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TestGenerator takes as an input an Excel file with
sheets that represent a table in the OMOP-CDM. The following example (testPatientsRSV.xlsx)
represents a population of 10 patients, some of them with RSV.
#> # A tibble: 10 × 5
#> person_id gender_concept_id year_of_birth race_concept_id
#> <dbl> <dbl> <dbl> <dbl>
#> 1 1 8532 1980 0
#> 2 2 8507 1980 0
#> 3 3 8532 1965 0
#> 4 4 8532 2010 0
#> 5 5 8532 1936 0
#> 6 6 8532 1970 0
#> 7 7 8532 1988 0
#> 8 8 8507 1998 0
#> 9 9 8507 1990 0
#> 10 10 8532 1945 0
#> # ℹ 1 more variable: ethnicity_concept_id <dbl>The user can include only the tables that are relevant to the analysis.
#> [1] "person" "observation_period" "condition_occurrence"
#> [4] "visit_occurrence" "visit_detail" "death"TestGenerator::readPatients() converts the file into
JSON format and saves it in the project. The sample data is then pushed
to a blank CDM with patientsCDM().
#> Unit Test Definition created successfully: test
#> Patients pushed to blank CDM successfully
#> # OMOP CDM reference (tbl_duckdb_connection)
#>
#> Tables: person, observation_period, visit_occurrence, visit_detail, condition_occurrence, drug_exposure, procedure_occurrence, device_exposure, measurement, observation, death, note, note_nlp, specimen, fact_relationship, location, care_site, provider, payer_plan_period, cost, drug_era, dose_era, condition_era, metadata, cdm_source, concept, vocabulary, domain, concept_class, concept_relationship, relationship, concept_synonym, concept_ancestor, source_to_concept_map, drug_strength, cohort_definition, attribute_definitionThat returns a CDM reference object that now can be used to perform unit tests.
#> # Source: table<person> [?? x 18]
#> # Database: DuckDB v0.9.1 [cbarboza@Windows 10 x64:R 4.3.1/C:\Users\cbarboza\AppData\Local\Temp\Rtmp6Jtt0B\file92c81df13da1.duckdb]
#> person_id gender_concept_id year_of_birth month_of_birth day_of_birth
#> <int> <int> <int> <int> <int>
#> 1 1 8532 1980 NA NA
#> 2 2 8507 1980 NA NA
#> 3 3 8532 1965 NA NA
#> 4 4 8532 2010 NA NA
#> 5 5 8532 1936 NA NA
#> 6 6 8532 1970 NA NA
#> 7 7 8532 1988 NA NA
#> 8 8 8507 1998 NA NA
#> 9 9 8507 1990 NA NA
#> 10 10 8532 1945 NA NA
#> # ℹ more rows
#> # ℹ 13 more variables: birth_datetime <dttm>, 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>These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.