DDIWAS R package tutorial

Patrick Wu

10/17/2020

Description

CSV files in this tutorial come from the vignette on how to extract EHR data for DDIWAS.

• This tutorial shows how to process and analyze electronic health record (EHR) data extracted from a relational database organized using the OHDSI/OMOP Common Data Model.
  
• Please submit questions/comments/feedback to wei-qi.wei(AT)vumc.org.

Import packages

Load required packages

suppressPackageStartupMessages({
  library(tidyverse);
  library(broom); 
  library(ddiwas); 
  library(glue); 
  library(lubridate)})
set.seed(1)

Map drug allergies

ehr_drug_allergies <- read_csv("ddi_adr_data.csv", col_types = cols())
names(ehr_drug_allergies) <- tolower(names(ehr_drug_allergies))
drug_allergies <- ddiwas::map_drug_allergies(ehr_drug_allergies = ehr_drug_allergies)

Example input ddi_adr_data.csv dataframe

Example output drug_allergies dataframe

Process covariates

df_drug_exposures <- read_csv("ddi_drug_exposures.csv", col_types = cols())
names(df_drug_exposures) <- c("person_id", "concept_id")

covariates <- read_csv("ddi_covariates.csv", col_types = cols())
names(covariates) <- tolower(names(covariates))
covariates <- ddiwas::process_covariates(covariates, df_drug_exposures)

Example input dataframes

• ddi_drug_exposures.csv

• ddi_covariates.csv

Example output covariates dataframe

Require allergy list entry during observation period

covariates <- ddiwas::require_drug_allergies(ehr_drug_allergies, covariates)

Example input dataframes

• ehr_drug_allergies

• covariates

Example output covariates dataframe after requiring allergy list entry

Create regression table

regression_table <- ddiwas::create_regression_table(drug_allergies, covariates)

Example input dataframes.

• drug_allergies

• covariates

Example output regression_table dataframe

Run regression

results <- ddiwas::ddiwas_regression(regression_table, rare_events = TRUE)

Add object_drug column. Rearrange and rename columns.

results$object_drug <- "simvastatin"
results <- results %>% 
  select(object_drug, drug, coef, se, pval, or, nA, nB, nC, nD)
names(results) <- c("object_drug", "potential_precipitant_drug", "coef", "se", "pval", "or", "nA", "nB", "nC", "nD") 

Example input regression_table dataframe.

Example output results dataframe.

Packages used to create document

sessionInfo()
#> R version 4.0.4 (2021-02-15)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] lubridate_1.7.10 glue_1.4.2       ddiwas_0.1       broom_0.7.5     
#>  [5] forcats_0.5.1    stringr_1.4.0    dplyr_1.0.5      purrr_0.3.4     
#>  [9] readr_1.4.0      tidyr_1.1.3      tibble_3.1.0     ggplot2_3.3.3   
#> [13] tidyverse_1.3.0 
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.6        assertthat_0.2.1  rprojroot_2.0.2   digest_0.6.27    
#>  [5] utf8_1.2.1        R6_2.5.0          cellranger_1.1.0  backports_1.2.1  
#>  [9] reprex_1.0.0      evaluate_0.14     httr_1.4.2        pillar_1.5.1     
#> [13] rlang_0.4.10      readxl_1.3.1      rstudioapi_0.13   DT_0.17          
#> [17] rmarkdown_2.7     pkgdown_1.6.1     textshaping_0.3.1 desc_1.2.0       
#> [21] htmlwidgets_1.5.3 munsell_0.5.0     compiler_4.0.4    modelr_0.1.8     
#> [25] xfun_0.22         pkgconfig_2.0.3   systemfonts_1.0.1 htmltools_0.5.1.1
#> [29] tidyselect_1.1.0  fansi_0.4.2       crayon_1.4.1      dbplyr_2.1.0     
#> [33] withr_2.4.1       grid_4.0.4        jsonlite_1.7.2    gtable_0.3.0     
#> [37] lifecycle_1.0.0   DBI_1.1.1         magrittr_2.0.1    scales_1.1.1     
#> [41] cli_2.3.1         stringi_1.5.3     cachem_1.0.4      fs_1.5.0         
#> [45] xml2_1.3.2        ellipsis_0.3.1    ragg_1.1.1        generics_0.1.0   
#> [49] vctrs_0.3.6       tools_4.0.4       crosstalk_1.1.1   hms_1.0.0        
#> [53] fastmap_1.1.0     yaml_2.2.1        colorspace_2.0-0  rvest_1.0.0      
#> [57] memoise_2.0.0     knitr_1.31        haven_2.3.1