documentation:software:heracles
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| **Requirements** | **Requirements** | ||
| * Data in OMOP CDM v4/v5 | * Data in OMOP CDM v4/v5 | ||
| - | * [[https://github.com/OHDSI/WebAPI|WebAPI]] installed and running | + | * COHORT and COHORT_DEFINITION tables (or other tables following the OMOP V5 cohort table format) |
| - | * Cohort and Cohort Definition Tables populated | + | |
| + | **Installation** | ||
| + | * Install [[documentation:software:olympus|OLYMPUS]] | ||
| + | * Advanced users may reference [[https://github.com/OHDSI/Heracles/|Heracles on Github]] for custom installation instructions | ||
| + | |||
| + | **Use** | ||
| + | |||
| + | * Select a Cohort from the Heracles dropdown. This will include all cohorts in your cohort definition table. | ||
| + | |||
| + | {{ :documentation:software:screen_shot_2015-04-09_at_4.04.07_pm.png |}} | ||
| + | |||
| + | * Select analyses individually (as listed below) or as part of a report package (bundle of analyses that will enable Heracles to build a particular visual report of a particular area of interest (e.g., drug exposure)). | ||
| + | |||
| + | {{ :documentation:software:screen_shot_2015-04-09_at_3.59.19_pm.png |}} | ||
| + | |||
| + | Optional parameters include | ||
| + | |||
| + | * Specific concept ID's to run for conditions, drugs, procedures, observations, and measurements | ||
| + | * Small Cell Count (minimum number of patients to return for any category) | ||
| + | * Run Heracles Heel for data quality analyses | ||
| + | * Limit the analyses to only events occurring within the Cohort Period (as opposed to all events for patients in the cohort) | ||
| + | |||
| + | * Your analysis will be sent to the Job Manager. If running Olympus, check there for completion status. Or if not in Olympus, use the link provided by Heracles to check it manually. | ||
| + | |||
| + | |||
| + | **Heracles Viewer** | ||
| + | |||
| **Heracles Analysis List** | **Heracles Analysis List** | ||
| - | Source name | + | Person |
| - | Number of persons | + | * Source name |
| - | Number of persons by gender | + | * Number of persons |
| - | Number of persons by year of birth | + | * Number of persons by gender |
| - | Number of persons by race | + | * Number of persons by year of birth |
| - | Number of persons by ethnicity | + | * Number of persons by race |
| - | Number of persons with invalid provider_id | + | * Number of persons by ethnicity |
| - | Number of persons with invalid location_id | + | * Number of persons with invalid provider_id |
| - | Number of persons with invalid care_site_id | + | * Number of persons with invalid location_id |
| - | Number of persons by age, with age at first observation period | + | * Number of persons with invalid care_site_id |
| - | Number of persons by gender by age, with age at first observation period | + | |
| - | Distribution of age at first observation period | + | Observation Period |
| - | Distribution of age at first observation period by gender | + | * Number of persons by age, with age at first observation period |
| - | Length of observation (days) of first observation period | + | * Number of persons by gender by age, with age at first observation period |
| - | Length of observation (days) of first observation period by gender | + | * Distribution of age at first observation period |
| - | Length of observation (days) of first observation period by age decile | + | * Distribution of age at first observation period by gender |
| - | Number of persons by length of observation period, in 30d increments | + | * Length of observation (days) of first observation period |
| - | Number of persons with continuous observation in each year | + | * Length of observation (days) of first observation period by gender |
| - | Number of persons with continuous observation in each month | + | * Length of observation (days) of first observation period by age decile |
| - | Number of persons by observation period start month | + | * Number of persons by length of observation period, in 30d increments |
| - | Number of persons by observation period end month | + | * Number of persons with continuous observation in each year |
| - | Number of persons by number of observation periods | + | * Number of persons with continuous observation in each month |
| - | Number of persons with observation period before year-of-birth | + | * Number of persons by observation period start month |
| - | Number of persons with observation period end < observation period start | + | * Number of persons by observation period end month |
| - | Number of persons with at least one day of observation in each year by gender and age decile | + | * Number of persons by number of observation periods |
| - | Number of persons with at least one day of observation in each month | + | * Number of persons with observation period before year-of-birth |
| - | Number of persons with at least one visit occurrence, by visit_concept_id | + | * Number of persons with observation period end < observation period start |
| - | Number of visit occurrence records, by visit_concept_id | + | * Number of persons with at least one day of observation in each year by gender and age decile |
| - | Number of persons by visit occurrence start month, by visit_concept_id | + | * Number of persons with at least one day of observation in each month |
| - | Number of distinct visit occurrence concepts per person | + | |
| - | Number of persons with at least one visit occurrence, by visit_concept_id by calendar year by gender by age decile | + | Visit Occurrence |
| - | Distribution of age by visit_concept_id | + | |
| - | Number of visit records with invalid person_id | + | * Number of persons with at least one visit occurrence, by visit_concept_id |
| - | Number of visit records outside valid observation period | + | * Number of visit occurrence records, by visit_concept_id |
| - | Number of visit records with end date < start date | + | * Number of persons by visit occurrence start month, by visit_concept_id |
| - | Number of visit records with invalid care_site_id | + | * Number of distinct visit occurrence concepts per person |
| - | Distribution of length of stay by visit_concept_id | + | * Number of persons with at least one visit occurrence, by visit_concept_id by calendar year by gender by age decile |
| - | Number of visit occurrence records by visit occurrence start month | + | * Distribution of age by visit_concept_id |
| - | Number of persons with at least one condition occurrence, by condition_concept_id | + | * Number of visit records with invalid person_id |
| - | Number of condition occurrence records, by condition_concept_id | + | * Number of visit records outside valid observation period |
| - | Number of persons by condition occurrence start month, by condition_concept_id | + | * Number of visit records with end date < start date |
| - | Number of distinct condition occurrence concepts per person | + | * Number of visit records with invalid care_site_id |
| - | Number of persons with at least one condition occurrence, by condition_concept_id by calendar year by gender by age decile | + | * Distribution of length of stay by visit_concept_id |
| - | Number of condition occurrence records, by condition_concept_id by condition_type_concept_id | + | * Number of visit occurrence records by visit occurrence start month |
| - | Distribution of age by condition_concept_id | + | * Number of persons with at least one condition occurrence, by condition_concept_id |
| - | Number of condition occurrence records with invalid person_id | + | |
| - | Number of condition occurrence records outside valid observation period | + | Condition Occurrence |
| - | Number of condition occurrence records with end date < start date | + | |
| - | Number of condition occurrence records with invalid provider_id | + | * Number of condition occurrence records, by condition_concept_id |
| - | Number of condition occurrence records with invalid visit_id | + | * Number of persons by condition occurrence start month, by condition_concept_id |
| - | Number of condition occurrence records by condition occurrence start month | + | * Number of distinct condition occurrence concepts per person |
| - | Number of persons with death, by cause_of_death_concept_id | + | * Number of persons with at least one condition occurrence, by condition_concept_id by calendar year by gender by age decile |
| - | Number of records of death, by cause_of_death_concept_id | + | * Number of condition occurrence records, by condition_concept_id by condition_type_concept_id |
| - | Number of persons by death month | + | * Distribution of age by condition_concept_id |
| - | Number of persons with a death, by calendar year by gender by age decile | + | * Number of condition occurrence records with invalid person_id |
| - | Number of death records, by death_type_concept_id | + | * Number of condition occurrence records outside valid observation period |
| - | Distribution of age at death by gender | + | * Number of condition occurrence records with end date < start date |
| - | Number of death records with invalid person_id | + | * Number of condition occurrence records with invalid provider_id |
| - | Number of death records outside valid observation period | + | * Number of condition occurrence records with invalid visit_id |
| - | Distribution of time from death to last condition | + | * Number of condition occurrence records by condition occurrence start month |
| - | Distribution of time from death to last drug | + | |
| - | Distribution of time from death to last visit | + | Death |
| - | Distribution of time from death to last procedure | + | |
| - | Distribution of time from death to last observation | + | * Number of persons with death, by cause_of_death_concept_id |
| - | Number of persons with at least one procedure occurrence, by procedure_concept_id | + | * Number of records of death, by cause_of_death_concept_id |
| - | Number of procedure occurrence records, by procedure_concept_id | + | * Number of persons by death month |
| - | Number of persons by procedure occurrence start month, by procedure_concept_id | + | * Number of persons with a death, by calendar year by gender by age decile |
| - | Number of distinct procedure occurrence concepts per person | + | * Number of death records, by death_type_concept_id |
| - | Number of persons with at least one procedure occurrence, by procedure_concept_id by calendar year by gender by age decile | + | * Distribution of age at death by gender |
| - | Number of procedure occurrence records, by procedure_concept_id by procedure_type_concept_id | + | * Number of death records with invalid person_id |
| - | Distribution of age by procedure_concept_id | + | * Number of death records outside valid observation period |
| - | Number of procedure occurrence records with invalid person_id | + | * Distribution of time from death to last condition |
| - | Number of procedure occurrence records outside valid observation period | + | * Distribution of time from death to last drug |
| - | Number of procedure occurrence records with invalid provider_id | + | * Distribution of time from death to last visit |
| - | Number of procedure occurrence records with invalid visit_id | + | * Distribution of time from death to last procedure |
| - | Number of procedure occurrence records by procedure occurrence start month | + | * Distribution of time from death to last observation |
| - | Number of persons with at least one drug exposure, by drug_concept_id | + | |
| - | Number of drug exposure records, by drug_concept_id | + | Procedure Occurrence |
| - | Number of persons by drug exposure start month, by drug_concept_id | + | |
| - | Number of distinct drug exposure concepts per person | + | * Number of persons with at least one procedure occurrence, by procedure_concept_id |
| - | Number of persons with at least one drug exposure, by drug_concept_id by calendar year by gender by age decile | + | * Number of procedure occurrence records, by procedure_concept_id |
| - | Number of drug exposure records, by drug_concept_id by drug_type_concept_id | + | * Number of persons by procedure occurrence start month, by procedure_concept_id |
| - | Distribution of age by drug_concept_id | + | * Number of distinct procedure occurrence concepts per person |
| - | Number of drug exposure records with invalid person_id | + | * Number of persons with at least one procedure occurrence, by procedure_concept_id by calendar year by gender by age decile |
| - | Number of drug exposure records outside valid observation period | + | * Number of procedure occurrence records, by procedure_concept_id by procedure_type_concept_id |
| - | Number of drug exposure records with end date < start date | + | * Distribution of age by procedure_concept_id |
| - | Number of drug exposure records with invalid provider_id | + | * Number of procedure occurrence records with invalid person_id |
| - | Number of drug exposure records with invalid visit_id | + | * Number of procedure occurrence records outside valid observation period |
| - | Distribution of days_supply by drug_concept_id | + | * Number of procedure occurrence records with invalid provider_id |
| - | Distribution of refills by drug_concept_id | + | * Number of procedure occurrence records with invalid visit_id |
| - | Distribution of quantity by drug_concept_id | + | * Number of procedure occurrence records by procedure occurrence start month |
| - | Number of drug exposure records by drug exposure start month | + | |
| - | Number of persons with at least one observation occurrence, by observation_concept_id | + | Drug Exposure |
| - | Number of observation occurrence records, by observation_concept_id | + | |
| - | Number of persons by observation occurrence start month, by observation_concept_id | + | * Number of persons with at least one drug exposure, by drug_concept_id |
| - | Number of distinct observation occurrence concepts per person | + | * Number of drug exposure records, by drug_concept_id |
| - | Number of persons with at least one observation occurrence, by observation_concept_id by calendar year by gender by age decile | + | * Number of persons by drug exposure start month, by drug_concept_id |
| - | Number of observation occurrence records, by observation_concept_id by observation_type_concept_id | + | * Number of distinct drug exposure concepts per person |
| - | Distribution of age by observation_concept_id | + | * Number of persons with at least one drug exposure, by drug_concept_id by calendar year by gender by age decile |
| - | Number of observation occurrence records, by observation_concept_id and unit_concept_id | + | * Number of drug exposure records, by drug_concept_id by drug_type_concept_id |
| - | Number of observation records with invalid person_id | + | * Distribution of age by drug_concept_id |
| - | Number of observation records outside valid observation period | + | * Number of drug exposure records with invalid person_id |
| - | Number of observation records with invalid provider_id | + | * Number of drug exposure records outside valid observation period |
| - | Number of observation records with invalid visit_id | + | * Number of drug exposure records with end date < start date |
| - | Number of observation records with no value (numeric, string, or concept) | + | * Number of drug exposure records with invalid provider_id |
| - | Distribution of numeric values, by observation_concept_id and unit_concept_id | + | * Number of drug exposure records with invalid visit_id |
| - | Distribution of low range, by observation_concept_id and unit_concept_id | + | * Distribution of days_supply by drug_concept_id |
| - | Distribution of high range, by observation_concept_id and unit_concept_id | + | * Distribution of refills by drug_concept_id |
| - | Number of observation records below/within/above normal range, by observation_concept_id and unit_concept_id | + | * Distribution of quantity by drug_concept_id |
| - | Number of observation records by observation start month | + | * Number of drug exposure records by drug exposure start month |
| - | Number of persons with at least one drug era, by drug_concept_id | + | |
| - | Number of drug era records, by drug_concept_id | + | Observation |
| - | Number of persons by drug era start month, by drug_concept_id | + | |
| - | Number of distinct drug era concepts per person | + | * Number of persons with at least one observation occurrence, by observation_concept_id |
| - | Number of persons with at least one drug era, by drug_concept_id by calendar year by gender by age decile | + | * Number of observation occurrence records, by observation_concept_id |
| - | Distribution of age by drug_concept_id | + | * Number of persons by observation occurrence start month, by observation_concept_id |
| - | Distribution of drug era length, by drug_concept_id | + | * Number of distinct observation occurrence concepts per person |
| - | Number of drug eras without valid person | + | * Number of persons with at least one observation occurrence, by observation_concept_id by calendar year by gender by age decile |
| - | Number of drug eras outside valid observation period | + | * Number of observation occurrence records, by observation_concept_id by observation_type_concept_id |
| - | Number of drug eras with end date < start date | + | * Distribution of age by observation_concept_id |
| - | Number of drug era records by drug era start month | + | * Number of observation occurrence records, by observation_concept_id and unit_concept_id |
| - | Number of persons with at least one condition era, by condition_concept_id | + | * Number of observation records with invalid person_id |
| - | Number of condition era records, by condition_concept_id | + | * Number of observation records outside valid observation period |
| - | Number of persons by condition era start month, by condition_concept_id | + | * Number of observation records with invalid provider_id |
| - | Number of distinct condition era concepts per person | + | * Number of observation records with invalid visit_id |
| - | Number of persons with at least one condition era, by condition_concept_id by calendar year by gender by age decile | + | * Number of observation records with no value (numeric, string, or concept) |
| - | Distribution of age by condition_concept_id | + | * Distribution of numeric values, by observation_concept_id and unit_concept_id |
| - | Distribution of condition era length, by condition_concept_id | + | * Distribution of low range, by observation_concept_id and unit_concept_id |
| - | Number of condition eras without valid person | + | * Distribution of high range, by observation_concept_id and unit_concept_id |
| - | Number of condition eras outside valid observation period | + | * Number of observation records below/within/above normal range, by observation_concept_id and unit_concept_id |
| - | Number of condition eras with end date < start date | + | * Number of observation records by observation start month |
| - | Number of condition era records by condition era start month | + | |
| - | Number of persons by location 3-digit zip | + | Measurement |
| - | Number of persons by location state | + | |
| - | Number of persons by place of service | + | * Number of persons with at least one measurement occurrence, by measurement_concept_id |
| - | Number of visits by place of service | + | * Number of measurement occurrence records, by measurement_concept_id |
| - | Number of records by cohort_concept_id | + | * Number of persons by measurement occurrence start month, by measurement_concept_id |
| - | Number of records with cohort end date < cohort start date | + | * Number of distinct measurement occurrence concepts per person |
| - | Number of persons by age, with age at cohort start | + | * Number of persons with at least one measurement occurrence, by measurement_concept_id by calendar year by gender by age decile |
| - | Distribution of age at cohort start | + | * Number of measurement occurrence records, by measurement_concept_id by measurement_type_concept_id |
| - | Distribution of age at cohort start by gender | + | * Distribution of age by measurement_concept_id |
| - | Distribution of age at cohort start by cohort start year | + | * Number of measurement occurrence records, by measurement_concept_id and unit_concept_id |
| - | Number of persons by duration from cohort start to cohort end, in 30d increments | + | * Number of measurement records with invalid person_id |
| - | Number of persons by duration from observation start to cohort start, in 30d increments | + | * Number of measurement records outside valid measurement period |
| - | Number of persons by duration from cohort start to observation end, in 30d increments | + | * Number of measurement records with invalid provider_id |
| - | Number of persons by duration from cohort end to observation end, in 30d increments | + | * Number of measurement records with invalid visit_id |
| - | Distribution of duration (days) from cohort start to cohort end | + | * Number of measurement records with no value (numeric, string, or concept) |
| - | Distribution of duration (days) from cohort start to cohort end, by gender | + | * Distribution of numeric values, by measurement_concept_id and unit_concept_id |
| - | Distribution of duration (days) from cohort start to cohort end, by age decile | + | * Distribution of low range, by measurement_concept_id and unit_concept_id |
| - | Distribution of duration (days) from observation start to cohort start | + | * Distribution of high range, by measurement_concept_id and unit_concept_id |
| - | Distribution of duration (days) from cohort start to observation end | + | * Number of measurement records below/within/above normal range, by measurement_concept_id and unit_concept_id |
| - | Distribution of duration (days) from cohort end to observation end | + | * Number of measurement records by measurement start month |
| - | Number of persons by cohort start year by gender by age decile | + | |
| - | Number of persons by cohort start month | + | Drug Era |
| - | Number of persons by number of cohort periods | + | |
| - | Number of persons by duration from cohort start to first occurrence of condition occurrence, by condition_concept_id | + | * Number of persons with at least one drug era, by drug_concept_id |
| - | Number of events by duration from cohort start to all occurrences of condition occurrence, by condition_concept_id | + | * Number of drug era records, by drug_concept_id |
| - | Number of persons by duration from cohort start to first occurrence of procedure occurrence, by procedure_concept_id | + | * Number of persons by drug era start month, by drug_concept_id |
| - | Number of events by duration from cohort start to all occurrences of procedure occurrence, by procedure_concept_id | + | * Number of distinct drug era concepts per person |
| - | Number of persons by duration from cohort start to first occurrence of drug exposure, by drug_concept_id | + | * Number of persons with at least one drug era, by drug_concept_id by calendar year by gender by age decile |
| - | Number of events by duration from cohort start to all occurrences of drug exposure, by drug_concept_id | + | * Distribution of age by drug_concept_id |
| - | Number of persons by duration from cohort start to first occurrence of observation, by observation_concept_id | + | * Distribution of drug era length, by drug_concept_id |
| - | Number of events by duration from cohort start to all occurrences of observation, by observation_concept_id | + | * Number of drug eras without valid person |
| - | Number of persons by duration from cohort start to first occurrence of condition era, by condition_concept_id | + | * Number of drug eras outside valid observation period |
| - | Number of events by duration from cohort start to all occurrences of condition era, by condition_concept_id | + | * Number of drug eras with end date < start date |
| - | Number of persons by duration from cohort start to first occurrence of drug era, by drug_concept_id | + | * Number of drug era records by drug era start month |
| - | Number of events by duration from cohort start to all occurrences of drug era, by drug_concept_id | + | |
| + | Condition Era | ||
| + | |||
| + | * Number of persons with at least one condition era, by condition_concept_id | ||
| + | * Number of condition era records, by condition_concept_id | ||
| + | * Number of persons by condition era start month, by condition_concept_id | ||
| + | * Number of distinct condition era concepts per person | ||
| + | * Number of persons with at least one condition era, by condition_concept_id by calendar year by gender by age decile | ||
| + | * Distribution of age by condition_concept_id | ||
| + | * Distribution of condition era length, by condition_concept_id | ||
| + | * Number of condition eras without valid person | ||
| + | * Number of condition eras outside valid observation period | ||
| + | * Number of condition eras with end date < start date | ||
| + | * Number of condition era records by condition era start month | ||
| + | |||
| + | Location | ||
| + | |||
| + | * Number of persons by location 3-digit zip | ||
| + | * Number of persons by location state | ||
| + | |||
| + | Care Site | ||
| + | |||
| + | * Number of persons by place of service | ||
| + | * Number of visits by place of service | ||
| + | |||
| + | Cohort Analyses | ||
| + | |||
| + | * Number of records by cohort_concept_id | ||
| + | * Number of records with cohort end date < cohort start date | ||
| + | * Number of persons by age, with age at cohort start | ||
| + | * Distribution of age at cohort start | ||
| + | * Distribution of age at cohort start by gender | ||
| + | * Distribution of age at cohort start by cohort start year | ||
| + | * Number of persons by duration from cohort start to cohort end, in 30d increments | ||
| + | * Number of persons by duration from observation start to cohort start, in 30d increments | ||
| + | * Number of persons by duration from cohort start to observation end, in 30d increments | ||
| + | * Number of persons by duration from cohort end to observation end, in 30d increments | ||
| + | * Distribution of duration (days) from cohort start to cohort end | ||
| + | * Distribution of duration (days) from cohort start to cohort end, by gender | ||
| + | * Distribution of duration (days) from cohort start to cohort end, by age decile | ||
| + | * Distribution of duration (days) from observation start to cohort start | ||
| + | * Distribution of duration (days) from cohort start to observation end | ||
| + | * Distribution of duration (days) from cohort end to observation end | ||
| + | * Number of persons by cohort start year by gender by age decile | ||
| + | * Number of persons by cohort start month | ||
| + | * Number of persons by number of cohort periods | ||
| + | * Number of persons by duration from cohort start to first occurrence of condition occurrence, by condition_concept_id | ||
| + | * Number of events by duration from cohort start to all occurrences of condition occurrence, by condition_concept_id | ||
| + | * Number of persons by duration from cohort start to first occurrence of procedure occurrence, by procedure_concept_id | ||
| + | * Number of events by duration from cohort start to all occurrences of procedure occurrence, by procedure_concept_id | ||
| + | * Number of persons by duration from cohort start to first occurrence of drug exposure, by drug_concept_id | ||
| + | * Number of events by duration from cohort start to all occurrences of drug exposure, by drug_concept_id | ||
| + | * Number of persons by duration from cohort start to first occurrence of observation, by observation_concept_id | ||
| + | * Number of events by duration from cohort start to all occurrences of observation, by observation_concept_id | ||
| + | * Number of persons by duration from cohort start to first occurrence of condition era, by condition_concept_id | ||
| + | * Number of events by duration from cohort start to all occurrences of condition era, by condition_concept_id | ||
| + | * Number of persons by duration from cohort start to first occurrence of drug era, by drug_concept_id | ||
| + | * Number of events by duration from cohort start to all occurrences of drug era, by drug_concept_id | ||
documentation/software/heracles.1428606090.txt.gz · Last modified: 2015/04/09 19:01 by jduke
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