Merge pull request #810 from asharaali/fix-802-episode-anchor

Fix Episodes anchor case in OncologyWG links

Author: anthonysena

docs/cdm54.html

@@ -10415,7 +10415,7 @@ <h3 class="tabset tabset-pills anchored" data-anchor-id="episode">EPISODE</h3>
 <p><strong>Table Description</strong></p>
 <p>The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.</p>
 <p><strong>User Guide</strong></p>
-<p>Valid Episode Concepts belong to the ‘Episode’ domain. For more information on how to populate this table, please see the <a href="https://ohdsi.github.io/OncologyWG/model.html#Episodes">article</a> on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.</p>
+<p>Valid Episode Concepts belong to the ‘Episode’ domain. For more information on how to populate this table, please see the <a href="https://ohdsi.github.io/OncologyWG/model.html#episodes">article</a> on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.</p>
 <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
 <thead>
 <tr>

docs/cdm55.html

@@ -10583,7 +10583,7 @@ <h3 class="tabset tabset-pills anchored" data-anchor-id="episode">EPISODE</h3>
 <p><strong>Table Description</strong></p>
 <p>The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.</p>
 <p><strong>User Guide</strong></p>
-<p>Valid Episode Concepts belong to the ‘Episode’ domain. For more information on how to populate this table, please see the <a href="https://ohdsi.github.io/OncologyWG/model.html#Episodes">article</a> on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.</p>
+<p>Valid Episode Concepts belong to the ‘Episode’ domain. For more information on how to populate this table, please see the <a href="https://ohdsi.github.io/OncologyWG/model.html#episodes">article</a> on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.</p>
 <table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
 <thead>
 <tr>
@@ -10678,7 +10678,7 @@ <h3 class="tabset tabset-pills anchored" data-anchor-id="episode">EPISODE</h3>
 The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.
 </td>
 <td style="text-align:left;">
-Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see the <a href="https://ohdsi.github.io/OncologyWG/model.html#Episodes">information</a> from the Oncology workgroup describing how these are defined. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Episode&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>
+Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see the <a href="https://ohdsi.github.io/OncologyWG/model.html#episodes">information</a> from the Oncology workgroup describing how these are defined. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Episode&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>
 </td>
 <td style="text-align:left;">
 integer

inst/csv/OMOP_CDMv5.4_Table_Level.csv

@@ -65,7 +65,7 @@ For example, consider a Person who visits her Primary Care Physician (PCP) and w
 The condition_concept_id field contains Concepts that are identical to those of the CONDITION_OCCURRENCE table records that make up the Condition Era. In contrast to Drug Eras, Condition Eras are not aggregated to contain Conditions of different hierarchical layers. The SQl Script for generating CONDITION_ERA records can be found [here](https://ohdsi.github.io/CommonDataModel/sqlScripts.html#condition_eras)
 The Condition Era Start Date is the start date of the first Condition Occurrence.
 The Condition Era End Date is the end date of the last Condition Occurrence. Condition Eras are built with a Persistence Window of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date."
-episode,CDM,FALSE,NA,FALSE,NA,NA,"The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.","Valid Episode Concepts belong to the 'Episode' domain. For more information on how to populate this table, please see the [article](https://ohdsi.github.io/OncologyWG/model.html#Episodes) on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.",NA
+episode,CDM,FALSE,NA,FALSE,NA,NA,"The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.","Valid Episode Concepts belong to the 'Episode' domain. For more information on how to populate this table, please see the [article](https://ohdsi.github.io/OncologyWG/model.html#episodes) on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.",NA
 episode_event,CDM,FALSE,NA,FALSE,NA,NA,"The EPISODE_EVENT table connects qualifying clinical events (such as CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT) to the appropriate EPISODE entry. For example, linking the precise location of the metastasis (cancer modifier in MEASUREMENT) to the disease episode.",This connecting table is used instead of the FACT_RELATIONSHIP table for linking low-level events to abstracted Episodes.,"Some episodes may not have links to any underlying clinical events. For such episodes, the EPISODE_EVENT table is not populated."
 metadata,CDM,FALSE,NA,FALSE,NA,NA,The METADATA table contains metadata information about a dataset that has been transformed to the OMOP Common Data Model.,NA,NA
 cdm_source,CDM,FALSE,NA,FALSE,NA,NA,The CDM_SOURCE table contains detail about the source database and the process used to transform the data into the OMOP Common Data Model.,NA,NA

inst/csv/OMOP_CDMv5.5_Field_Level.csv

@@ -376,7 +376,7 @@ Occurrences used to construct the
 condition era.",NA,false,false,NA,NA,NA,NA
 episode,episode_id,true,integer,A unique identifier for each Episode.,NA,true,false,NA,NA,NA,NA
 episode,person_id,true,integer,The PERSON_ID of the PERSON for whom the episode is recorded.,NA,false,true,PERSON,PERSON_ID,NA,NA
-episode,episode_concept_id,true,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see the [information](https://ohdsi.github.io/OncologyWG/model.html#Episodes) from the Oncology workgroup describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",false,true,CONCEPT,CONCEPT_ID,Episode,NA
+episode,episode_concept_id,true,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see the [information](https://ohdsi.github.io/OncologyWG/model.html#episodes) from the Oncology workgroup describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",false,true,CONCEPT,CONCEPT_ID,Episode,NA
 episode,episode_start_date,true,date,The date when the Episode beings.,Please see [article] for how to define an Episode start date.,false,false,NA,NA,NA,NA
 episode,episode_start_datetime,false,datetime,The date and time when the Episode begins.,NA,false,false,NA,NA,NA,NA
 episode,episode_end_date,false,date,The date when the instance of the Episode is considered to have ended.,Please see [article] for how to define an Episode end date.,false,false,NA,NA,NA,NA

inst/csv/OMOP_CDMv5.5_Table_Level.csv

@@ -65,7 +65,7 @@ For example, consider a Person who visits her Primary Care Physician (PCP) and w
 The condition_concept_id field contains Concepts that are identical to those of the CONDITION_OCCURRENCE table records that make up the Condition Era. In contrast to Drug Eras, Condition Eras are not aggregated to contain Conditions of different hierarchical layers. The SQl Script for generating CONDITION_ERA records can be found [here](https://ohdsi.github.io/CommonDataModel/sqlScripts.html#condition_eras)
 The Condition Era Start Date is the start date of the first Condition Occurrence.
 The Condition Era End Date is the end date of the last Condition Occurrence. Condition Eras are built with a Persistence Window of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date."
-episode,CDM,FALSE,NA,FALSE,NA,NA,"The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.","Valid Episode Concepts belong to the 'Episode' domain. For more information on how to populate this table, please see the [article](https://ohdsi.github.io/OncologyWG/model.html#Episodes) on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.",NA
+episode,CDM,FALSE,NA,FALSE,NA,NA,"The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.","Valid Episode Concepts belong to the 'Episode' domain. For more information on how to populate this table, please see the [article](https://ohdsi.github.io/OncologyWG/model.html#episodes) on the Oncology Workgroup website. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.",NA
 episode_event,CDM,FALSE,NA,FALSE,NA,NA,"The EPISODE_EVENT table connects qualifying clinical events (such as CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT) to the appropriate EPISODE entry. For example, linking the precise location of the metastasis (cancer modifier in MEASUREMENT) to the disease episode.",This connecting table is used instead of the FACT_RELATIONSHIP table for linking low-level events to abstracted Episodes.,"Some episodes may not have links to any underlying clinical events. For such episodes, the EPISODE_EVENT table is not populated."
 metadata,CDM,FALSE,NA,FALSE,NA,NA,The METADATA table contains metadata information about a dataset that has been transformed to the OMOP Common Data Model.,NA,NA
 cdm_source,CDM,FALSE,NA,FALSE,NA,NA,"The CDM_SOURCE table contains details about your CDM instance. Most OHDSI tooling expects one record in this table to get the name of your cdm, release date, and vocabulary version. Multiple records are allowed in the cdm_source table, but tooling will typically only read the first record.",NA,NA