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 indffor 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)
#> To review trial concepts details, call 'help("ctrdata-trial-concepts")'
#> Querying database (26 fields)...
#> Typing fields...
#> Calculating f.trialPopulation...
trialsDf
#> # A tibble: 25 × 4
#> `_id` .trialPopulationAgeGroup .trialPopulationInclusion
#> <chr> <fct> <chr>
#> 1 12949496 P "All infants with a gestation ≥ 3…
#> 2 13281214 P "All infants aged less than 29 we…
#> 3 17473621 P "1. Infants with gestational age …
#> 4 2013-000615-24-BE P "Children aged 0 to 18 years old …
#> 5 2016-004489-24-DE P "Inclusion Criteria: A subject mu…
#> 6 2019-002663-10-ES P+A "Part A, B and C: - Genetic docum…
#> 7 2022-000099-20-DE P "- Born at 29 weeks gestational …
#> 8 2022-500244-37-00 A+E "Diagnosis of symptomatic COVID-1…
#> 9 2023-505613-24-00 P "Panel A: Is undergoing treatment…
#> 10 2023-508143-51-01 A+E "In order to be eligible to parti…
#> # ℹ 15 more rows
#> # ℹ 1 more variable: .trialPopulationExclusion <chr>