Merge pull request #627 from yarikoptic/enh-codespell

Reincarnated codespell PR: no conflicts, more typos fixed etc.

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,.*.min.js,*.pdf,site_libs
+ignore-regex = src="data:image/png.*
+ignore-words-list = bu,eacg,ehr,infarction,2rd,aas,ags,alog,bui,caf,eacf,ede,edn,esy,fo,gage,ges,gud,iif,isnt,knwo,mor,nam,nd,ot,slq,tahn,te,tey,thn,tye,ue,vas,wel,whn,wih,wth,yau,pilon

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

R/buildRelease.R

@@ -17,7 +17,7 @@
 #' Create OMOP CDM SQL files
 #'
 #' Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion
-#' and targetDialect to the 'ddl' folder in specifed output folder.
+#' and targetDialect to the 'ddl' folder in specified output folder.
 #'
 #' @param cdmVersions The versions of the CDM you are creating, e.g. 5.3, 5.4.
 #'                   Defaults to all supported CDM versions.
@@ -26,7 +26,7 @@
 #' @param outputfolder The base folder where the SQL files will be written.
 #'                     Subfolders will be created for each cdmVersion and targetDialect.
 #' @return Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion
-#'         and targetDialect to the 'ddl' folder in specifed output folder.
+#'         and targetDialect to the 'ddl' folder in specified output folder.
 #' @export
 buildRelease <- function(cdmVersions = listSupportedVersions(),
                          targetDialects = listSupportedDialects(),

docs/cdm53.html

@@ -1125,7 +1125,7 @@ <h3 class="tabset tabset-pills">observation_period</h3>
 <p><strong>Table Description</strong></p>
 <p>This table contains records which define spans of time during which
 two conditions are expected to hold: (i) Clinical Events that happened
-to the Person are recorded in the Event tables, and (ii) absense of
+to the Person are recorded in the Event tables, and (ii) absence of
 records indicate such Events did not occur during this span of time.</p>
 <p><strong>User Guide</strong></p>
 <p>For each Person, one or more OBSERVATION_PERIOD records may be

docs/cdm54.html

@@ -1233,7 +1233,7 @@ <h3 class="tabset tabset-pills">observation_period</h3>
 <p><strong>Table Description</strong></p>
 <p>This table contains records which define spans of time during which
 two conditions are expected to hold: (i) Clinical Events that happened
-to the Person are recorded in the Event tables, and (ii) absense of
+to the Person are recorded in the Event tables, and (ii) absence of
 records indicate such Events did not occur during this span of time.</p>
 <p><strong>User Guide</strong></p>
 <p>For each Person, one or more OBSERVATION_PERIOD records may be

docs/cdm54ToolingSupport.html

@@ -499,12 +499,12 @@ <h1>Introduction</h1>
 make use of which OMOP CDM fields. The goal is to inform ETL developers,
 tooling developers and CDM extensions.</p>
 <ul>
-<li>For ETL developers it helps to have guidance on which fieds to
+<li>For ETL developers it helps to have guidance on which fields to
 prioritise in the mapping. Most value will be gained from populating
 fields support across the OHDSI tooling.</li>
 <li>For OHDSI tooling developers, this page provides insight in the gaps
 of support and can drive future development efforts.</li>
-<li>For CDM extenstions, it helps to known what it means for an OMOP CDM
+<li>For CDM extensions, it helps to known what it means for an OMOP CDM
 table/field to be part of the standard. In other words: what OHDSI
 tooling do we at least expect to support the new extensions?</li>
 </ul>
@@ -582,7 +582,7 @@ <h1>Tooling Support for OMOP fields</h1>
 </colgroup>
 <thead>
 <tr class="header">
-<th><strong>Abbrevations</strong></th>
+<th><strong>Abbreviations</strong></th>
 <th> </th>
 </tr>
 </thead>

docs/cdm60.html

@@ -1219,7 +1219,7 @@ <h3 class="tabset tabset-pills">observation_period</h3>
 <p><strong>Table Description</strong></p>
 <p>This table contains records which define spans of time during which
 two conditions are expected to hold: (i) Clinical Events that happened
-to the Person are recorded in the Event tables, and (ii) absense of
+to the Person are recorded in the Event tables, and (ii) absence of
 records indicate such Events did not occur during this span of time.</p>
 <p><strong>User Guide</strong></p>
 <p>For each Person, one or more OBSERVATION_PERIOD records may be

extras/archive/OMOP_CDM_PDF.html

@@ -1087,7 +1087,7 @@ <h3>Conventions</h3>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
-<td align="left">Concept Relationships define direct relationships between Concepts. Indirect relationships through 3rd Concepts are not captured in this table. However, the <a href="https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR">CONCEPT_ANCESTOR</a> table does this for hierachical relationships over several “generations” of direct relationships.</td>
+<td align="left">Concept Relationships define direct relationships between Concepts. Indirect relationships through 3rd Concepts are not captured in this table. However, the <a href="https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR">CONCEPT_ANCESTOR</a> table does this for hierarchical relationships over several “generations” of direct relationships.</td>
 </tr>
 </tbody>
 </table>
@@ -5203,7 +5203,7 @@ <h2>PAYER_PLAN_PERIOD</h2>
 <td align="left">payer_concept_id</td>
 <td align="left">Yes</td>
 <td align="left">integer</td>
-<td align="left">A foreign key that refers to a standard Payer concept identifier in the Standarized Vocabularies</td>
+<td align="left">A foreign key that refers to a standard Payer concept identifier in the Standardized Vocabularies</td>
 </tr>
 <tr class="odd">
 <td align="left">payer_source_value</td>

extras/archive/OMOP_CDM_v6_0test.html

@@ -1000,7 +1000,7 @@ <h3>Conventions</h3>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
-<td align="left">Concept Relationships define direct relationships between Concepts. Indirect relationships through 3rd Concepts are not captured in this table. However, the <a href="https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR">CONCEPT_ANCESTOR</a> table does this for hierachical relationships over several “generations” of direct relationships.</td>
+<td align="left">Concept Relationships define direct relationships between Concepts. Indirect relationships through 3rd Concepts are not captured in this table. However, the <a href="https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_ANCESTOR">CONCEPT_ANCESTOR</a> table does this for hierarchical relationships over several “generations” of direct relationships.</td>
 </tr>
 </tbody>
 </table>

extras/archive/testSpec.html

@@ -1018,7 +1018,7 @@ <h3>OBSERVATION_PERIOD</h3>
 observation_period_start_date
 </td>
 <td style="text-align:left;">
-Use this date to determine the start date of the period for which we can assume that all events for a Person are recorded and any absense of records indicates an absence of events.
+Use this date to determine the start date of the period for which we can assume that all events for a Person are recorded and any absence of records indicates an absence of events.
 </td>
 <td style="text-align:left;">
 It is often the case that the idea of observation periods does not exist in source data. In those cases the observation_period_start_date can be inferred as the earliest event date available for the Person. In US claims, the observation period can be considered as the time period the person is enrolled with an insurer. If a Person switches plans but stays with the same insurer, that change would be captured in payer_plan_period.
@@ -1050,7 +1050,7 @@ <h3>OBSERVATION_PERIOD</h3>
 observation_period_end_date
 </td>
 <td style="text-align:left;">
-Use this date to determine the end date of the period for which we can assume that all events for a Person are recorded and any absense of records indicates an absence of events.
+Use this date to determine the end date of the period for which we can assume that all events for a Person are recorded and any absence of records indicates an absence of events.
 </td>
 <td style="text-align:left;">
 It is often the case that the idea of observation periods does not exist in source data. In those cases the observation_period_start_end_date can be inferred as the latest event date available for the Person. The event dates include insurance enrollment dates.
@@ -1667,7 +1667,7 @@ <h3>VISIT_OCCURRENCE</h3>
 preceding_visit_occurrence_id
 </td>
 <td style="text-align:left;">
-Use this field to find the visit that occured for the person prior to the given visit. There could be a few days or a few years in between.
+Use this field to find the visit that occurred for the person prior to the given visit. There could be a few days or a few years in between.
 </td>
 <td style="text-align:left;">
 The preceding_visit_id can be used to link a visit immediately preceding the current visit. Note this is not symmetrical, and there is no such thing as a “following_visit_id”.
@@ -10200,7 +10200,7 @@ <h3>DRUG_ERA</h3>
 <p>The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:</p>
 <p>For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information.</p>
 <p>For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date).</p>
-A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era. (ARENT WE REQUIRING TO USE DRUG_EXPOSURE_END_DATE NOW????)
+A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era. (AREN'T WE REQUIRING TO USE DRUG_EXPOSURE_END_DATE NOW????)
 </td>
 <td style="text-align:left;">
 datetime
@@ -20702,7 +20702,7 @@ <h3>PAYER_PLAN_PERIOD</h3>
 payer_concept_id
 </td>
 <td style="text-align:left;">
-A foreign key that refers to a standard Payer concept identifier in the Standarized Vocabularies
+A foreign key that refers to a standard Payer concept identifier in the Standardized Vocabularies
 </td>
 <td style="text-align:left;">
 NA

inst/csv/OMOP_CDM_Oncology_Ex_Field_Level.csv

@@ -10,7 +10,7 @@ episode,episode_parent_id,No,bigint,Use this field to find the Episode that subs
 episode,episode_number,No,integer,"For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here. ",Please see [article] for the details of how to count episodes.,No,No,,,,
 episode,episode_object_concept_id,Yes,integer,"A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists.  For example, if the episode_concept_id is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the episode_object_concept_id should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). ",Episode entries from the 'Disease Episode' concept class should have an episode_object_concept_id that comes from the Condition domain.  Episode entries from the 'Treatment Episode' concept class should have an episode_object_concept_id that scome from the 'Procedure' domain or 'Regimen' concept class.,No,Yes,concept,concept_id,"Procedure, Regimen",
 episode,episode_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources.",Choose the episode_type_concept_id that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,concept,concept_id,Type Concept,
-episode,episode_source_value,No,varchar(50),The source code for the Episdoe as it appears in the source data. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,,No,No,,,,
+episode,episode_source_value,No,varchar(50),The source code for the Episode as it appears in the source data. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,,No,No,,,,
 episode,episode_source_concept_id,No,integer,A foreign key to a Episode Concept that refers to the code used in the source.,Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero. ,No,Yes,concept,concept_id,,
 episode_event,episode_id,Yes,bigint,Use this field to link the episode_event record to its episode.,Put the episode_id that subsumes the episode_event record here.,No,Yes,episode,episode_id,,
 episode_event,event_id,Yes,bigint,"This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the condition_occurrence_id of the linked record goes in this field. ",Put the primary key of the linked record here. ,No,No,,,,