The function works with procotol- and results- related information.
It converts lists and other values that are in a data frame returned
by dbGetFieldsIntoDf into individual rows of a long data frame.
From the resulting long data frame, values of interest can be selected
using dfName2Value.
The function is particularly useful for fields with complex content,
such as node field "clinical_results" from EUCTR, for which
dbGetFieldsIntoDf returns as a multiply nested list and for
which this function then converts every observation of every (leaf)
field into a row of its own.
Arguments
- df
Data frame (or tibble) with columns including the trial identifier (
_id) and one or more variables as obtained from dbGetFieldsIntoDf
Value
A data frame (or tibble, if tibble is loaded)
with the four columns: `_id`, `identifier`, `name`, `value`
Examples
dbc <- nodbi::src_sqlite(
dbname = system.file("extdata", "demo.sqlite", package = "ctrdata"),
collection = "my_trials",
flags = RSQLite::SQLITE_RO)
dfwide <- dbGetFieldsIntoDf(
fields = "clinical_results.participant_flow",
con = dbc)
#> Querying database (1 fields)...
dfTrials2Long(df = dfwide)
#> clinical_results.participant_flow.recruitment_details
#> clinical_results.participant_flow.pre_assignment_details
#> clinical_results.participant_flow.group_list.group
#> clinical_results.participant_flow.period_list.period.title
#> clinical_results.participant_flow.period_list.period.milestone_list.milestone
#> clinical_results.participant_flow.period_list.period.drop_withdraw_reason_list.drop_withdraw_reason.title
#> clinical_results.participant_flow.period_list.period.drop_withdraw_reason_list.drop_withdraw_reason.participants_list.participants.group_id
#> clinical_results.participant_flow.period_list.period.drop_withdraw_reason_list.drop_withdraw_reason.participants_list.participants.count
#>
#> .
#> .
#>
#> Total 43 rows, 12 unique names of variables
#> # A tibble: 43 × 4
#> `_id` identifier name value
#> <chr> <chr> <chr> <chr>
#> 1 NCT02620761 1 clinical_results.participant_flow.group_list.gr… "Inf…
#> 2 NCT02620761 2 clinical_results.participant_flow.group_list.gr… "Inf…
#> 3 NCT02620761 1 clinical_results.participant_flow.group_list.gr… "P1"
#> 4 NCT02620761 2 clinical_results.participant_flow.group_list.gr… "P2"
#> 5 NCT02620761 1 clinical_results.participant_flow.group_list.gr… "Con…
#> 6 NCT02620761 2 clinical_results.participant_flow.group_list.gr… "Fen…
#> 7 NCT02620761 1.1 clinical_results.participant_flow.period_list.p… "1"
#> 8 NCT02620761 1.2 clinical_results.participant_flow.period_list.p… "0"
#> 9 NCT02620761 2.1 clinical_results.participant_flow.period_list.p… "1"
#> 10 NCT02620761 2.2 clinical_results.participant_flow.period_list.p… "0"
#> # ℹ 33 more rows