The primary objective of the omock package is to generate mock OMOPCDM (Observational Medical Outcomes Partnership Common Data Model) datato facilitating the testing of various packages within the OMOPverseecosystem. For more information on the package please see our paper inJournal of Open Source Software.
#> To cite omock in publications please use:#> #> Du, Mike, Mercadé-Besora, Núria, Alcalde-Herraiz, Marta, Chen,#> Xihang, Guo, Yuchen, López-Güell, Kim, Burn, Edward, Català, Martí#> (2025). "omock: A R package for Mock Data Generation for the#> Observational Medical Outcomes Partnership Common Data Model."#> _Journal of Open Source Software_. doi:10.21105/joss.08178#> <https://doi.org/10.21105/joss.08178>,#> <https://joss.theoj.org/papers/10.21105/joss.08178>.#> #> A BibTeX entry for LaTeX users is#> #> @Article{,#> title = {omock: A R package for Mock Data Generation for the Observational Medical Outcomes Partnership Common Data Model},#> author = {{Du} and {Mike} and {Mercadé-Besora} and {Núria} and {Alcalde-Herraiz} and {Marta} and {Chen} and {Xihang} and {Guo} and {Yuchen} and {López-Güell} and {Kim} and {Burn} and {Edward} and {Català} and {Martí}},#> journal = {Journal of Open Source Software},#> year = {2025},#> doi = {10.21105/joss.08178},#> url = {https://joss.theoj.org/papers/10.21105/joss.08178},#> }You can install the development version of omock using:
# install.packages("devtools")devtools::install_github("OHDSI/omock")With omock we can quickly make a simple mock of OMOP CDM data.
library(omopgenerics)library(omock)library(dplyr)We first start by making an empty cdm reference. This includes theperson and observation tables (as they are required) but they arecurrently 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>Once we have have our empty cdm reference, we can quickly add aperson table with a specific number of individuals.
cdm<- cdm%>% omock::mockPerson(nPerson =1000)cdm$person%>%glimpse()#> Rows: 1,000#> Columns: 18#> $ person_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,…#> $ gender_concept_id <int> 8532, 8532, 8507, 8532, 8532, 8507, 8532, …#> $ year_of_birth <int> 1984, 1972, 1978, 1994, 1975, 1973, 1984, …#> $ month_of_birth <int> 5, 8, 9, 10, 11, 1, 10, 3, 5, 10, 8, 6, 4,…#> $ day_of_birth <int> 8, 1, 26, 6, 5, 14, 25, 22, 30, 29, 3, 6, …#> $ race_concept_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ ethnicity_concept_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ birth_datetime <dttm> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…#> $ location_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ provider_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ care_site_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ person_source_value <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ gender_source_value <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ gender_source_concept_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ race_source_value <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ race_source_concept_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ ethnicity_source_value <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…#> $ ethnicity_source_concept_id <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…We can then fill in the observation period table for theseindividuals.
cdm<- cdm%>% omock::mockObservationPeriod()cdm$observation_period%>%glimpse()#> Rows: 1,000#> Columns: 5#> $ person_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…#> $ observation_period_start_date <date> 1988-05-28, 2000-01-12, 2014-03-05, 201…#> $ observation_period_end_date <date> 1994-07-23, 2006-02-16, 2018-07-08, 201…#> $ observation_period_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…#> $ period_type_concept_id <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…