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Perform time-to-onset analysis for drug-event associations

Source: R/time_to_onset_analysis.R
time_to_onset_analysis.Rd

This function conducts a time-to-onset analysis for associations between drugs and events based on user-specified parameters.

Usage

time_to_onset_analysis(
  drug_selected,
  reac_selected,
  temp_drug = Drug,
  temp_reac = Reac,
  temp_ther = Ther,
  meddra_level = "pt",
  drug_level = "substance",
  restriction = "none",
  minimum_cases = 3,
  max_TTO = 365,
  test = "AD"
)

Arguments

drug_selected

A list of drugs for analysis. Can be a list of lists (to collapse terms together) if drug_level is set to custom.

reac_selected

A list of adverse events for analysis. Can be a list of lists (to collapse terms together) if meddra_level is set to custom.

temp_drug

Data table containing drug data (default is Drug). If set to Drug[role_cod %in% c("PS","SS")] allows to investigate only suspects.

temp_reac

Data table containing reaction data (default is Reac).

temp_ther

Data table containing therapy and temporal data (default is Ther).

meddra_level

The desired MedDRA level for analysis (default is "pt"). If set to "custom" allows a list of lists for reac_selected (collapsing multiple terms).

drug_level

The desired drug level for analysis (default is "substance"). If set to "custom" allows a list of lists for reac_selected (collapsing multiple terms).

restriction

Primary IDs to consider for analysis (default is "none", which includes the entire population). If set to Demo[!RB_duplicates_only_susp]$primaryid, for example, allows to exclude duplicates according to one of the deduplication algorithms.

minimum_cases

The minimum number of cases required for the analysis (default is 3).

max_TTO

The maximum time to onset considered in the analysis, in days (default is 365).

test

The two-sample goodness of fit test to apply for TTO analysis. Choices are AD (Anderson-Darling test - default) and KS (Kolmogorov-Smirnov test).

Value

A data.table containing results of the time-to-onset analysis, including drug-event associations, KS test statistics, and p-values.

References

Van Holle, L., Zeinoun, Z., Bauchau, V. and Verstraeten, T. (2012), Using time-to-onset for detecting safety signals in spontaneous reports of adverse events following immunization: a proof of concept study. Pharmacoepidemiol Drug Saf, 21: 603-610. https://doi.org/10.1002/pds.3226

Scholl JHG, van Hunsel FPAM, Hak E, van Puijenbroek EP. Time to onset in statistical signal detection revisited: A follow-up study in long-term onset adverse drug reactions. Pharmacoepidemiology and Drug Safety. 2019;28:1283–9.

See also

ks.test for information about the Kolmogorov-Smirnov test.

Examples

# This is just an example of how to use the function,
# as sample_Data has only little information about time to onset.
df <- time_to_onset_analysis(
  drug_selected = "skin care",
  reac_selected = list("skin affection" = list(
    "dry skin",
    "skin burning sensation",
    "skin irritation",
    "erythema",
    "rash macular",
    "acne",
    "skin haemorrhage"
  )),
  temp_drug = sample_Drug, temp_reac = sample_Reac,
  temp_ther = sample_Ther
)