Calculate in- and exclusion criteria and age groups
Source:R/f_trialPopulation.R
f.trialPopulation.RdTrial concept calculated: inclusion and exclusion criteria as well as age groups that can participate in a trial, based on protocol-related information. Since CTGOV uses single text field for eligibility criteria, text extraction is used to separate in- and exclusion criteria. (See dfMergeVariablesRelevel with an example for healthy volunteers.)
Arguments
- df
data frame such as from dbGetFieldsIntoDf. If `NULL`, prints fields needed in `df` for calculating this trial concept, which can be used with dbGetFieldsIntoDf.
Value
data frame with columns `_id` and new columns: `.trialPopulationAgeGroup` (factor, "P", "A", "P+A", "E", "A+E", "P+A+E"), `.trialPopulationInclusion` (string), `.trialPopulationExclusion` (string).
Examples
# fields needed
f.trialPopulation()
#> $euctr
#> [1] "e3_principal_inclusion_criteria"
#> [2] "e4_principal_exclusion_criteria"
#> [3] "f111_in_utero"
#> [4] "f112_preterm_newborn_infants_up_to_gestational_age__37_weeks"
#> [5] "f113_newborns_027_days"
#> [6] "f114_infants_and_toddlers_28_days23_months"
#> [7] "f115_children_211years"
#> [8] "f116_adolescents_1217_years"
#> [9] "f11_trial_has_subjects_under_18"
#> [10] "f12_adults_1864_years"
#> [11] "f13_elderly_65_years"
#>
#> $ctgov
#> [1] "eligibility.criteria.textblock" "eligibility.maximum_age"
#> [3] "eligibility.minimum_age"
#>
#> $ctgov2
#> [1] "protocolSection.eligibilityModule.maximumAge"
#> [2] "protocolSection.eligibilityModule.minimumAge"
#> [3] "protocolSection.eligibilityModule.eligibilityCriteria"
#> [4] "protocolSection.eligibilityModule.stdAges"
#>
#> $isrctn
#> [1] "participants.ageRange" "participants.inclusion" "participants.exclusion"
#>
#> $ctis
#> [1] "ageGroup"
#> [2] "authorizedPartI.trialDetails.trialInformation.eligibilityCriteria.principalInclusionCriteria.principalInclusionCriteria"
#> [3] "authorizedPartI.trialDetails.trialInformation.eligibilityCriteria.principalExclusionCriteria.principalExclusionCriteria"
#> [4] "authorizedApplication.authorizedPartI.trialDetails.trialInformation.eligibilityCriteria.principalInclusionCriteria.principalInclusionCriteria"
#> [5] "authorizedApplication.authorizedPartI.trialDetails.trialInformation.eligibilityCriteria.principalExclusionCriteria.principalExclusionCriteria"
#>
# apply trial concept when creating data frame
dbc <- nodbi::src_sqlite(
dbname = system.file("extdata", "demo.sqlite", package = "ctrdata"),
collection = "my_trials", flags = RSQLite::SQLITE_RO)
trialsDf <- dbGetFieldsIntoDf(
calculate = "f.trialPopulation",
con = dbc)
#> Querying database (26 fields)...
trialsDf
#> # A tibble: 31 × 4
#> `_id` .trialPopulationAgeG…¹ .trialPopulationIncl…² .trialPopulationExcl…³
#> <chr> <fct> <chr> <chr>
#> 1 12949496 P All infants with a ge… 1. Lethal congenital …
#> 2 13281214 P All infants aged less… 1. Lack of consent or…
#> 3 17473621 P 1. Infants with gesta… 1. Genetic, metabolic…
#> 4 2012-00… P+A 1. Primary HLH patien… 1. Diagnosis of secon…
#> 5 2012-00… P+A 1. Primary HLH patien… 1. Diagnosis of secon…
#> 6 2014-00… P 1. Children 3 months … 1. Anticoagulant trea…
#> 7 2014-00… P Each subject must mee… Subjects who meet any…
#> 8 2014-00… P Each subject must mee… Subjects who meet any…
#> 9 2022-50… A+E Diagnosis of symptoma… Patients with an indi…
#> 10 2022-50… A Age > 18 years old / … Unable to understand …
#> # ℹ 21 more rows
#> # ℹ abbreviated names: ¹.trialPopulationAgeGroup, ².trialPopulationInclusion,
#> # ³.trialPopulationExclusion