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@ginberg
ginberg committed Nov 18, 2024
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1 change: 1 addition & 0 deletions README.Rmd
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Expand Up @@ -19,6 +19,7 @@ knitr::opts_chunk$set(
[![CRAN status](https://www.r-pkg.org/badges/version/DrugExposureDiagnostics)](https://CRAN.R-project.org/package=DrugExposureDiagnostics)
[![codecov.io](https://codecov.io/github/darwin-eu/DrugExposureDiagnostics/coverage.svg?branch=main)](https://app.codecov.io/github/darwin-eu/DrugExposureDiagnostics?branch=main)
[![R-CMD-check](https://github.com/darwin-eu/DrugExposureDiagnostics/workflows/R-CMD-check/badge.svg)](https://github.com/darwin-eu/DrugExposureDiagnostics/actions)
[![Lifecycle:stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
<!-- badges: end -->

The goal of DrugExposureDiagnostics is to summarise ingredient specific drug exposure data in the OMOP CDM.
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129 changes: 68 additions & 61 deletions README.md
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Expand Up @@ -9,6 +9,7 @@
status](https://www.r-pkg.org/badges/version/DrugExposureDiagnostics)](https://CRAN.R-project.org/package=DrugExposureDiagnostics)
[![codecov.io](https://codecov.io/github/darwin-eu/DrugExposureDiagnostics/coverage.svg?branch=main)](https://app.codecov.io/github/darwin-eu/DrugExposureDiagnostics?branch=main)
[![R-CMD-check](https://github.com/darwin-eu/DrugExposureDiagnostics/workflows/R-CMD-check/badge.svg)](https://github.com/darwin-eu/DrugExposureDiagnostics/actions)
[![Lifecycle:stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
<!-- badges: end -->

The goal of DrugExposureDiagnostics is to summarise ingredient specific
Expand Down Expand Up @@ -39,15 +40,15 @@ citation("DrugExposureDiagnostics")
#>
#> Inberg G, Burn E, Burkard T (????). _DrugExposureDiagnostics:
#> Diagnostics for OMOP Common Data Model Drug Records_. R package
#> version 1.0.5, https://github.com/darwin-eu/DrugExposureDiagnostics,
#> version 1.0.9, https://github.com/darwin-eu/DrugExposureDiagnostics,
#> <https://darwin-eu.github.io/DrugExposureDiagnostics/>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {DrugExposureDiagnostics: Diagnostics for OMOP Common Data Model Drug Records},
#> author = {Ger Inberg and Edward Burn and Theresa Burkard},
#> note = {R package version 1.0.5, https://github.com/darwin-eu/DrugExposureDiagnostics},
#> note = {R package version 1.0.9, https://github.com/darwin-eu/DrugExposureDiagnostics},
#> url = {https://darwin-eu.github.io/DrugExposureDiagnostics/},
#> }
```
Expand All @@ -62,6 +63,11 @@ library(dplyr)

``` r
cdm <- mockDrugExposure()
#> Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
#> target signature 'duckdb_connection#Id'.
#> "duckdb_connection#ANY" would also be valid
#> Warning: ! 1 column in drug_strength do not match expected column type:
#> • `box_size` is numeric but expected integer
```

Let´s look at the ingredient acetaminophen
Expand All @@ -77,13 +83,13 @@ all_checks <- executeChecks(cdm = cdm,
"verbatimEndDate", "dose", "sig", "quantity", "diagnosticsSummary"))
#> population after earliestStartDate smaller than sample, sampling ignored
#> ℹ The following estimates will be computed:
#> • daily_dose: count_missing, percentage_missing, mean, sd, min, q05, q25,
#> median, q75, q95, max
#> • daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median,
#> q75, q95, min, max
#> ! Table is collected to memory as not all requested estimates are supported on
#> the database side
#> → Start summary of data, at 2024-06-12 14:48:26.801546
#> → Start summary of data, at 2024-11-18 16:50:21.851554
#>
#> ✔ Summary finished, at 2024-06-12 14:48:26.97046
#> ✔ Summary finished, at 2024-11-18 16:50:21.996256
```

The output is a list which contains the following set of tibbles:
Expand All @@ -108,30 +114,31 @@ the database for a given ingredient.
``` r
glimpse(all_checks$conceptSummary)
#> Rows: 6
#> Columns: 25
#> Columns: 26
#> Rowwise:
#> $ drug_concept_id <dbl> 40231925, 19133768, 1127433, 1127078, 4022…
#> $ drug <chr> "acetaminophen 325 MG / Hydrocodone Bitart…
#> $ ingredient_concept_id <dbl> 1125315, 1125315, 1125315, 1125315, 112531…
#> $ drug_concept_id <int> 19133768, 1127078, 40162522, 1127433, 4022…
#> $ drug <chr> "acetaminophen 160 MG Oral Tablet", "aceta…
#> $ ingredient_concept_id <int> 1125315, 1125315, 1125315, 1125315, 112531…
#> $ ingredient <chr> "acetaminophen", "acetaminophen", "acetami…
#> $ n_records <int> 10, 14, 13, 19, 12, 18
#> $ n_patients <int> 9, 13, 11, 13, 11, 15
#> $ n_records <int> 14, 19, 18, 13, 12, 10
#> $ n_patients <int> 13, 13, 15, 11, 11, 9
#> $ domain_id <chr> "Drug", "Drug", "Drug", "Drug", "Drug", "D…
#> $ vocabulary_id <chr> "RxNorm", "RxNorm", "RxNorm", "RxNorm", "R…
#> $ concept_class_id <chr> "Clinical Drug", "Clinical Drug", "Clinica…
#> $ standard_concept <chr> "S", "S", "S", "S", "S", "S"
#> $ concept_code <chr> "857005", "282464", "1049221", "833036", "…
#> $ concept_code <chr> "282464", "833036", "313782", "1049221", "…
#> $ valid_start_date <date> 1970-01-01, 1970-01-01, 1970-01-01, 1970-0…
#> $ valid_end_date <date> 2099-12-31, 2099-12-31, 2099-12-31, 2099-1…
#> $ invalid_reason <lgl> NA, NA, NA, NA, NA, NA
#> $ amount_value <dbl> NA, NA, 200, NA, 100, 200
#> $ amount_unit_concept_id <dbl> NA, NA, 9655, NA, 9655, 9655
#> $ numerator_value <dbl> 3, 3, NA, 3, NA, NA
#> $ numerator_unit_concept_id <dbl> 8576, 8576, NA, 8576, NA, NA
#> $ invalid_reason <chr> NA, NA, NA, NA, NA, NA
#> $ amount_value <dbl> NA, 300, 100, 100, 300, 200
#> $ amount_unit_concept_id <int> NA, 8576, 8576, 8576, 8576, 8576
#> $ numerator_value <dbl> 1, NA, NA, NA, NA, NA
#> $ numerator_unit_concept_id <int> 8576, NA, NA, NA, NA, NA
#> $ numerator_unit <chr> NA, NA, NA, NA, NA, NA
#> $ denominator_value <dbl> 10, 10, NA, 10, NA, NA
#> $ denominator_unit_concept_id <dbl> 8587, 8587, NA, 8587, NA, NA
#> $ denominator_value <dbl> 100, NA, NA, NA, NA, NA
#> $ denominator_unit_concept_id <int> 8587, NA, NA, NA, NA, NA
#> $ denominator_unit <chr> NA, NA, NA, NA, NA, NA
#> $ box_size <dbl> 0, 0, 0, 0, 0, 0
#> $ amount_unit <chr> NA, NA, NA, NA, NA, NA
#> $ dose_form <chr> "Oral Tablet", "Oral Tablet", "Oral Tablet…
#> $ result_obscured <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE
Expand All @@ -140,13 +147,13 @@ all_checks$conceptSummary %>%
#> # A tibble: 6 × 2
#> # Rowwise:
#> drug_concept_id drug
#> <dbl> <chr>
#> 1 40231925 acetaminophen 325 MG / Hydrocodone Bitartrate
#> 2 19133768 acetaminophen 160 MG Oral Tablet
#> 3 1127433 acetaminophen 325 MG / Oxycodone Hydrochloride
#> 4 1127078 acetaminophen 750 MG / Hydrocodone Bitartrate
#> <int> <chr>
#> 1 19133768 acetaminophen 160 MG Oral Tablet
#> 2 1127078 acetaminophen 750 MG / Hydrocodone Bitartrate
#> 3 40162522 acetaminophen 325 MG Oral Tablet
#> 4 1127433 acetaminophen 325 MG / Oxycodone Hydrochloride
#> 5 40229134 acetaminophen 21.7 MG/ML / Dextromethorphan
#> 6 40162522 acetaminophen 325 MG Oral Tablet
#> 6 40231925 acetaminophen 325 MG / Hydrocodone Bitartrate
```

Other tibbles then contain information from the various checks
Expand All @@ -158,47 +165,47 @@ by concept.

``` r
all_checks$missingValuesOverall
#> # A tibble: 15 × 9
#> # A tibble: 15 × 10
#> # Rowwise: ingredient_concept_id, ingredient
#> ingredient_concept_id ingredient variable n_records n_sample
#> <dbl> <chr> <chr> <int> <dbl>
#> 1 1125315 acetaminophen n_missing_drug_exposu… 44 10000
#> 2 1125315 acetaminophen n_missing_person_id 44 10000
#> 3 1125315 acetaminophen n_missing_drug_concep… 44 10000
#> 4 1125315 acetaminophen n_missing_drug_exposu… 44 10000
#> 5 1125315 acetaminophen n_missing_drug_exposu… 44 10000
#> 6 1125315 acetaminophen n_missing_verbatim_en… 44 10000
#> 7 1125315 acetaminophen n_missing_drug_type_c… 44 10000
#> 8 1125315 acetaminophen n_missing_quantity 44 10000
#> 9 1125315 acetaminophen n_missing_days_supply 44 10000
#> 10 1125315 acetaminophen n_missing_sig 44 10000
#> 11 1125315 acetaminophen n_missing_route_conce… 44 10000
#> 12 1125315 acetaminophen n_missing_drug_source… 44 10000
#> 13 1125315 acetaminophen n_missing_drug_source… 44 10000
#> 14 1125315 acetaminophen n_missing_route_sourc… 44 10000
#> 15 1125315 acetaminophen n_missing_dose_unit_s… 44 10000
#> ingredient_concept_id ingredient variable n_records n_sample n_person
#> <int> <chr> <chr> <int> <dbl> <dbl>
#> 1 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 2 1125315 acetaminophen n_missing_pe… 44 10000 25
#> 3 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 4 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 5 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 6 1125315 acetaminophen n_missing_ve… 44 10000 25
#> 7 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 8 1125315 acetaminophen n_missing_qu… 44 10000 25
#> 9 1125315 acetaminophen n_missing_da… 44 10000 25
#> 10 1125315 acetaminophen n_missing_sig 44 10000 25
#> 11 1125315 acetaminophen n_missing_ro… 44 10000 25
#> 12 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 13 1125315 acetaminophen n_missing_dr… 44 10000 25
#> 14 1125315 acetaminophen n_missing_ro… 44 10000 25
#> 15 1125315 acetaminophen n_missing_do… 44 10000 25
#> # ℹ 4 more variables: n_records_not_missing_value <dbl>,
#> # n_records_missing_value <dbl>, proportion_records_missing_value <dbl>,
#> # result_obscured <lgl>
all_checks$missingValuesByConcept
#> # A tibble: 90 × 11
#> # A tibble: 90 × 12
#> # Rowwise: drug_concept_id, drug, ingredient_concept_id, ingredient
#> drug_concept_id drug ingredient_concept_id ingredient variable n_records
#> <dbl> <chr> <dbl> <chr> <chr> <int>
#> 1 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 2 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 3 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 4 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 5 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 6 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 7 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 8 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 9 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> 10 40162522 acetamin… 1125315 acetamino… n_missi… 12
#> <int> <chr> <int> <chr> <chr> <int>
#> 1 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 2 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 3 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 4 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 5 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 6 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 7 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 8 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 9 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> 10 19133768 acetamin… 1125315 acetamino… n_missi… 8
#> # ℹ 80 more rows
#> # ℹ 5 more variables: n_sample <dbl>, n_records_not_missing_value <dbl>,
#> # n_records_missing_value <dbl>, proportion_records_missing_value <dbl>,
#> # result_obscured <lgl>
#> # ℹ 6 more variables: n_sample <dbl>, n_person <dbl>,
#> # n_records_not_missing_value <dbl>, n_records_missing_value <dbl>,
#> # proportion_records_missing_value <dbl>, result_obscured <lgl>
```

Or we can also see a summary of drug exposure duration
Expand All @@ -210,7 +217,7 @@ all_checks$drugExposureDurationOverall
#> # A tibble: 1 × 18
#> # Rowwise: ingredient_concept_id
#> ingredient_concept_id ingredient n_records n_sample n_person
#> <dbl> <chr> <int> <dbl> <int>
#> <int> <chr> <int> <dbl> <int>
#> 1 1125315 acetaminophen 44 10000 25
#> # ℹ 13 more variables: n_non_negative_days <int>, n_negative_days <int>,
#> # proportion_negative_days <dbl>, minimum_drug_exposure_days <dbl>,
Expand All @@ -223,7 +230,7 @@ all_checks$drugExposureDurationByConcept
#> # A tibble: 6 × 20
#> # Rowwise: drug_concept_id, drug, ingredient_concept_id
#> drug_concept_id drug ingredient_concept_id ingredient n_records n_sample
#> <dbl> <chr> <dbl> <chr> <int> <dbl>
#> <int> <chr> <int> <chr> <int> <dbl>
#> 1 1127078 acetamino… 1125315 acetamino… 8 10000
#> 2 1127433 acetamino… 1125315 acetamino… 8 10000
#> 3 19133768 acetamino… 1125315 acetamino… 8 10000
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