Integrating OMOP into RAMSES

[zsenousy]

Found this OMOCK package: https://github.com/OHDSI/omock

The main purpose of the package is to generate mock OMOP CDM (Observational Medical Outcomes Partnership Common Data Model) data to facilitating the testing of various packages within the OMOPverse ecosystem.

Step 1 - Install:

# install.packages("devtools")
devtools::install_github("OHDSI/omock")

Step 2 - import required libraries:

library(omopgenerics)
library(omock)
library(dplyr)

Step 3 - making an empty cdm reference. This includes the person and observation tables (as they are required) but they are currently empty:

cdm <- emptyCdmReference(cdmName = "mock")
cdm$person %>% 
  glimpse()
#> Rows: 0
#> Columns: 18
#> $ person_id                   <int> 
#> $ gender_concept_id           <int> 
#> $ year_of_birth               <int> 
#> $ month_of_birth              <int> 
#> $ day_of_birth                <int> 
#> $ birth_datetime              <date> 
#> $ race_concept_id             <int> 
#> $ ethnicity_concept_id        <int> 
#> $ location_id                 <int> 
#> $ provider_id                 <int> 
#> $ care_site_id                <int> 
#> $ person_source_value         <chr> 
#> $ gender_source_value         <chr> 
#> $ gender_source_concept_id    <int> 
#> $ race_source_value           <chr> 
#> $ race_source_concept_id      <int> 
#> $ ethnicity_source_value      <chr> 
#> $ ethnicity_source_concept_id <int>
cdm$observation_period %>% 
  glimpse()
#> Rows: 0
#> Columns: 5
#> $ observation_period_id         <int> 
#> $ person_id                     <int> 
#> $ observation_period_start_date <date> 
#> $ observation_period_end_date   <date> 
#> $ period_type_concept_id        <int>

Step 4 - Once we have have our empty cdm reference, we can quickly add a person and observation tables with a specific number of individuals.

cdm <- cdm %>% 
  omock::mockPerson(nPerson = 1000)

cdm$person %>% 
  glimpse()
#> Rows: 1,000
#> Columns: 7
#> $ person_id            <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15…
#> $ gender_concept_id    <dbl> 8507, 8532, 8532, 8532, 8507, 8507, 8532, 8532, 8…
#> $ year_of_birth        <dbl> 1997, 1963, 1986, 1978, 1973, 1961, 1986, 1981, 1…
#> $ month_of_birth       <dbl> 8, 1, 3, 11, 3, 2, 12, 9, 7, 6, 1, 10, 1, 3, 7, 1…
#> $ day_of_birth         <dbl> 22, 27, 10, 8, 2, 1, 16, 5, 23, 2, 17, 13, 24, 20…
#> $ race_concept_id      <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
#> $ ethnicity_concept_id <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…

cdm <- cdm %>% 
  omock::mockObservationPeriod()

cdm$observation_period %>% 
  glimpse()
#> Rows: 1,000
#> Columns: 5
#> $ observation_period_id         <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
#> $ person_id                     <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
#> $ observation_period_start_date <date> 2000-06-03, 1999-04-05, 2015-01-15, 198…
#> $ observation_period_end_date   <date> 2013-06-29, 2003-06-15, 2015-10-11, 201…
#> $ period_type_concept_id        <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …

[zsenousy]

@docsteveharris if that helps.