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SAFEHR-data / ramses-package

R Package for Data-Driven Antimicrobial Stewardship & Surveillance in Hospitals
https://ramses-antibiotics.web.app/
GNU General Public License v3.0
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Integrating OMOP into RAMSES #12

Closed zsenousy closed 1 week ago

zsenousy commented 3 months ago

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 commented 2 months ago

@docsteveharris if that helps.