fix: upgrade HTTP links to HTTPS in Rmd source and generated HTML docs (Fixes #790)

docs/background.html

@@ -531,7 +531,7 @@ <h2>Background</h2>
 <p>The community is actively using the OMOP Common Data Model for their
 various research purposes. Those tools will continue to be maintained
 and supported, and information about this work is available in the <a
-href="http://www.github.com/ohdsi">public domain</a>.</p>
+href="https://www.github.com/ohdsi">public domain</a>.</p>
 <p>The OMOP Common Data Model will continue to be an open-source
 community standard for observational healthcare data. The model
 specifications and associated work products will be placed in the public

docs/cdm53.html

@@ -618,7 +618,7 @@ <h3 class="tabset tabset-pills">person</h3>
 gender identity it should be stored in the <a
 href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
 table. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 gender concepts</a>. Please refer to the <a
 href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
 repository</a> for detailed conventions on how to populate this field.
@@ -772,7 +772,7 @@ <h3 class="tabset tabset-pills">person</h3>
 of human races and ethnic backgrounds, this is not a perfect system.
 Mixed races are not supported. If a clear race or ethnic background
 cannot be established, use Concept_Id 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Race&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Race&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Race Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -808,7 +808,7 @@ <h3 class="tabset tabset-pills">person</h3>
 Only use this field if you have US-based data and a source of this
 information. Do not attempt to infer Ethnicity from the race or ethnic
 background of the Person. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 ethnicity concepts</a>
 </td>
 <td style="text-align:left;">
@@ -8990,7 +8990,7 @@ <h3 class="tabset tabset-pills">provider</h3>
 specialties, or, 2. Choose the specialty that occurs most often for the
 provider. Concepts in this field should be Standard with a domain of
 Provider. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Provider&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Provider&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -9077,7 +9077,7 @@ <h3 class="tabset tabset-pills">provider</h3>
 <td style="text-align:left;">
 If given, put a concept from the gender domain representing the recorded
 gender of the provider. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -9521,7 +9521,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 <td style="text-align:left;">
 Map the Plan directly to a standard CONCEPT_ID in the ‘Plan’ vocabulary
 (<a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>). This vocabulary is not exhaustive so if there is a value
 missing, please see the <a
 href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">custom
@@ -9729,7 +9729,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 <td style="text-align:left;">
 Map the stop reason directly to a standard CONCEPT_ID with a domain of
 ‘Plan Stop Reason’ (<a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>). If one does not exist visit the <a
 href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">Custom
 Concepts</a> pate for more information.

docs/cdm54.html

@@ -586,7 +586,7 @@ <h3>Current Support for CDM v5.4</h3>
 <td><strong>ATLAS</strong></td>
 <td>ATLAS is an open source software tool for researchers to conduct
 scientific analyses on standardized observational data. <a
-href="http://atlas-demo.ohdsi.org/">Demo</a></td>
+href="https://atlas-demo.ohdsi.org/">Demo</a></td>
 <td>✔️</td>
 <td>❗</td>
 </tr>
@@ -726,7 +726,7 @@ <h3 class="tabset tabset-pills">person</h3>
 gender identity it should be stored in the <a
 href="https://ohdsi.github.io/CommonDataModel/cdm54.html#observation">OBSERVATION</a>
 table. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 gender concepts</a>. Please refer to the <a
 href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
 repository</a> for detailed conventions on how to populate this field.
@@ -880,7 +880,7 @@ <h3 class="tabset tabset-pills">person</h3>
 of human races and ethnic backgrounds, this is not a perfect system.
 Mixed races are not supported. If a clear race or ethnic background
 cannot be established, use Concept_Id 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Race&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Race&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Race Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -916,7 +916,7 @@ <h3 class="tabset tabset-pills">person</h3>
 Only use this field if you have US-based data and a source of this
 information. Do not attempt to infer Ethnicity from the race or ethnic
 background of the Person. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 ethnicity concepts</a>
 </td>
 <td style="text-align:left;">
@@ -9668,7 +9668,7 @@ <h3 class="tabset tabset-pills">provider</h3>
 specialties, or, 2. Choose the specialty that occurs most often for the
 provider. Concepts in this field should be Standard with a domain of
 Provider. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Provider&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Provider&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -9755,7 +9755,7 @@ <h3 class="tabset tabset-pills">provider</h3>
 <td style="text-align:left;">
 If given, put a concept from the gender domain representing the recorded
 gender of the provider. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -10199,7 +10199,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 <td style="text-align:left;">
 Map the Plan directly to a standard CONCEPT_ID in the ‘Plan’ vocabulary
 (<a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>). This vocabulary is not exhaustive so if there is a value
 missing, please see the <a
 href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">custom
@@ -10407,7 +10407,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 <td style="text-align:left;">
 Map the stop reason directly to a standard CONCEPT_ID with a domain of
 ‘Plan Stop Reason’ (<a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>). If one does not exist visit the <a
 href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">Custom
 Concepts</a> pate for more information.

docs/cdm54Changes.html

@@ -506,7 +506,7 @@ <h1 class="title toc-ignore"><strong>Changes by Table</strong></h1>
 
 <p><em>from CDM v5.3 -&gt; CDM v5.4</em></p>
 <p>For a full description of each table and field listed here, please
-see the <a href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM
+see the <a href="https://ohdsi.github.io/CommonDataModel/cdm54.html">CDM
 specification</a>.</p>
 <p>Notation:</p>
 <ul>

docs/cdm54erd.html

@@ -449,7 +449,7 @@ <h1 class="title toc-ignore"><strong>OMOP CDM v5.4 ERD</strong></h1>
 entity-relationship diagram and we crowned two winners! Martijn Schuemie
 and Renske Los created the best printable version and Vishnu
 Chandrabalan created the best <a
-href="http://omop-erd.surge.sh/">interactive version</a>.</p>
+href="https://omop-erd.surge.sh/">interactive version</a>.</p>
 <div class="float">
 <img src="images/erd.jpg" style="width:150.0%"
 alt="CDM v5.4 Printable ERD - click here to download" />

docs/cdm60.html

@@ -514,9 +514,9 @@ <h2>NOTE ABOUT CDM v6.0</h2>
 forward with v6.0, CDM v5.4 was designed with additions to the model
 that have been requested by the community while retaining the date
 structure of medical events in v5.3. Please see our the specifications
-for <a href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM
+for <a href="https://ohdsi.github.io/CommonDataModel/cdm54.html">CDM
 v5.4</a> and detailed <a
-href="http://ohdsi.github.io/CommonDataModel/cdm54Changes.html">changes
+href="https://ohdsi.github.io/CommonDataModel/cdm54Changes.html">changes
 from CDM v5.3</a>. <strong>For new collaborators to OHDSI, please
 transform your data to <a
 href="https://github.com/OHDSI/CommonDataModel/releases/tag/v5.4.0">CDM
@@ -667,7 +667,7 @@ <h3 class="tabset tabset-pills">person</h3>
 gender identity it should be stored in the <a
 href="https://ohdsi.github.io/CommonDataModel/cdm60.html#observation">OBSERVATION</a>
 table. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 gender concepts</a>
 </td>
 <td style="text-align:left;">
@@ -861,7 +861,7 @@ <h3 class="tabset tabset-pills">person</h3>
 of human races and ethnic backgrounds, this is not a perfect system.
 Mixed races are not supported. If a clear race or ethnic background
 cannot be established, use Concept_Id 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Race&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Race&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Race Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -897,7 +897,7 @@ <h3 class="tabset tabset-pills">person</h3>
 Only use this field if you have US-based data and a source of this
 information. Do not attempt to infer Ethnicity from the race or ethnic
 background of the Person. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 ethnicity concepts</a>
 </td>
 <td style="text-align:left;">
@@ -9897,7 +9897,7 @@ <h3 class="tabset tabset-pills">provider</h3>
 specialties, or, 2. Choose the specialty that occurs most often for the
 provider. Concepts in this field should be Standard with a domain of
 Provider. If not available, set to 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Provider&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Provider&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -9984,7 +9984,7 @@ <h3 class="tabset tabset-pills">provider</h3>
 <td style="text-align:left;">
 If given, put a concept from the gender domain representing the recorded
 gender of the provider. If not available, set to 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -10370,7 +10370,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 vocabulary available for this information. The point is to stratify on
 this information and identify if Persons have the same payer, though the
 name of the Payer is not necessary. If not available, set to 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Payer&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Payer&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -10460,7 +10460,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 this information and identify if Persons have the same health benefit
 Plan though the name of the Plan is not necessary. If not available, set
 to 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -10647,7 +10647,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 vocabulary available for this information. The point is to stratify on
 this information and identify if Persons have the same sponsor though
 the name of the sponsor is not necessary. If not available, set to 0. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Sponsor&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Sponsor&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">
@@ -10762,7 +10762,7 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 Map the stop reason directly to a standard CONCEPT_ID. If one does not
 exists please contact the vocabulary team. There is no global controlled
 vocabulary available for this information. <a
-href="http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
+href="https://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
 Concepts</a>.
 </td>
 <td style="text-align:left;">

docs/dataModelConventions.html

@@ -565,15 +565,15 @@ <h3>Fields</h3>
 standard_concept attribute for the corresponding term is true), which
 serves as the primary basis for all standardized analytics. For example,
 CONDITION_CONCEPT_ID = <a
-href="http://athena.ohdsi.org/search-terms/terms/31967">31967</a>
+href="https://athena.ohdsi.org/search-terms/terms/31967">31967</a>
 contains the reference value for the SNOMED concept of ‘Nausea’</td>
 </tr>
 <tr class="even">
 <td><entity>_SOURCE_CONCEPT_ID</td>
 <td>Foreign key into the Standardized Vocabularies representing the
 concept and terminology used in the source data, when applicable. For
 example, CONDITION_SOURCE_CONCEPT_ID = <a
-href="http://athena.ohdsi.org/search-terms/terms/45431665">45431665</a>
+href="https://athena.ohdsi.org/search-terms/terms/45431665">45431665</a>
 denotes the concept of ‘Nausea’ in the Read terminology; the analogous
 CONDITION_CONCEPT_ID might be 31967, since SNOMED-CT is the Standardized
 Vocabulary for most clinical diagnoses and findings.</td>