={headers}>
+                {store.canEdit ? (
+                    <CheckboxInput
+                        id={key}
+                        disabled={disabled}
+                        onChange={value => store.setModelSelection(type, model, value)}
+                        checked={isModelChecked(store.models, type, model)}
+                    />
+                ) : (
+                    checkOrEmpty(isModelChecked(store.models, type, model))
+                )}
             </td>
-        ) : (
-            <td key={id}>{checkOrEmpty(isModelChecked(store.models, type, model))}</td>
         );
     }),
+    ModelHeaderTd = ({name, extra}) => {
+        return (
+            <td className="text-left align-middle" headers="m-name">
+                {name}
+                {extra ? extra : null}
+            </td>
+        );
+    },
     multistageHelpText = `All Multistage model polynomial degrees will be run up to a maximum
         degree as specified by the user. For Bayesian Model Averaging, only the 2nd degree
         Multistage model is used (see User Manual for details).`,
@@ -74,29 +86,29 @@ const ModelsCheckBox = observer(props => {
         return (
             <tbody>
                 <tr>
-                    <td className="text-left align-middle">Exponential</td>
-                    <CheckBoxTd store={store} type={fr} model={"Exponential"} />
-                    <td></td>
+                    <ModelHeaderTd name="Exponential" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Exponential"} />
+                    <td id="mle-u"></td>
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Hill</td>
-                    <CheckBoxTd store={store} type={fr} model={"Hill"} />
-                    <CheckBoxTd store={store} type={fu} model={"Hill"} />
+                    <ModelHeaderTd name="Hill" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Hill"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Hill"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Linear</td>
-                    <td></td>
-                    <CheckBoxTd store={store} type={fu} model={"Linear"} />
+                    <ModelHeaderTd name="Linear" />
+                    <td id="mle-r"></td>
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Linear"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Polynomial</td>
-                    <CheckBoxTd store={store} type={fr} model={"Polynomial"} />
-                    <CheckBoxTd store={store} type={fu} model={"Polynomial"} />
+                    <ModelHeaderTd name="Polynomial" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Polynomial"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Polynomial"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Power</td>
-                    <CheckBoxTd store={store} type={fr} model={"Power"} />
-                    <CheckBoxTd store={store} type={fu} model={"Power"} />
+                    <ModelHeaderTd name="Power" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Power"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Power"} />
                 </tr>
             </tbody>
         );
@@ -104,69 +116,79 @@ const ModelsCheckBox = observer(props => {
         return (
             <tbody>
                 <tr>
-                    <td className="text-left align-middle">Dichotomous Hill</td>
-                    <CheckBoxTd store={store} type={fr} model={"Dichotomous-Hill"} />
-                    <CheckBoxTd store={store} type={fu} model={"Dichotomous-Hill"} />
-                    <CheckBoxTd store={store} type={b} model={"Dichotomous-Hill"} />
+                    <ModelHeaderTd name="Dichotomous Hill" />
+                    <CheckBoxTd
+                        store={store}
+                        type={fr}
+                        headers="mle-r"
+                        model={"Dichotomous-Hill"}
+                    />
+                    <CheckBoxTd
+                        store={store}
+                        type={fu}
+                        headers="mle-u"
+                        model={"Dichotomous-Hill"}
+                    />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Dichotomous-Hill"} />
                     <PriorWeightTd store={store} model={"Dichotomous-Hill"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Gamma</td>
-                    <CheckBoxTd store={store} type={fr} model={"Gamma"} />
-                    <CheckBoxTd store={store} type={fu} model={"Gamma"} />
-                    <CheckBoxTd store={store} type={b} model={"Gamma"} />
+                    <ModelHeaderTd name="Gamma" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Gamma"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Gamma"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Gamma"} />
                     <PriorWeightTd store={store} model={"Gamma"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Logistic</td>
-                    <td></td>
-                    <CheckBoxTd store={store} type={fu} model={"Logistic"} />
-                    <CheckBoxTd store={store} type={b} model={"Logistic"} />
+                    <ModelHeaderTd name="Logistic" />
+                    <td headers="mle-r"></td>
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Logistic"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Logistic"} />
                     <PriorWeightTd store={store} model={"Logistic"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Log Logistic</td>
-                    <CheckBoxTd store={store} type={fr} model={"LogLogistic"} />
-                    <CheckBoxTd store={store} type={fu} model={"LogLogistic"} />
-                    <CheckBoxTd store={store} type={b} model={"LogLogistic"} />
+                    <ModelHeaderTd name="Log Logistic" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"LogLogistic"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"LogLogistic"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"LogLogistic"} />
                     <PriorWeightTd store={store} model={"LogLogistic"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">LogProbit</td>
-                    <CheckBoxTd store={store} type={fr} model={"LogProbit"} />
-                    <CheckBoxTd store={store} type={fu} model={"LogProbit"} />
-                    <CheckBoxTd store={store} type={b} model={"LogProbit"} />
+                    <ModelHeaderTd name="Log Probit" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"LogProbit"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"LogProbit"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"LogProbit"} />
                     <PriorWeightTd store={store} model={"LogProbit"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">
-                        Multistage
-                        {writeMode ? <HelpTextPopover content={multistageHelpText} /> : null}
-                    </td>
-                    <CheckBoxTd store={store} type={fr} model={"Multistage"} />
-                    <CheckBoxTd store={store} type={fu} model={"Multistage"} />
-                    <CheckBoxTd store={store} type={b} model={"Multistage"} />
+                    <ModelHeaderTd
+                        name="Multistage"
+                        extra={writeMode ? <HelpTextPopover content={multistageHelpText} /> : null}
+                    />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Multistage"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Multistage"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Multistage"} />
                     <PriorWeightTd store={store} model={"Multistage"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Probit</td>
-                    <td></td>
-                    <CheckBoxTd store={store} type={fu} model={"Probit"} />
-                    <CheckBoxTd store={store} type={b} model={"Probit"} />
+                    <ModelHeaderTd name="Probit" />
+                    <td headers="mle-r"></td>
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Probit"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Probit"} />
                     <PriorWeightTd store={store} model={"Probit"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Quantal Linear</td>
-                    <td></td>
-                    <CheckBoxTd store={store} type={fu} model={"Quantal Linear"} />
-                    <CheckBoxTd store={store} type={b} model={"Quantal Linear"} />
+                    <ModelHeaderTd name="Quantal Linear" />
+                    <td headers="mle-r"></td>
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Quantal Linear"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Quantal Linear"} />
                     <PriorWeightTd store={store} model={"Quantal Linear"} />
                 </tr>
                 <tr>
-                    <td className="text-left align-middle">Weibull</td>
-                    <CheckBoxTd store={store} type={fr} model={"Weibull"} />
-                    <CheckBoxTd store={store} type={fu} model={"Weibull"} />
-                    <CheckBoxTd store={store} type={b} model={"Weibull"} />
+                    <ModelHeaderTd name="Weibull" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Weibull"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Weibull"} />
+                    <CheckBoxTd store={store} type={b} headers="b-i" model={"Weibull"} />
                     <PriorWeightTd store={store} model={"Weibull"} />
                 </tr>
             </tbody>
@@ -175,14 +197,26 @@ const ModelsCheckBox = observer(props => {
         return (
             <tbody>
                 <tr>
-                    <td className="text-left align-middle">Nested Logistic</td>
-                    <CheckBoxTd store={store} type={fr} model={"Nested Logistic"} />
-                    <CheckBoxTd store={store} type={fu} model={"Nested Logistic"} />
-                </tr>
-                <tr>
-                    <td className="text-left align-middle">NCTR</td>
-                    <CheckBoxTd store={store} type={fr} model={"NCTR"} disabled={true} />
-                    <CheckBoxTd store={store} type={fu} model={"NCTR"} disabled={true} />
+                    <ModelHeaderTd name="Nested Logistic" />
+                    <CheckBoxTd store={store} type={fr} headers="mle-r" model={"Nested Logistic"} />
+                    <CheckBoxTd store={store} type={fu} headers="mle-u" model={"Nested Logistic"} />
+                </tr>
+                <tr>
+                    <ModelHeaderTd name="NCTR" />
+                    <CheckBoxTd
+                        store={store}
+                        type={fr}
+                        headers="mle-r"
+                        model={"NCTR"}
+                        disabled={true}
+                    />
+                    <CheckBoxTd
+                        store={store}
+                        type={fu}
+                        headers="mle-u"
+                        model={"NCTR"}
+                        disabled={true}
+                    />
                 </tr>
             </tbody>
         );
@@ -193,4 +227,8 @@ const ModelsCheckBox = observer(props => {
 ModelsCheckBox.propTypes = {
     store: PropTypes.any,
 };
+ModelHeaderTd.propTypes = {
+    name: PropTypes.string.isRequired,
+    extra: PropTypes.node,
+};
 export default ModelsCheckBox;
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js
index 456c69ea..2e1ad476 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js
@@ -49,7 +49,7 @@ const ModelsCheckBoxHeader = observer(props => {
             <ModelColGroup hasBayesianModels={hasBayesianModels} />
             <thead className="bg-custom">
                 <tr>
-                    <th className="align-top" rowSpan="2">
+                    <th className="align-top" rowSpan="2" id="m-name">
                         Model
                         {canEdit ? (
                             <>
@@ -65,7 +65,7 @@ const ModelsCheckBoxHeader = observer(props => {
                     {hasBayesianModels ? <th colSpan="2">Bayesian Model Averaging</th> : null}
                 </tr>
                 <tr>
-                    <th>
+                    <th id="mle-r">
                         Restricted
                         {canEdit ? (
                             <>
@@ -78,7 +78,7 @@ const ModelsCheckBoxHeader = observer(props => {
                             </>
                         ) : null}
                     </th>
-                    <th>
+                    <th id="mle-ur">
                         Unrestricted
                         {canEdit ? (
                             <>
@@ -93,7 +93,7 @@ const ModelsCheckBoxHeader = observer(props => {
                     </th>
                     {hasBayesianModels ? (
                         <>
-                            <th>
+                            <th id="b-i">
                                 Include
                                 {canEdit ? (
                                     <>
@@ -106,7 +106,7 @@ const ModelsCheckBoxHeader = observer(props => {
                                     </>
                                 ) : null}
                             </th>
-                            <th>
+                            <th id="b-p">
                                 <span className="mb-1">Prior Weight</span>
                             </th>
                         </>
diff --git a/frontend/src/components/Output/FrequentistResultTable.js b/frontend/src/components/Output/FrequentistResultTable.js
index dce5cb52..607fb0d2 100644
--- a/frontend/src/components/Output/FrequentistResultTable.js
+++ b/frontend/src/components/Output/FrequentistResultTable.js
@@ -131,7 +131,7 @@ class FrequentistRowSet extends Component {
         return (
             <>
                 <tr>
-                    <td colSpan={colSpan}>
+                    <td colSpan={colSpan} headers="m-name">
                         <b>
                             <u>{label}</u>
                         </b>
@@ -165,7 +165,7 @@ class ModelNameTd extends Component {
     render() {
         const {store, data, rowIcon, modelClasses} = this.props;
         return (
-            <td>
+            <td headers="m-name">
                 <a
                     id={`freq-result-${data.index}`}
                     href="#"
@@ -204,13 +204,17 @@ class RecommendationTd extends Component {
                     .join("<br/>") || "<i>No notes.</i>";
 
         return store.showInlineNotes ? (
-            <td>
+            <td headers="rec">
                 <u>{getModelBinLabel(selectedFrequentist, data.index)}</u>
                 <br />
                 {getRecommenderText(selectedFrequentist, data.index)}
             </td>
         ) : (
-            <Popover element="td" title={popoverTitle} content={popoverContent}>
+            <Popover
+                element="td"
+                title={popoverTitle}
+                content={popoverContent}
+                attrs={{headers: "rec"}}>
                 <u>{getModelBinLabel(selectedFrequentist, data.index)}</u>
             </Popover>
         );
@@ -244,17 +248,17 @@ class FrequentistRow extends Component {
                         rowIcon={rowIcon}
                         modelClasses={modelClasses}
                     />
-                    <td>
+                    <td headers="bmdl">
                         <FloatingPointHover value={results.bmdl} />
                     </td>
-                    <td>
+                    <td headers="bmd">
                         <FloatingPointHover value={results.bmd} />
                     </td>
-                    <td>
+                    <td headers="bmdu">
                         <FloatingPointHover value={results.bmdu} />
                     </td>
-                    <td>{ff(results.combined_pvalue)}</td>
-                    <td>
+                    <td headers="p_value">{ff(results.combined_pvalue)}</td>
+                    <td headers="aic">
                         <FloatingPointHover value={results.aic} />
                     </td>
                     <RecommendationTd
@@ -277,21 +281,21 @@ class FrequentistRow extends Component {
                     rowIcon={rowIcon}
                     modelClasses={modelClasses}
                 />
-                <td>
+                <td headers="bmdl">
                     <FloatingPointHover value={results.bmdl} />
                 </td>
-                <td>
+                <td headers="bmd">
                     <FloatingPointHover value={results.bmd} />
                 </td>
-                <td>
+                <td headers="bmdu">
                     <FloatingPointHover value={results.bmdu} />
                 </td>
-                <td>{fractionalFormatter(getPValue(dataset.dtype, results))}</td>
-                <td>
+                <td headers="p_value">{fractionalFormatter(getPValue(dataset.dtype, results))}</td>
+                <td headers="aic">
                     <FloatingPointHover value={results.fit.aic} />
                 </td>
-                <td>{ff(results.gof.residual[0])}</td>
-                <td>{ff(results.gof.roi)}</td>
+                <td headers="roi0">{ff(results.gof.residual[0])}</td>
+                <td headers="roi1">{ff(results.gof.roi)}</td>
                 <RecommendationTd
                     store={store}
                     data={data}
@@ -343,18 +347,18 @@ class FrequentistResultTable extends Component {
                 </colgroup>
                 <thead>
                     <tr className="bg-custom">
-                        <th>Model</th>
-                        <th>BMDL</th>
-                        <th>BMD</th>
-                        <th>BMDU</th>
-                        <th>
+                        <th id="m-name">Model</th>
+                        <th id="bmdl">BMDL</th>
+                        <th id="bmd">BMD</th>
+                        <th id="bmdu">BMDU</th>
+                        <th id="p_value">
                             <i>P</i>-Value
                         </th>
-                        <th>AIC</th>
-                        {isNestedDichotomous ? null : <th>Scaled Residual at Control</th>}
-                        {isNestedDichotomous ? null : <th>Scaled Residual near BMD</th>}
+                        <th id="aic">AIC</th>
+                        {isNestedDichotomous ? null : <th id="roi0">Scaled Residual at Control</th>}
+                        {isNestedDichotomous ? null : <th id="roi1">Scaled Residual near BMD</th>}
                         {store.recommendationEnabled ? (
-                            <th>
+                            <th id="rec">
                                 <Button
                                     title="Toggle showing notes inline or popover"
                                     className="btn btn-info btn-sm float-right"

From a0829ec2ddca9b79bea190edc79a9dfa6a3beca0 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 09:20:56 -0500
Subject: [PATCH 05/17] fix scrub_db

---
 bmds_ui/common/management/commands/scrub_db.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/bmds_ui/common/management/commands/scrub_db.py b/bmds_ui/common/management/commands/scrub_db.py
index 812e1624..0539d3a9 100644
--- a/bmds_ui/common/management/commands/scrub_db.py
+++ b/bmds_ui/common/management/commands/scrub_db.py
@@ -4,7 +4,7 @@
 from django.contrib.auth.hashers import make_password
 from django.core.management.base import BaseCommand, CommandError
 from django.db import transaction
-from django.db.models import Value
+from django.db.models import CharField, Value
 from django.db.models.functions import Concat
 
 
@@ -41,10 +41,10 @@ def update_users(self):
 
         # save all programs
         get_user_model().objects.update(
-            first_name=Concat(Value("first-"), "id"),
-            last_name=Concat(Value("last-"), "id"),
-            username=Concat(Value("username-"), "id"),
-            email=Concat(Value("user-"), "id", Value("@bmdsonline.org")),
+            first_name=Concat(Value("f-"), "id", output_field=CharField()),
+            last_name=Concat(Value("l-"), "id", output_field=CharField()),
+            username=Concat(Value("u-"), "id", output_field=CharField()),
+            email=Concat(Value("e-"), "id", Value("@bmdsonline.org"), output_field=CharField()),
             password=hash_password,
         )
 

From 57299b46f29080b517b81c689e35fa70bfabc5a5 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 09:21:31 -0500
Subject: [PATCH 06/17] simplify api schema

---
 bmds_ui/analysis/schema.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/bmds_ui/analysis/schema.py b/bmds_ui/analysis/schema.py
index 3e01b498..3863bd7e 100644
--- a/bmds_ui/analysis/schema.py
+++ b/bmds_ui/analysis/schema.py
@@ -95,17 +95,4 @@ def add_schema_to_path(schema: dict, path: str, verb: str, name: str):
 
 
 class ApiSchemaGenerator(SchemaGenerator):
-    def get_schema(self, *args, **kwargs):
-        schema = super().get_schema(*args, **kwargs)
-        add_schemas(schema, [EditKeySchema, WrappedAnalysisSelectedSchema])
-        add_schema_to_path(schema, "/api/v1/analysis/{id}/execute/", "post", EditKeySchema.__name__)
-        add_schema_to_path(
-            schema, "/api/v1/analysis/{id}/execute-reset/", "post", EditKeySchema.__name__
-        )
-        add_schema_to_path(
-            schema,
-            "/api/v1/analysis/{id}/select-model/",
-            "post",
-            WrappedAnalysisSelectedSchema.__name__,
-        )
-        return schema
+    pass

From 78600d5d87c4f52c9e8e2475aa43bf767c54e6a2 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 09:21:45 -0500
Subject: [PATCH 07/17] remove throttle api endpoint

---
 bmds_ui/common/api.py    | 11 +----------
 tests/common/test_api.py | 21 ---------------------
 2 files changed, 1 insertion(+), 31 deletions(-)

diff --git a/bmds_ui/common/api.py b/bmds_ui/common/api.py
index 2c4135f2..2d527826 100644
--- a/bmds_ui/common/api.py
+++ b/bmds_ui/common/api.py
@@ -1,4 +1,4 @@
-from rest_framework import permissions, status, viewsets
+from rest_framework import status, viewsets
 from rest_framework.decorators import action
 from rest_framework.response import Response
 from rest_framework.throttling import UserRateThrottle
@@ -20,12 +20,3 @@ def worker(self, request):
         is_healthy = worker_healthcheck.healthy()
         status_code = status.HTTP_200_OK if is_healthy else status.HTTP_503_SERVICE_UNAVAILABLE
         return Response({"healthy": is_healthy}, status=status_code)
-
-    @action(
-        detail=False,
-        permission_classes=(permissions.IsAdminUser,),
-        throttle_classes=(FivePerMinuteThrottle,),
-    )
-    def throttle(self, request):
-        throttle = self.get_throttles()[0]
-        return Response({"identity": throttle.get_ident(request)})
diff --git a/tests/common/test_api.py b/tests/common/test_api.py
index 913d9919..614281ea 100644
--- a/tests/common/test_api.py
+++ b/tests/common/test_api.py
@@ -32,24 +32,3 @@ def test_web(self):
         resp = anon.get(url)
         assert resp.status_code == 200
         assert resp.json() == {"healthy": True}
-
-    def test_throttle(self):
-        anon = APIClient()
-        admin = APIClient()
-        admin.login(username="admin@bmdsonline.org", password="pw")
-
-        # failure - not admin
-        url = reverse("api:healthcheck-throttle")
-        resp = anon.get(url)
-        assert resp.status_code == 401
-
-        # success - admin
-        url = reverse("api:healthcheck-throttle")
-        for _ in range(5):
-            resp = admin.get(url)
-            assert resp.status_code == 200
-            assert "identity" in resp.data
-
-        # success- throttled (>5/min)
-        resp = admin.get(url)
-        assert resp.status_code == 429

From f8af17b55ee9d800349b7b5cc360de729f1c288c Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 11:41:20 -0500
Subject: [PATCH 08/17] dont show bootstrap final row twice

---
 .../Output/NestedDichotomous/BootstrapRuns.js | 60 ++++++++++---------
 1 file changed, 32 insertions(+), 28 deletions(-)

diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
index 1e667f04..d1c0cf72 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
@@ -8,34 +8,38 @@ import {ff, fractionalFormatter} from "@/utils/formatters";
 
 const getData = function(model) {
     const results = model.results.bootstrap,
-        rows = _.range(results.p_value.length).map(run => [
-            run + 1,
-            fractionalFormatter(results.p_value[run]),
-            ff(results.p50[run]),
-            ff(results.p90[run]),
-            ff(results.p95[run]),
-            ff(results.p99[run]),
-        ]);
-    rows.push([
-        <span key={0} className="font-weight-bold">
-            Combined
-        </span>,
-        <span key={1} className="font-weight-bold">
-            {fractionalFormatter(results.p_value[3])}
-        </span>,
-        <span key={2} className="font-weight-bold">
-            {ff(results.p50[3])}
-        </span>,
-        <span key={3} className="font-weight-bold">
-            {ff(results.p90[3])}
-        </span>,
-        <span key={4} className="font-weight-bold">
-            {ff(results.p95[3])}
-        </span>,
-        <span key={5} className="font-weight-bold">
-            {ff(results.p99[3])}
-        </span>,
-    ]);
+        finalIdx = results.p_value.length-1,
+        rows = _.range(results.p_value.length).map(idx =>{
+            return (idx===finalIdx)?[
+                <span key={0} className="font-weight-bold">
+                    Combined
+                </span>,
+                <span key={1} className="font-weight-bold">
+                    {fractionalFormatter(results.p_value[idx])}
+                </span>,
+                <span key={2} className="font-weight-bold">
+                    {ff(results.p50[idx])}
+                </span>,
+                <span key={3} className="font-weight-bold">
+                    {ff(results.p90[idx])}
+                </span>,
+                <span key={4} className="font-weight-bold">
+                    {ff(results.p95[idx])}
+                </span>,
+                <span key={5} className="font-weight-bold">
+                    {ff(results.p99[idx])}
+                </span>,
+            ]:[
+                idx + 1,
+                fractionalFormatter(results.p_value[idx]),
+                ff(results.p50[idx]),
+                ff(results.p90[idx]),
+                ff(results.p95[idx]),
+                ff(results.p99[idx]),
+            ];
+
+        });
+    rows.push();
 
     return {
         headers: [

From 1c3eaf91beae13867c69fe09378c085709f4d6c2 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 11:41:20 -0500
Subject: [PATCH 09/17] dont show bootstrap final row twice

---
 .../Output/NestedDichotomous/BootstrapRuns.js | 61 ++++++++++---------
 1 file changed, 33 insertions(+), 28 deletions(-)

diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
index 1e667f04..0279c35f 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
@@ -8,34 +8,39 @@ import {ff, fractionalFormatter} from "@/utils/formatters";
 
 const getData = function(model) {
     const results = model.results.bootstrap,
-        rows = _.range(results.p_value.length).map(run => [
-            run + 1,
-            fractionalFormatter(results.p_value[run]),
-            ff(results.p50[run]),
-            ff(results.p90[run]),
-            ff(results.p95[run]),
-            ff(results.p99[run]),
-        ]);
-    rows.push([
-        <span key={0} className="font-weight-bold">
-            Combined
-        </span>,
-        <span key={1} className="font-weight-bold">
-            {fractionalFormatter(results.p_value[3])}
-        </span>,
-        <span key={2} className="font-weight-bold">
-            {ff(results.p50[3])}
-        </span>,
-        <span key={3} className="font-weight-bold">
-            {ff(results.p90[3])}
-        </span>,
-        <span key={4} className="font-weight-bold">
-            {ff(results.p95[3])}
-        </span>,
-        <span key={5} className="font-weight-bold">
-            {ff(results.p99[3])}
-        </span>,
-    ]);
+        finalIdx = results.p_value.length - 1,
+        rows = _.range(results.p_value.length).map(idx => {
+            return idx === finalIdx
+                ? [
+                      <span key={0} className="font-weight-bold">
+                          Combined
+                      </span>,
+                      <span key={1} className="font-weight-bold">
+                          {fractionalFormatter(results.p_value[idx])}
+                      </span>,
+                      <span key={2} className="font-weight-bold">
+                          {ff(results.p50[idx])}
+                      </span>,
+                      <span key={3} className="font-weight-bold">
+                          {ff(results.p90[idx])}
+                      </span>,
+                      <span key={4} className="font-weight-bold">
+                          {ff(results.p95[idx])}
+                      </span>,
+                      <span key={5} className="font-weight-bold">
+                          {ff(results.p99[idx])}
+                      </span>,
+                  ]
+                : [
+                      idx + 1,
+                      fractionalFormatter(results.p_value[idx]),
+                      ff(results.p50[idx]),
+                      ff(results.p90[idx]),
+                      ff(results.p95[idx]),
+                      ff(results.p99[idx]),
+                  ];
+        });
+    rows.push();
 
     return {
         headers: [

From 79f4f37011980b7c3029159ceb1deb31f97c5375 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 12:05:56 -0500
Subject: [PATCH 10/17] add estimate_background option

---
 bmds_ui/analysis/validators/options.py                   | 1 +
 .../src/components/IndividualModel/ModelOptionsTable.js  | 7 ++++---
 frontend/src/components/Main/OptionsForm/OptionsForm.js  | 9 +++++++++
 .../src/components/Main/OptionsForm/OptionsFormList.js   | 1 +
 .../src/components/Main/OptionsForm/OptionsReadOnly.js   | 2 ++
 frontend/src/components/Output/OptionSetTable.js         | 7 ++++---
 frontend/src/constants/optionsConstants.js               | 1 +
 tests/analysis/test_validators.py                        | 1 +
 8 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/bmds_ui/analysis/validators/options.py b/bmds_ui/analysis/validators/options.py
index abffcfab..95653adf 100644
--- 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
index 7639cc34..c3fe7e12 100644
--- 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
index 87a36113..a4c1916c 100644
--- 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
index 3c36d018..1de6ea06 100644
--- 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
index c213996c..e28065f3 100644
--- 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
index 1399b8a9..de00d4a3 100644
--- 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 {
@@ -56,8 +56,6 @@ 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(
@@ -65,6 +63,9 @@ class OptionSetTable extends Component {
                         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
index ffad8365..9eef9b9a 100644
--- 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
index ec860106..d5ab4f83 100644
--- 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

From d78fc45fef3095703871d806d04c3bbd0ff30fb1 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 12:23:19 -0500
Subject: [PATCH 11/17] fix ci/cd

---
 tests/data/db.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/data/db.yaml b/tests/data/db.yaml
index e0304461..f8bf53a1 100644
--- a/tests/data/db.yaml
+++ b/tests/data/db.yaml
@@ -9965,6 +9965,7 @@
         confidence_level: 0.95
         bootstrap_iterations: 1000
         litter_specific_covariate: 1
+        estimate_background: false
       datasets:
       - doses:
         - 0
@@ -10930,7 +10931,7 @@
               bmr_type: 1
               bootstrap_n: 3
               bootstrap_seed: 4
-              estimate_background: true
+              estimate_background: false
               bootstrap_iterations: 1000
               intralitter_correlation: 0
               litter_specific_covariate: 0
@@ -11590,7 +11591,7 @@
               bmr_type: 1
               bootstrap_n: 3
               bootstrap_seed: 4
-              estimate_background: true
+              estimate_background: false
               bootstrap_iterations: 1000
               intralitter_correlation: 1
               litter_specific_covariate: 0
@@ -12250,7 +12251,7 @@
               bmr_type: 1
               bootstrap_n: 3
               bootstrap_seed: 4
-              estimate_background: true
+              estimate_background: false
               bootstrap_iterations: 1000
               intralitter_correlation: 0
               litter_specific_covariate: 1
@@ -12910,7 +12911,7 @@
               bmr_type: 1
               bootstrap_n: 3
               bootstrap_seed: 4
-              estimate_background: true
+              estimate_background: false
               bootstrap_iterations: 1000
               intralitter_correlation: 1
               litter_specific_covariate: 1

From 41129a610cc7e29dbd0dc596f6f0d3941031a805 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 15:01:46 -0500
Subject: [PATCH 12/17] add chi2, simplify summary table

---
 .../IndividualModel/ModelDetailModal.js       |  6 +--
 .../src/components/IndividualModel/Summary.js | 53 ++++++++++++-------
 2 files changed, 37 insertions(+), 22 deletions(-)

diff --git a/frontend/src/components/IndividualModel/ModelDetailModal.js b/frontend/src/components/IndividualModel/ModelDetailModal.js
index 6c906d08..16a7e666 100644
--- a/frontend/src/components/IndividualModel/ModelDetailModal.js
+++ b/frontend/src/components/IndividualModel/ModelDetailModal.js
@@ -62,7 +62,7 @@ class ModelBody extends Component {
                         />
                     </Col>
                     <Col xl={4}>
-                        <Summary store={outputStore} />
+                        <Summary />
                     </Col>
                     <Col xl={8}>
                         <DoseResponsePlot
@@ -194,7 +194,7 @@ class MultitumorModalBody extends Component {
                         />
                     </Col>
                     <Col xl={4}>
-                        <Summary model={model} />
+                        <Summary />
                     </Col>
                     <Col xs={8}>
                         <DoseResponsePlot
@@ -250,7 +250,7 @@ class NestedDichotomousModalBody extends Component {
                         <ModelOptionsTable dtype={dtype} model={model} />
                     </Col>
                     <Col xs={6}>
-                        <Summary results={model.results} />
+                        <Summary />
                     </Col>
                     <Col xs={6}>
                         <DoseResponsePlot
diff --git a/frontend/src/components/IndividualModel/Summary.js b/frontend/src/components/IndividualModel/Summary.js
index a516a250..4c0d9872 100644
--- a/frontend/src/components/IndividualModel/Summary.js
+++ b/frontend/src/components/IndividualModel/Summary.js
@@ -11,47 +11,62 @@ import {ff, fractionalFormatter} from "@/utils/formatters";
 class Summary extends Component {
     render() {
         const {outputStore} = this.props,
-            model = outputStore.modalModel;
+            model = outputStore.modalModel,
+            {results} = model;
         let data;
         if (outputStore.isNestedDichotomous) {
             data = [
-                ["BMD", ff(model.results.bmd), model.results.bmd],
-                ["BMDL", ff(model.results.bmdl), model.results.bmdl],
-                ["BMDU", ff(model.results.bmdu), model.results.bmdu],
-                ["AIC", ff(model.results.aic), model.results.aic],
+                ["BMD", ff(results.bmd), results.bmd],
+                ["BMDL", ff(results.bmdl), results.bmdl],
+                ["BMDU", ff(results.bmdu), results.bmdu],
+                ["AIC", ff(results.aic), results.aic],
                 [
                     <span key={0}>
                         <i>P</i>-value
                     </span>,
-                    fractionalFormatter(model.results.combined_pvalue),
+                    fractionalFormatter(results.combined_pvalue),
+                    results.combined_pvalue,
                 ],
-                ["Model d.f.", ff(model.results.dof)],
-                [<span key={1}>Chi²</span>, ff(model.results.chi_squared)],
+                ["Model d.f.", ff(results.dof), results.dof],
+                [<span key={1}>Chi²</span>, ff(results.chi_squared), results.chi_squared],
+            ];
+        } else if (outputStore.getModelType === mc.MODEL_CONTINUOUS) {
+            data = [
+                ["BMD", ff(results.bmd), results.bmd],
+                ["BMDL", ff(results.bmdl), results.bmdl],
+                ["BMDU", ff(results.bmdu), results.bmdu],
+                ["AIC", ff(results.fit.aic), results.fit.aic],
+                [
+                    <span key={0}>
+                        <i>P</i>-value
+                    </span>,
+                    fractionalFormatter(results.tests.p_values[3]),
+                    results.tests.p_values[3],
+                ],
+                ["Model d.f.", ff(results.tests.dfs[3]), results.tests.dfs[3]],
+                ["Log-Likelihood", ff(results.fit.loglikelihood), results.fit.loglikelihood],
             ];
         } else {
-            const isContinuous = outputStore.getModelType === mc.MODEL_CONTINUOUS,
-                results = model.bmd ? model : model.results,
-                p_value = isContinuous ? results.tests.p_values[3] : results.gof.p_value,
-                df = isContinuous ? results.tests.dfs[3] : results.gof.df;
             data = [
                 ["BMD", ff(results.bmd), results.bmd],
                 ["BMDL", ff(results.bmdl), results.bmdl],
                 ["BMDU", ff(results.bmdu), results.bmdu],
+                outputStore.isMultiTumor
+                    ? ["Slope Factor", ff(results.slope_factor), results.slope_factor]
+                    : null,
                 ["AIC", ff(results.fit.aic), results.fit.aic],
-                ["Log-Likelihood", ff(results.fit.loglikelihood)],
                 [
                     <span key={0}>
                         <i>P</i>-value
                     </span>,
-                    fractionalFormatter(p_value),
+                    fractionalFormatter(results.gof.p_value),
+                    results.gof.p_value,
                 ],
-                ["Model d.f.", ff(df)],
+                ["Model d.f.", ff(results.gof.df), results.gof.df],
+                ["Log-Likelihood", ff(results.fit.loglikelihood), results.fit.loglikelihood],
+                ["Chi²", ff(results.fit.chisq), results.fit.chisq],
             ];
-            if (outputStore.isMultiTumor) {
-                data.splice(3, 0, ["Slope Factor", ff(results.slope_factor), results.slope_factor]);
-            }
         }
-
         return <TwoColumnTable data={data} label="Modeling Summary" />;
     }
 }

From bfa5da48d21f0d30e4dad556dd0c3e20daf73433 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 15:39:31 -0500
Subject: [PATCH 13/17] show model degrees, not auto

---
 frontend/src/components/Output/OptionSetTable.js | 2 +-
 frontend/src/stores/OutputStore.js               | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/frontend/src/components/Output/OptionSetTable.js b/frontend/src/components/Output/OptionSetTable.js
index de00d4a3..37dbb2f7 100644
--- a/frontend/src/components/Output/OptionSetTable.js
+++ b/frontend/src/components/Output/OptionSetTable.js
@@ -72,7 +72,7 @@ class OptionSetTable extends Component {
                 ["BMR Type", getLabel(selectedModelOptions.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(selectedModelOptions.bmr_value)],
                 ["Confidence Level (one sided)", ff(selectedModelOptions.confidence_level)],
-                ["Degree Setting", outputStore.multitumorDegreeInputSettings.join(", ")],
+                ["Degree Setting", outputStore.multitumorDegreesUsed.join(", ")],
             ];
         } else {
             throw `Unknown model type: ${getModelType}`;
diff --git a/frontend/src/stores/OutputStore.js b/frontend/src/stores/OutputStore.js
index 36501b61..7f791f10 100644
--- a/frontend/src/stores/OutputStore.js
+++ b/frontend/src/stores/OutputStore.js
@@ -135,6 +135,12 @@ class OutputStore {
             .map(d => (d.degree === 0 ? "auto" : d.degree));
     }
 
+    @computed get multitumorDegreesUsed() {
+        return this.selectedFrequentist.results.models.map(models =>
+            _.max(models.map(model => model.settings.degree))
+        );
+    }
+
     @computed get recommendationEnabled() {
         return (
             this.selectedOutput.frequentist &&

From aec78f19b8c9a43a19ab293d667b9a300f74c0aa Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 16:16:41 -0500
Subject: [PATCH 14/17] report lsc in ui output

---
 frontend/src/components/IndividualModel/ModelOptionsTable.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/frontend/src/components/IndividualModel/ModelOptionsTable.js b/frontend/src/components/IndividualModel/ModelOptionsTable.js
index c3fe7e12..2d436359 100644
--- a/frontend/src/components/IndividualModel/ModelOptionsTable.js
+++ b/frontend/src/components/IndividualModel/ModelOptionsTable.js
@@ -72,10 +72,10 @@ class ModelOptionsTable extends Component {
                 ["Confidence Level (one sided)", ff(1 - model.settings.alpha)],
                 [
                     "Litter Specific Covariate",
-                    getLabel(
+                    `${getLabel(
                         model.settings.litter_specific_covariate,
                         litterSpecificCovariateOptions
-                    ),
+                    )} (${ff(model.results.fixed_lsc)})`,
                 ],
                 [
                     "Intralitter Correlation",

From 2b945a75c47e6c981842cc16ecb423a23ff5a080 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Fri, 15 Nov 2024 16:16:49 -0500
Subject: [PATCH 15/17] simplify ui

---
 .../Output/NestedDichotomous/BootstrapRuns.js | 39 ++++---------------
 1 file changed, 8 insertions(+), 31 deletions(-)

diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
index f52b4495..b96aef9d 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
@@ -9,37 +9,14 @@ import {ff, fractionalFormatter} from "@/utils/formatters";
 const getData = function(model) {
     const results = model.results.bootstrap,
         finalIdx = results.p_value.length - 1,
-        rows = _.range(results.p_value.length).map(idx => {
-            return idx === finalIdx
-                ? [
-                      <span key={0} className="font-weight-bold">
-                          Combined
-                      </span>,
-                      <span key={1} className="font-weight-bold">
-                          {fractionalFormatter(results.p_value[idx])}
-                      </span>,
-                      <span key={2} className="font-weight-bold">
-                          {ff(results.p50[idx])}
-                      </span>,
-                      <span key={3} className="font-weight-bold">
-                          {ff(results.p90[idx])}
-                      </span>,
-                      <span key={4} className="font-weight-bold">
-                          {ff(results.p95[idx])}
-                      </span>,
-                      <span key={5} className="font-weight-bold">
-                          {ff(results.p99[idx])}
-                      </span>,
-                  ]
-                : [
-                      idx + 1,
-                      fractionalFormatter(results.p_value[idx]),
-                      ff(results.p50[idx]),
-                      ff(results.p90[idx]),
-                      ff(results.p95[idx]),
-                      ff(results.p99[idx]),
-                  ];
-        });
+        rows = _.range(results.p_value.length).map(idx => [
+            idx === finalIdx ? "Combined" : idx + 1,
+            fractionalFormatter(results.p_value[idx]),
+            ff(results.p50[idx]),
+            ff(results.p90[idx]),
+            ff(results.p95[idx]),
+            ff(results.p99[idx]),
+        ]);
 
     return {
         headers: [

From 069f3ba492bd48f6e2d076c224b430dae69debb1 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Sat, 16 Nov 2024 12:21:23 -0500
Subject: [PATCH 16/17] don't print all models by default

---
 frontend/src/stores/MainStore.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/frontend/src/stores/MainStore.js b/frontend/src/stores/MainStore.js
index 8df47827..8530cf28 100644
--- a/frontend/src/stores/MainStore.js
+++ b/frontend/src/stores/MainStore.js
@@ -39,7 +39,6 @@ class MainStore {
         // word export options setting
         if (this.isMultiTumorOrNestedDichotomous) {
             this.changeReportOptions("datasetFormatLong", false);
-            this.changeReportOptions("allModels", true);
         }
         this.rootStore.modelsStore.setDefaultsByDatasetType(true);
         this.rootStore.optionsStore.setDefaultsByDatasetType(true);

From b740f7d5e963b584acb38720c7abbbef4453dcae Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Mon, 18 Nov 2024 14:00:12 -0500
Subject: [PATCH 17/17] release 24.1a6

---
 bmds_ui/__init__.py |  2 +-
 pyproject.toml      |  2 +-
 tests/data/db.yaml  | 62 ++++++++++++++++++++++-----------------------
 3 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/bmds_ui/__init__.py b/bmds_ui/__init__.py
index 719fd787..5d443ba1 100644
--- a/bmds_ui/__init__.py
+++ b/bmds_ui/__init__.py
@@ -1,7 +1,7 @@
 import os
 import sys
 
-__version__ = "24.1a5"
+__version__ = "24.1a6"
 
 
 def manage():
diff --git a/pyproject.toml b/pyproject.toml
index 943e8077..46125072 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ classifiers = [
 requires-python = ">=3.11"
 dependencies = [
   # pybmds
-  "pybmds==24.1a5",
+  "pybmds==24.1a6",
 
   # website
   "Django~=5.1.2",
diff --git a/tests/data/db.yaml b/tests/data/db.yaml
index f8bf53a1..75f65cf7 100644
--- a/tests/data/db.yaml
+++ b/tests/data/db.yaml
@@ -1959,8 +1959,8 @@
       analysis_id: cc3ca355-a57a-4fba-9dc3-99657562df68
       analysis_schema_version: '1.1'
       bmds_python_version:
-        dll: 24.1a5
-        python: 24.1a5
+        dll: 24.1a6
+        python: 24.1a6
       bmds_ui_version: 9434971c
       outputs:
       - bayesian:
@@ -3419,8 +3419,8 @@
             model_index: null
             notes: ''
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
         dataset_index: 0
         error: null
         frequentist:
@@ -5135,8 +5135,8 @@
             model_index: null
             notes: ''
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
         option_index: 0
     starred: false
     started: 2024-05-14 19:18:13.442351+00:00
@@ -6837,8 +6837,8 @@
             - 10.0
             - 19.0
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
           selected:
             notes: ''
             model_index: null
@@ -6999,10 +6999,10 @@
         option_index: 0
         dataset_index: 0
       analysis_id: 432a6083-f9aa-4de2-a71f-a6488b4c5bf1
-      bmds_ui_version: 24.1a5
+      bmds_ui_version: 24.1a6
       bmds_python_version:
-        dll: 24.1a5
-        python: 24.1a5
+        dll: 24.1a6
+        python: 24.1a6
       analysis_schema_version: '1.1'
     errors: []
     created: 2024-08-22 15:46:25.966993+00:00
@@ -7942,8 +7942,8 @@
               - 8.24
               - 9.23
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
           selected:
             notes: User selected best fitting model
             model_index: 0
@@ -8100,10 +8100,10 @@
         option_index: 0
         dataset_index: 0
       analysis_id: cfe458aa-2313-44c0-9346-f4931567bef0
-      bmds_ui_version: 24.1a5
+      bmds_ui_version: 24.1a6
       bmds_python_version:
-        dll: 24.1a5
-        python: 24.1a5
+        dll: 24.1a6
+        python: 24.1a6
       analysis_schema_version: '1.1'
     errors: []
     created: 2024-08-22 15:45:08.929260+00:00
@@ -9832,8 +9832,8 @@
             - 0
             - 0
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
           datasets:
           - ns:
             - 20.0
@@ -9936,10 +9936,10 @@
         option_index: 0
         dataset_index: -1
       analysis_id: 2f86f324-911d-4194-97d1-fc7c3f5d0c72
-      bmds_ui_version: 24.1a5
+      bmds_ui_version: 24.1a6
       bmds_python_version:
-        dll: 24.1a5
-        python: 24.1a5
+        dll: 24.1a6
+        python: 24.1a6
       analysis_schema_version: '1.1'
     errors: []
     created: 2024-08-22 15:26:02.720355+00:00
@@ -13096,8 +13096,8 @@
             - 8.0
             - 10.0
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
           selected:
             notes: User selected best fitting model
             model_index: 1
@@ -13266,10 +13266,10 @@
         option_index: 0
         dataset_index: 0
       analysis_id: 4459f728-05f7-4057-a27c-174822a0313d
-      bmds_ui_version: 24.1a5
+      bmds_ui_version: 24.1a6
       bmds_python_version:
-        dll: 24.1a5
-        python: 24.1a5
+        dll: 24.1a6
+        python: 24.1a6
       analysis_schema_version: '1.1'
     errors: []
     created: 2024-08-22 15:25:20.345600+00:00
@@ -14368,8 +14368,8 @@
             - 15.1564
             - 15.0368
           version:
-            dll: 24.1a5
-            python: 24.1a5
+            dll: 24.1a6
+            python: 24.1a6
           selected:
             notes: User selected best fitting model
             model_index: 0
@@ -14526,10 +14526,10 @@
         option_index: 0
         dataset_index: 0
       analysis_id: 09c09d22-2e1a-413c-b350-6b19969f6533
-      bmds_ui_version: 24.1a5
+      bmds_ui_version: 24.1a6
       bmds_python_version:
-        dll: 24.1a5
-        python: 24.1a5
+        dll: 24.1a6
+        python: 24.1a6
       analysis_schema_version: '1.1'
     errors: []
     created: 2024-08-22 15:23:53.050405+00:00