extract_tto: Time to onset extraction

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

Time to onset extraction

Description

extract_tto() collects all available time to onsets for a set of drug-adr pairs.

Usage

extract_tto(.data, adr_s, drug_s, tto_time_range = 1)

Arguments

.data	A link data.table. See link_.
adr_s	A character string. The name of the adr column. (see details)
drug_s	A character string. The name of the drug column. (see details)
tto_time_range	Incertitude range of Time to onset, in days. Defaults to 1 as recommended by umc

Details

Extraction of (maximum available) time between drug initiation and event onset. This runs at the drug-adr pair level. You will need a link data.table, see link_, on which you have added drugs and adrs with add_drug() and add_adr(). Uppsala Monitoring Centre recommends to use only cases where the incertitude on time to onset is less than 1 day. You can change this with tto_time_range. You might want to use desc_tto() to obtain summary statistics of time to onset, but extract_tto() is useful to get the raw data and plot it, for instance with ggplot2.

Value

A data.frame with

• All available time to onsets for this combination (column tto_max).

• adr_s and drug_s, same as input.

• UMCReportId, the unique identifier of the case.

See Also

link_, desc_tto(), add_drug(), add_adr(), desc_dch(), desc_rch()

Examples

link_ <-
  link_ |>
  add_drug(
    d_code = ex_$d_groups_drecno,
    drug_data = drug_
  ) |>
  add_adr(
    a_code = ex_$a_llt,
    adr_data = adr_
  )

extract_tto(.data = link_,
         adr_s = "a_colitis",
         drug_s = "pd1")
extract_tto(.data = link_,
         adr_s = c("a_colitis", "a_pneumonitis"),
         drug_s = c("pd1", "ctla4"))

vigicaen documentation built on April 3, 2025, 8:55 p.m.