From fd1027533348f186c8597164b4d5d19d7ee14b76 Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Wed, 12 Jun 2024 21:32:45 -0700
Subject: [PATCH 1/9] Change alpha diversity metric

---
 microsetta_interface/templates/new_results_page.jinja2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index b4c493c3..b801ad5a 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1036,7 +1036,7 @@
         }
 
         // We override the default alpha_metric from state for this page.
-        let alpha_metric = "observed_features"
+        let alpha_metric = "shannon"
         for (let key in POST_DATA) {
             $.ajax(
                 {

From c48524347606bb84916fafe7eda9a691cd6c7096 Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Wed, 12 Jun 2024 21:37:07 -0700
Subject: [PATCH 2/9] Round alpha diversity metric

---
 microsetta_interface/templates/new_results_page.jinja2 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index b801ad5a..266e2531 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1048,7 +1048,7 @@
                     data: JSON.stringify(POST_DATA[key]),
                     contentType: "application/json",
                     success: function (data) {
-                        let display = data["group_summary"]["median"]
+                        let display = Math.round(data["group_summary"]["median"] * 100)/100;
                         $(SELECTORS[key]).text(display).removeClass("spinner-grow spinner-grow-sm");
                     }
                 }).fail(function (result, textStatus, errorThrown) {
@@ -1064,7 +1064,7 @@
                 method: "GET",
                 contentType: "application/json",
                 success: function (data) {
-                    let display = data["data"]
+                    let display = Math.round(data["data"] * 100)/100;
                     $("#diversity_in_sample").text(display).removeClass("spinner-grow spinner-grow-sm");
                 }
             }).fail(function (result, textStatus, errorThrown) {

From cece0e73a5e624b5fa67fe6a24667a423ee7b8fc Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Wed, 12 Jun 2024 21:42:23 -0700
Subject: [PATCH 3/9] Flag text to update

---
 microsetta_interface/templates/new_results_page.jinja2 | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index 266e2531..f34d1f7e 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -13,6 +13,10 @@
 <link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/jquery.contextMenu.min.css">
 <link rel="stylesheet" type="text/css" href="/static/css/4_column_flex.css" />
 <style>
+    .diversity-change-me {
+        color: red;
+        font-weight: 700;
+    }
     .nav-white-bg {
       background-color: #fff;
       width: auto;
@@ -1426,10 +1430,10 @@
                   <p>
                       {{ _('Recent estimates suggest hundreds of billions of types of microbes live on earth. This number dwarfs the meager 2 million different kinds of animals and plants discovered on the planet.') }}
                   </p>
-                  <p>
+                  <p class="diversity-change-me">
                       {{ _('If we were to randomly select a set number of microbial DNA sequences from a stool sample, we would find that the&nbsp;<span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span>&nbsp;American has&nbsp;<strong id="average-american-observed-otus">FILLIN</strong>&nbsp;different types of microbes, which is lower than we find in people living a more hunter-gatherer lifestyle, like the&nbsp;<strong id="average-hadza-observed-otus">FILLIN</strong>&nbsp;we find in samples from the&nbsp;<span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span>&nbsp;people of Tanzania.') }}
                   </p>
-                  <p>
+                  <p class="diversity-change-me">
                       {{ _('The number of microbes found in your sample can be very close or vastly different from this average, and it doesn\'t necessarily mean something is right or wrong with you. We are all different, and this number is affected by many different factors.') }}
                   </p>
                   <div class="card your_sample_diversity_inset">

From 4b579fc6de4f49d2b2257a4103e2a5e0f85978a6 Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Wed, 12 Jun 2024 21:45:13 -0700
Subject: [PATCH 4/9] Flag text to update

---
 .../templates/new_results_page.jinja2                | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index f34d1f7e..07070bc4 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1437,7 +1437,7 @@
                       {{ _('The number of microbes found in your sample can be very close or vastly different from this average, and it doesn\'t necessarily mean something is right or wrong with you. We are all different, and this number is affected by many different factors.') }}
                   </p>
                   <div class="card your_sample_diversity_inset">
-                      <div class="card-header">{{ _('Number of different microbes found in your sample:') }}</div>
+                      <div class="card-header diversity-change-me">{{ _('Number of different microbes found in your sample:') }}</div>
                       <div class="card-body">
                           <span id="diversity_in_sample" class="info-loader">...</span></h5>
                       </div>
@@ -1454,7 +1454,7 @@
                             <div class="diversity-category">
                               {{ _('Participants who eat more than 30 plants per week') }}
                             </div>
-                            <div class="diversity-info">
+                            <div class="diversity-info diversity-change-me">
                               {{ _('Average number of different microbes:') }} <span id="diversity_30_plants_per_week" class="info-loader text-success">...</span>
                             </div>
                           </div>
@@ -1465,7 +1465,7 @@
                             <div class="diversity-category">
                               {{ _('Participants who exercise regularly') }}
                             </div>
-                            <div class="diversity-info">
+                            <div class="diversity-info diversity-change-me">
                               {{ _('Average number of different microbes:') }} <span id="diversity_exercise_regularly" class="info-loader text-success">...</span>
                             </div>
                           </div>
@@ -1478,7 +1478,7 @@
                             <div class="diversity-category">
                               {{ _('Participants who drink 1L of water regularly') }}
                             </div>
-                            <div class="diversity-info">
+                            <div class="diversity-info diversity-change-me">
                               {{ _('Average number of different microbes:') }} <span id="diversity_water_regularly" class="info-loader text-success">...</span>
                             </div>
                           </div>
@@ -1489,7 +1489,7 @@
                               <div class="diversity-category">
                                 {{ _('Participants who sleep more than 6 hours per night') }}
                               </div>
-                              <div class="diversity-info">
+                              <div class="diversity-info diversity-change-me">
                                 {{ _('Average number of different microbes:') }} <span id="diversity_sleep_alot" class="info-loader text-success">...</span>
                               </div>
                           </div>
@@ -1625,7 +1625,7 @@
                     {{ _('To learn more about what the taxonomic ranks (column headers) mean, place your cursor over their names. Additionally, pronunciation can be a challenge considering the language of origin varies for the names between Latin, Greek, Norse, Chinese, and more. A pronunciation guide can be found <a href="https://www.atsu.edu/faculty/chamberlain/Website/studio.htm">here</a>.') }}
                     </p>
 
-                    <p>
+                    <p class="diversity-change-me">
                     {{ _('The number of microbes listed here might be different from what was reported as your Diversity because of the way microbes are grouped according to their taxonomy (i.e. names). There are likely many species of microbes in your sample that are all grouped in the same genus.') }}
                     </p>
                     

From 2ddb75af8079d6589679a8983e0649718dfb34e3 Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Thu, 13 Jun 2024 15:12:05 -0700
Subject: [PATCH 5/9] Update text

---
 .../templates/new_results_page.jinja2         | 50 ++++++++++---------
 1 file changed, 27 insertions(+), 23 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index 07070bc4..f4f3e999 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -13,10 +13,6 @@
 <link rel="stylesheet" type="text/css" href="/static/vendor/emperor/vendor/css/jquery.contextMenu.min.css">
 <link rel="stylesheet" type="text/css" href="/static/css/4_column_flex.css" />
 <style>
-    .diversity-change-me {
-        color: red;
-        font-weight: 700;
-    }
     .nav-white-bg {
       background-color: #fff;
       width: auto;
@@ -1394,7 +1390,7 @@
                 <div class="how_you_compare_section">
                     <h4>{{ _('Diversity') }}</h4>
                     <p>
-                    {{ _('How many kinds of microbes were in your sample? Check out your') }} <a class="fake-tab" href="#diversity" data-link="#diversity-tab">{{ _('Diversity') }}</a>.
+                    {{ _('How diverse is your microbiome? Check out your') }} <a class="fake-tab" href="#diversity" data-link="#diversity-tab">{{ _('Diversity') }}</a>.
                     </p>
                 </div>
                 </br>
@@ -1428,16 +1424,28 @@
                   <h3>{{ _('Diversity') }}</h3>
                   <br>
                   <p>
-                      {{ _('Recent estimates suggest hundreds of billions of types of microbes live on earth. This number dwarfs the meager 2 million different kinds of animals and plants discovered on the planet.') }}
+                      {{ _('This section provides insights into your microbiome diversity and how it compares to others\'.') }}
+                  </p>
+                  <p>
+                      <strong>{{ _('How do we calculate your diversity value?') }}</strong>
                   </p>
-                  <p class="diversity-change-me">
-                      {{ _('If we were to randomly select a set number of microbial DNA sequences from a stool sample, we would find that the&nbsp;<span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span>&nbsp;American has&nbsp;<strong id="average-american-observed-otus">FILLIN</strong>&nbsp;different types of microbes, which is lower than we find in people living a more hunter-gatherer lifestyle, like the&nbsp;<strong id="average-hadza-observed-otus">FILLIN</strong>&nbsp;we find in samples from the&nbsp;<span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span>&nbsp;people of Tanzania.') }}
+                  <p>
+                      {{ _('Diversity can be measured in a lot of different ways. We measure it by first taking the DNA sequences from your sample and figuring out which Bacteria and Archaea they may have come from. This produces a good estimate of how many of each kind of microbe you have. The measure we use, called Shannon\'s index, takes into account how many different kinds of microbes make up your gut community (also known as richness) and how relatively abundant each of those microbes are (also known as evenness).') }}
                   </p>
-                  <p class="diversity-change-me">
-                      {{ _('The number of microbes found in your sample can be very close or vastly different from this average, and it doesn\'t necessarily mean something is right or wrong with you. We are all different, and this number is affected by many different factors.') }}
+                  <p>
+                      {{ _('This number isn\'t exact for many reasons. However, because it\'s calculated in the same way for every sample in our dataset, it provides insight into how your microbial diversity compares to others\'. For example, the <span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span> diversity value in the Microsetta dataset is <strong id="average-american-observed-otus">FILLIN</strong>, which is lower than we find in people living a more hunter-gatherer lifestyle like the <span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span> people of Tanzania, who have an average value of <strong id="average-hadza-observed-otus">FILLIN</strong>. ') }}
+                  </p>
+                  <p>
+                      <strong>{{ _('What does this number mean for my health?') }}</strong>
+                  </p>
+                  <p>
+                      {{ _('This number reflects the variety of Bacteria and Archaea present in your gut at the time of testing. Currently, there\'s no single established standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, more research is needed to understand this connection.') }}
+                  </p>
+                  <p>
+                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
                   </p>
                   <div class="card your_sample_diversity_inset">
-                      <div class="card-header diversity-change-me">{{ _('Number of different microbes found in your sample:') }}</div>
+                      <div class="card-header">{{ _('Your sample\'s diversity value:') }}</div>
                       <div class="card-body">
                           <span id="diversity_in_sample" class="info-loader">...</span></h5>
                       </div>
@@ -1454,8 +1462,8 @@
                             <div class="diversity-category">
                               {{ _('Participants who eat more than 30 plants per week') }}
                             </div>
-                            <div class="diversity-info diversity-change-me">
-                              {{ _('Average number of different microbes:') }} <span id="diversity_30_plants_per_week" class="info-loader text-success">...</span>
+                            <div class="diversity-info">
+                              {{ _('Average diversity value:') }} <span id="diversity_30_plants_per_week" class="info-loader text-success">...</span>
                             </div>
                           </div>
                       </div>
@@ -1465,8 +1473,8 @@
                             <div class="diversity-category">
                               {{ _('Participants who exercise regularly') }}
                             </div>
-                            <div class="diversity-info diversity-change-me">
-                              {{ _('Average number of different microbes:') }} <span id="diversity_exercise_regularly" class="info-loader text-success">...</span>
+                            <div class="diversity-info">
+                              {{ _('Average diversity value:') }} <span id="diversity_exercise_regularly" class="info-loader text-success">...</span>
                             </div>
                           </div>
                       </div>
@@ -1478,8 +1486,8 @@
                             <div class="diversity-category">
                               {{ _('Participants who drink 1L of water regularly') }}
                             </div>
-                            <div class="diversity-info diversity-change-me">
-                              {{ _('Average number of different microbes:') }} <span id="diversity_water_regularly" class="info-loader text-success">...</span>
+                            <div class="diversity-info">
+                              {{ _('Average diversity value:') }} <span id="diversity_water_regularly" class="info-loader text-success">...</span>
                             </div>
                           </div>
                       </div>
@@ -1489,8 +1497,8 @@
                               <div class="diversity-category">
                                 {{ _('Participants who sleep more than 6 hours per night') }}
                               </div>
-                              <div class="diversity-info diversity-change-me">
-                                {{ _('Average number of different microbes:') }} <span id="diversity_sleep_alot" class="info-loader text-success">...</span>
+                              <div class="diversity-info">
+                                {{ _('Average diversity value:') }} <span id="diversity_sleep_alot" class="info-loader text-success">...</span>
                               </div>
                           </div>
                       </div>
@@ -1625,10 +1633,6 @@
                     {{ _('To learn more about what the taxonomic ranks (column headers) mean, place your cursor over their names. Additionally, pronunciation can be a challenge considering the language of origin varies for the names between Latin, Greek, Norse, Chinese, and more. A pronunciation guide can be found <a href="https://www.atsu.edu/faculty/chamberlain/Website/studio.htm">here</a>.') }}
                     </p>
 
-                    <p class="diversity-change-me">
-                    {{ _('The number of microbes listed here might be different from what was reported as your Diversity because of the way microbes are grouped according to their taxonomy (i.e. names). There are likely many species of microbes in your sample that are all grouped in the same genus.') }}
-                    </p>
-                    
                     <div style="padding:10px">
                       <table id="taxonomyTable" class="display" style="width:100%">
                         <thead>

From 6e2224fb45f1eb4cc3d0889afc192f11a0586a45 Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Sun, 16 Jun 2024 16:50:19 -0700
Subject: [PATCH 6/9] Update average values

---
 microsetta_interface/templates/new_results_page.jinja2 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index f4f3e999..23e96fa4 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1203,11 +1203,11 @@
         var us_text = document.getElementById('average-american-observed-otus');
         var hadza_text = document.getElementById('average-hadza-observed-otus');
         if (state.dataset_type.value === 'WGS') {
-            us_text.innerText = '107';
-            hadza_text.innerText = '129';
+            us_text.innerText = '5.31';
+            hadza_text.innerText = '6.30';
         } else if (state.dataset_type.value === '16S') {
-            us_text.innerText = '93';
-            hadza_text.innerText = '132';
+            us_text.innerText = '4.47';
+            hadza_text.innerText = '5.20';
         }
     }
 
@@ -1433,7 +1433,7 @@
                       {{ _('Diversity can be measured in a lot of different ways. We measure it by first taking the DNA sequences from your sample and figuring out which Bacteria and Archaea they may have come from. This produces a good estimate of how many of each kind of microbe you have. The measure we use, called Shannon\'s index, takes into account how many different kinds of microbes make up your gut community (also known as richness) and how relatively abundant each of those microbes are (also known as evenness).') }}
                   </p>
                   <p>
-                      {{ _('This number isn\'t exact for many reasons. However, because it\'s calculated in the same way for every sample in our dataset, it provides insight into how your microbial diversity compares to others\'. For example, the <span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span> diversity value in the Microsetta dataset is <strong id="average-american-observed-otus">FILLIN</strong>, which is lower than we find in people living a more hunter-gatherer lifestyle like the <span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span> people of Tanzania, who have an average value of <strong id="average-hadza-observed-otus">FILLIN</strong>. ') }}
+                      {{ _('This number isn\'t exact for many reasons. However, because it\'s calculated in the same way for every sample in our dataset, it provides insight into how your microbial diversity compares to others\'. For example, the <span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span> diversity value for people living in the US in our dataset is <strong id="average-american-observed-otus">FILLIN</strong>, which is lower than we find in people living a more hunter-gatherer lifestyle like the <span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span> people of Tanzania, who have an average value of <strong id="average-hadza-observed-otus">FILLIN</strong>. ') }}
                   </p>
                   <p>
                       <strong>{{ _('What does this number mean for my health?') }}</strong>

From c0cb8a9d755d7f1a4f33a2e13ebd7ae0bd6f4ca8 Mon Sep 17 00:00:00 2001
From: Cassidy Symons <83246693+cassidysymons@users.noreply.github.com>
Date: Mon, 17 Jun 2024 13:09:07 -0700
Subject: [PATCH 7/9] Apply suggestions from code review

Co-authored-by: Daniel McDonald <danielmcdonald@ucsd.edu>
---
 microsetta_interface/templates/new_results_page.jinja2 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index 23e96fa4..fc4dc06f 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1439,10 +1439,10 @@
                       <strong>{{ _('What does this number mean for my health?') }}</strong>
                   </p>
                   <p>
-                      {{ _('This number reflects the variety of Bacteria and Archaea present in your gut at the time of testing. Currently, there\'s no single established standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, more research is needed to understand this connection.') }}
+                      {{ _('This number reflects the variety of Bacteria and Archaea observed in your fecal specimen at the time of testing. Currently, there\'s no standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, that is not true universally -- more research is needed to understand the relationship. For example, it may be that the specific microbes present are more important than having many different types of microbes, much like how in a garden you care about the exact plants growing not that there is a random assortment of plants.') }}
                   </p>
                   <p>
-                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
+                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique and changing overtime. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
                   </p>
                   <div class="card your_sample_diversity_inset">
                       <div class="card-header">{{ _('Your sample\'s diversity value:') }}</div>

From 18fb25dc4680ffc579fcdbaccd0d33ceb3719a1b Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Mon, 17 Jun 2024 13:13:26 -0700
Subject: [PATCH 8/9] Update average IDs and tweak text

---
 .../templates/new_results_page.jinja2              | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index fc4dc06f..3d8f8bdb 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1199,9 +1199,9 @@
         END BLOCK COMMENTED OUT WHILE TAXA VIOLIN IS HIDDEN */
     }
 
-    function updateObservedOTUs(state) {
-        var us_text = document.getElementById('average-american-observed-otus');
-        var hadza_text = document.getElementById('average-hadza-observed-otus');
+    function updateObservedAverages(state) {
+        var us_text = document.getElementById('average-american-observed-average');
+        var hadza_text = document.getElementById('average-hadza-observed-average');
         if (state.dataset_type.value === 'WGS') {
             us_text.innerText = '5.31';
             hadza_text.innerText = '6.30';
@@ -1340,7 +1340,7 @@
             updateDatasetDetails(state);
 
             getMicrobiomeMapsRasterizedPlots(state);
-            updateObservedOTUs(state);
+            updateObservedAverages(state);
         }, state.dataset_input);
 
         refreshDatasets(state);
@@ -1433,16 +1433,16 @@
                       {{ _('Diversity can be measured in a lot of different ways. We measure it by first taking the DNA sequences from your sample and figuring out which Bacteria and Archaea they may have come from. This produces a good estimate of how many of each kind of microbe you have. The measure we use, called Shannon\'s index, takes into account how many different kinds of microbes make up your gut community (also known as richness) and how relatively abundant each of those microbes are (also known as evenness).') }}
                   </p>
                   <p>
-                      {{ _('This number isn\'t exact for many reasons. However, because it\'s calculated in the same way for every sample in our dataset, it provides insight into how your microbial diversity compares to others\'. For example, the <span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span> diversity value for people living in the US in our dataset is <strong id="average-american-observed-otus">FILLIN</strong>, which is lower than we find in people living a more hunter-gatherer lifestyle like the <span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span> people of Tanzania, who have an average value of <strong id="average-hadza-observed-otus">FILLIN</strong>. ') }}
+                      {{ _('This number isn\'t exact for many reasons. However, because it\'s calculated in the same way for every sample in our dataset, it provides insight into how your microbial diversity compares to others\'. For example, the <span id="average-us-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="Based on fecal samples from Microsetta participants in the United States">average</span> diversity value for people living in the US in our dataset is <strong id="average-american-observed-average">FILLIN</strong>, which is lower than we find in people living a more hunter-gatherer lifestyle like the <span id="taxa-tooltip" class="orange-text" data-bs-toggle="tooltip" data-bs-html="true" data-bs-placement="top" title="The Hadza are an indigenous hunter-gather group in Tanzania. The summary of the Hadza microbiome is based on Smits et al. Science 2017">Hadza</span> people of Tanzania, who have an average value of <strong id="average-hadza-observed-average">FILLIN</strong>. ') }}
                   </p>
                   <p>
                       <strong>{{ _('What does this number mean for my health?') }}</strong>
                   </p>
                   <p>
-                      {{ _('This number reflects the variety of Bacteria and Archaea observed in your fecal specimen at the time of testing. Currently, there\'s no standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, that is not true universally -- more research is needed to understand the relationship. For example, it may be that the specific microbes present are more important than having many different types of microbes, much like how in a garden you care about the exact plants growing not that there is a random assortment of plants.') }}
+                      {{ _('This number reflects the variety of Bacteria and Archaea observed in your fecal specimen at the time of testing. Currently, there\'s no standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, that is not true universally and more research is needed to understand the relationship. For example, it may be that the specific microbes present are more important than having many different types of microbes.') }}
                   </p>
                   <p>
-                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique and changing overtime. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
+                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique and changing over time. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
                   </p>
                   <div class="card your_sample_diversity_inset">
                       <div class="card-header">{{ _('Your sample\'s diversity value:') }}</div>

From 03d5f847e4f51ac13ce7f17bd2715dc4e5d33f3b Mon Sep 17 00:00:00 2001
From: Cassidy Symons <csymons@eng.ucsd.edu>
Date: Mon, 17 Jun 2024 13:46:02 -0700
Subject: [PATCH 9/9] Minor text adjustments

---
 microsetta_interface/templates/new_results_page.jinja2 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/microsetta_interface/templates/new_results_page.jinja2 b/microsetta_interface/templates/new_results_page.jinja2
index 3d8f8bdb..3654aacd 100644
--- a/microsetta_interface/templates/new_results_page.jinja2
+++ b/microsetta_interface/templates/new_results_page.jinja2
@@ -1439,10 +1439,10 @@
                       <strong>{{ _('What does this number mean for my health?') }}</strong>
                   </p>
                   <p>
-                      {{ _('This number reflects the variety of Bacteria and Archaea observed in your fecal specimen at the time of testing. Currently, there\'s no standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, that is not true universally and more research is needed to understand the relationship. For example, it may be that the specific microbes present are more important than having many different types of microbes.') }}
+                      {{ _('This number reflects the variety of Bacteria and Archaea observed in your fecal sample at the time of testing. Currently, there\'s no standard for how gut microbiome diversity relates to health. While some studies suggest a potential link between higher diversity and specific health benefits, that is not true universally and more research is needed to understand the relationship. For example, it may be that the specific microbes present are more important than having many different types of microbes.') }}
                   </p>
                   <p>
-                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique and changing over time. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
+                      {{ _('It\'s important to remember that everyone\'s gut microbiome is unique and changes over time. If your score differs from the average, it doesn\'t necessarily indicate a health concern.') }}
                   </p>
                   <div class="card your_sample_diversity_inset">
                       <div class="card-header">{{ _('Your sample\'s diversity value:') }}</div>