Skip to contents

Screening of Drugs

Source: R/screen_drug.R
screen_drug.Rd

[Experimental] The screen_drug() function identifies and ranks the most frequently reported drugs (by active ingredient) in a dataset.

Usage

screen_drug(.data, mp_data, freq_threshold = NULL, top_n = NULL)

Arguments

.data,

An drug data.table. See drug_

mp_data

An MP data.table. See mp_

freq_threshold

A numeric value indicating the minimum frequency (as a proportion) of cases where a drug must appear to be included in the results. Defaults to NULL.

top_n

An integer specifying the number of most frequently occurring drugs to return. Defaults to NULL.

Value

A data.frame with the following columns:

  • Drug name: The drug name.

  • DrecNo: The drug record number

  • N: The number of unique reports (cases) where the drug appears.

  • percentage: The percentage of total unique reports where the drug appears.

The results are sorted in descending order of percentage.

Details

  • If freq_threshold is set (e.g., 0.05), the function filters drugs appearing in at least 5% of unique reports in .data.

  • If top_n is specified, only the most frequent n drugs are returned. If both freq_threshold and top_n are provided, only top_n is applied (a warning is raised in such cases).

  • Counts are computed at the case level, not the drug mention level. This means frequencies reflect the proportion of unique reports (cases) where a drug is mentioned, rather than the total mentions across all reports.

Examples

# Filter drugs appearing in at least 10% of reports
screen_drug(
  .data = drug_,
  mp_data = mp_,
  freq_threshold = 0.10
)
#> # A tibble: 3 × 4
#>   `Drug name`      DrecNo     N percentage
#>   <chr>             <int> <int>      <dbl>
#> 1 pembrolizumab  20116296   298       39.7
#> 2 nivolumab     111841511   225       30  
#> 3 ipilimumab    133138448    86       11.5

# Get the top 5 most reported drugs
screen_drug(
  .data = drug_,
  mp_data = mp_,
  top_n = 5
)
#> # A tibble: 5 × 4
#>   `Drug name`      DrecNo     N percentage
#>   <chr>             <int> <int>      <dbl>
#> 1 pembrolizumab  20116296   298      39.7 
#> 2 nivolumab     111841511   225      30   
#> 3 ipilimumab    133138448    86      11.5 
#> 4 atezolizumab  112765189    69       9.2 
#> 5 durvalumab    125456180    68       9.07

# nb: in the example datasets, not all drugs are recorded in mp_,
# leading to NAs in screen_drug output.