From bca414d823551a695527f78870e9a8d0a9b14906 Mon Sep 17 00:00:00 2001 From: adam bouras Date: Tue, 30 Apr 2024 19:16:00 -0400 Subject: [PATCH 1/5] add observation_period_end_date --- docs/_data/sidebars/mydoc_sidebar.yml | 6 +-- docs/_data/tags.yml | 2 + .../observation_period_end_date.md | 45 +++++++++++++++++++ 3 files changed, 50 insertions(+), 3 deletions(-) create mode 100644 docs/pages/observation_period/observation_period_end_date.md diff --git a/docs/_data/sidebars/mydoc_sidebar.yml b/docs/_data/sidebars/mydoc_sidebar.yml index c1d3100..df5506b 100644 --- a/docs/_data/sidebars/mydoc_sidebar.yml +++ b/docs/_data/sidebars/mydoc_sidebar.yml @@ -138,9 +138,9 @@ entries: # url: /observation.html # output: web, pdf - # - title: Observation Period - # url: /observation_period.html - # output: web, pdf + - title: Observation Period + url: /observation_period_end_date.html + output: web, pdf # - title: Payer Plan Period # url: /payer_plan_period.html diff --git a/docs/_data/tags.yml b/docs/_data/tags.yml index c1a89c0..f8977a3 100644 --- a/docs/_data/tags.yml +++ b/docs/_data/tags.yml @@ -23,4 +23,6 @@ allowed-tags: - datetime - patient_reported - observation_period + - event + - survival # Copyright 2021 Google LLC diff --git a/docs/pages/observation_period/observation_period_end_date.md b/docs/pages/observation_period/observation_period_end_date.md new file mode 100644 index 0000000..2ec568a --- /dev/null +++ b/docs/pages/observation_period/observation_period_end_date.md @@ -0,0 +1,45 @@ +--- +title: Resolving observation_period_end_date without exact information on a last day +keywords: observation_period, event, survival +last_updated: April 30, 2024 +tags: [observation_period, event, survival] +sidebar: mydoc_sidebar +permalink: /observation_period_end_date.html +--- + +## Issue # and location +[Themis Issue #106](https://github.com/OHDSI/Themis/issues/106) + +## Issue Summary +Resolving `observation_period_end_date` without exact information on a last day + +## Convention type +Table + +## CDM table +`OBSERVATION_PERIOD` + +## CDM field +`observation_period_end_date` + +## Links to issue discussion +- [OHDSI Forums discussion](https://forums.ohdsi.org/t/resolving-observation-period-end-date-without-exact-information-on-a-last-day/13048) +- [CDM Documentation](https://ohdsi.github.io/CommonDataModel/cdm54.html#observation_period) + +## Provenance of data +General + +## The ratified convention +It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the `observation_period_end_date` can be inferred as the last event date available for the person. + +## Date of ratification/published +NA + +## Downstream implications +This convention can lead to a bias in survival studies. Namely, healthy persons will have shorter observation periods and not contributing to survival time as much. + +## Link to DQD check +No + +## Related conventions/further information +NA From a4650fb1af730ff691a4ceacfcf6efdbabca882d Mon Sep 17 00:00:00 2001 From: adam bouras Date: Wed, 1 May 2024 20:25:04 -0400 Subject: [PATCH 2/5] made changes to display obs-period on convention tab --- docs/_data/sidebars/mydoc_sidebar.yml | 10 +++++++--- .../observation_period/observation_period_end_date.md | 4 ++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/docs/_data/sidebars/mydoc_sidebar.yml b/docs/_data/sidebars/mydoc_sidebar.yml index df5506b..ea9515f 100644 --- a/docs/_data/sidebars/mydoc_sidebar.yml +++ b/docs/_data/sidebars/mydoc_sidebar.yml @@ -50,6 +50,10 @@ entries: url: /obs_periods_for_ehr.html output: web, pdf + - title: Events with no exact information on a last day + url: /events_with_no_exact_last_day.html + output: web, pdf + - title: CDM Tables output: web, pdf folderitems: @@ -138,9 +142,9 @@ entries: # url: /observation.html # output: web, pdf - - title: Observation Period - url: /observation_period_end_date.html - output: web, pdf + # - title: Observation Period + # url: url: /observation_period.html + # output: web, pdf # - title: Payer Plan Period # url: /payer_plan_period.html diff --git a/docs/pages/observation_period/observation_period_end_date.md b/docs/pages/observation_period/observation_period_end_date.md index 2ec568a..3ab9163 100644 --- a/docs/pages/observation_period/observation_period_end_date.md +++ b/docs/pages/observation_period/observation_period_end_date.md @@ -1,10 +1,10 @@ --- -title: Resolving observation_period_end_date without exact information on a last day +title: Resolving Observation Period End Date without Exact Information on a Last Day keywords: observation_period, event, survival last_updated: April 30, 2024 tags: [observation_period, event, survival] sidebar: mydoc_sidebar -permalink: /observation_period_end_date.html +permalink: /events_with_no_exact_last_day.html --- ## Issue # and location From bf0d6222a03f58b3e0ef79ff5b94287d1800b611 Mon Sep 17 00:00:00 2001 From: adam bouras Date: Wed, 1 May 2024 20:29:27 -0400 Subject: [PATCH 3/5] made some title chnages --- docs/_data/sidebars/mydoc_sidebar.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_data/sidebars/mydoc_sidebar.yml b/docs/_data/sidebars/mydoc_sidebar.yml index ea9515f..f565a6d 100644 --- a/docs/_data/sidebars/mydoc_sidebar.yml +++ b/docs/_data/sidebars/mydoc_sidebar.yml @@ -50,7 +50,7 @@ entries: url: /obs_periods_for_ehr.html output: web, pdf - - title: Events with no exact information on a last day + - title: Observation Period with no exact information on End Date url: /events_with_no_exact_last_day.html output: web, pdf From a253352284a6397271df819b3bbe70bca925a5f7 Mon Sep 17 00:00:00 2001 From: adam bouras Date: Sat, 4 May 2024 11:46:45 -0400 Subject: [PATCH 4/5] reviewed and made changes to observation period end date as requested --- docs/_data/sidebars/mydoc_sidebar.yml | 9 ++++++--- .../events_with_no_exact_last_day.md} | 1 + .../observation_period/observation_period.md | 16 ++++++++++++++++ 3 files changed, 23 insertions(+), 3 deletions(-) rename docs/pages/{observation_period/observation_period_end_date.md => general_conventions/events_with_no_exact_last_day.md} (94%) create mode 100644 docs/pages/observation_period/observation_period.md diff --git a/docs/_data/sidebars/mydoc_sidebar.yml b/docs/_data/sidebars/mydoc_sidebar.yml index f565a6d..abf0ea7 100644 --- a/docs/_data/sidebars/mydoc_sidebar.yml +++ b/docs/_data/sidebars/mydoc_sidebar.yml @@ -142,9 +142,9 @@ entries: # url: /observation.html # output: web, pdf - # - title: Observation Period - # url: url: /observation_period.html - # output: web, pdf + - title: Observation Period + url: /observation_period.html + output: web, pdf # - title: Payer Plan Period # url: /payer_plan_period.html @@ -234,6 +234,9 @@ entries: - title: Year of Birth url: /tag_year_of_birth.html output: web + - title: Observation Period + url: /tag_observation_period.html + output: web \ No newline at end of file diff --git a/docs/pages/observation_period/observation_period_end_date.md b/docs/pages/general_conventions/events_with_no_exact_last_day.md similarity index 94% rename from docs/pages/observation_period/observation_period_end_date.md rename to docs/pages/general_conventions/events_with_no_exact_last_day.md index 3ab9163..65cd3b3 100644 --- a/docs/pages/observation_period/observation_period_end_date.md +++ b/docs/pages/general_conventions/events_with_no_exact_last_day.md @@ -3,6 +3,7 @@ title: Resolving Observation Period End Date without Exact Information on a Last keywords: observation_period, event, survival last_updated: April 30, 2024 tags: [observation_period, event, survival] +summary: "Resolving observation period end date without exact information on a last day" sidebar: mydoc_sidebar permalink: /events_with_no_exact_last_day.html --- diff --git a/docs/pages/observation_period/observation_period.md b/docs/pages/observation_period/observation_period.md new file mode 100644 index 0000000..a53a2fb --- /dev/null +++ b/docs/pages/observation_period/observation_period.md @@ -0,0 +1,16 @@ +--- +title: OBSERVATION_PERIOD +keywords: observation_period, observation_end_date +last_updated: May 04, 2024 +tags: [observation_period, event, survival] +summary: "Conventions related to resolving OBSERVATION_PERIOD table." +sidebar: mydoc_sidebar +permalink: /observation_period.html +--- + +## Field-level Conventions + +| **Field** | **Convention** | +|:--------|:-------| +| OBSERVATION_PERIOD_END_DATE | [Resolving Observation Period End Date without Exact Information on a Last Day](events_outside_obs_period.html) | +|===== \ No newline at end of file From ff8db35c539c07c27e608f8dd5088b0f0e69cda9 Mon Sep 17 00:00:00 2001 From: adam bouras Date: Mon, 6 May 2024 20:59:37 -0400 Subject: [PATCH 5/5] made changes as requested --- docs/_data/sidebars/mydoc_sidebar.yml | 4 ---- docs/pages/observation_period/observation_period.md | 4 ++-- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/docs/_data/sidebars/mydoc_sidebar.yml b/docs/_data/sidebars/mydoc_sidebar.yml index abf0ea7..d528008 100644 --- a/docs/_data/sidebars/mydoc_sidebar.yml +++ b/docs/_data/sidebars/mydoc_sidebar.yml @@ -50,10 +50,6 @@ entries: url: /obs_periods_for_ehr.html output: web, pdf - - title: Observation Period with no exact information on End Date - url: /events_with_no_exact_last_day.html - output: web, pdf - - title: CDM Tables output: web, pdf folderitems: diff --git a/docs/pages/observation_period/observation_period.md b/docs/pages/observation_period/observation_period.md index a53a2fb..86eef73 100644 --- a/docs/pages/observation_period/observation_period.md +++ b/docs/pages/observation_period/observation_period.md @@ -3,7 +3,7 @@ title: OBSERVATION_PERIOD keywords: observation_period, observation_end_date last_updated: May 04, 2024 tags: [observation_period, event, survival] -summary: "Conventions related to resolving OBSERVATION_PERIOD table." +summary: "Conventions related to mapping data into the OBSERVATION_PERIOD table." sidebar: mydoc_sidebar permalink: /observation_period.html --- @@ -12,5 +12,5 @@ permalink: /observation_period.html | **Field** | **Convention** | |:--------|:-------| -| OBSERVATION_PERIOD_END_DATE | [Resolving Observation Period End Date without Exact Information on a Last Day](events_outside_obs_period.html) | +| OBSERVATION_PERIOD_END_DATE | [Resolving Observation Period End Date without Exact Information on a Last Day](events_with_no_exact_last_day.html) | |===== \ No newline at end of file