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Superseded deprecated function #36

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merged 4 commits into from
Jan 19, 2024
Merged

Superseded deprecated function #36

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e3554a4
update admiral look-up
athenamelia Jan 12, 2024
1859fd6
update admiral look-up
athenamelia Jan 12, 2024
4b3c652
update admiral lookup csv
athenamelia Jan 19, 2024
80a098c
running documentation for the one row added
athenamelia Jan 19, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -4,7 +4,7 @@ Version: 0.1.0.9000
Authors@R: c(
person("Daniel D.", "Sjoberg", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-0862-2018")),
person("Amelia", "Tran", , "[email protected]", role = "aut",
person("Amelia H.", "Tran", , "[email protected]", role = "aut",
comment = c(ORCID = "0000-0002-9472-0302"))
)
Description: Package exports a function that creates an interactive gt or
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2 changes: 2 additions & 0 deletions _pkgdown.yml
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Expand Up @@ -9,6 +9,8 @@ development:
authors:
Daniel D. Sjoberg:
href: https://www.danieldsjoberg.com/
Amelia H. Tran:
href: https://athenamelia.github.io/

navbar:
structure:
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Binary file modified data/discovery.rda
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31 changes: 15 additions & 16 deletions inst/admiral-lookup-book.csv
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Expand Up @@ -197,7 +197,7 @@ ADSL,ADSL,RANDDT,Derive randomization date,admiral,derive_vars_merged,https://ph
ADSL,ADSL,DTHDT,Derive death date,admiral,derive_vars_dt,https://pharmaverse.github.io/admiral/reference/derive_vars_dt.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,DTHADY,Derive relative day of death,admiral,derive_vars_duration,https://pharmaverse.github.io/admiral/reference/derive_vars_duration.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,LDDTHELD,Derive elapsed days from last dose to death,admiral,derive_vars_duration,https://pharmaverse.github.io/admiral/reference/derive_vars_duration.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,LSTALVDT,Derive the last date known alive ,admiral,derive_var_extreme_dt,https://pharmaverse.github.io/admiral/reference/derive_var_extreme_dt.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,LSTALVDT,Derive the last date known alive ,admiral,derive_vars_extreme_event,https://pharmaverse.github.io/admiral/reference/derive_vars_extreme_event.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,SAFFL,Derives population flag,admiral,derive_var_merged_exist_flag,https://pharmaverse.github.io/admiral/reference/derive_var_merged_exist_flag.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adsl.R
ADVS,BDS,TRTSDT,Derive treatment start date ,admiral,derive_vars_merged,https://pharmaverse.github.io/admiral/reference/derive_vars_merged.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_advs.R
ADVS,BDS,TRTEDT,Derive treatment end date,admiral,derive_vars_merged,https://pharmaverse.github.io/admiral/reference/derive_vars_merged.html,Template Example,https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_advs.R
Expand Down Expand Up @@ -233,13 +233,12 @@ ADRS,BDS,CCB,Derive confirmed clinical benefit by investigator,admiral,derive_ex
ADRS,BDS,CBOR,Derive best confirmed response by investigator,admiral,derive_extreme_event,https://pharmaverse.github.io/admiral/reference/derive_extreme_event.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs.R
ADRS,BDS,CBCP,Derive best confirmed overall response of CR/PR by investigator,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs.R
ADRS,BDS,DEATH,Derive death,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs.R
ADRS,BDS,LSTA,Derive last disease assessment by investigator,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs.R
ADRS,BDS,MDIS,Derive measurable disease at baseline by investigator,admiral,derive_param_exist_flag,https://pharmaverse.github.io/admiral/reference/derive_param_exist_flag.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs.R
ADRS,BDS,PD,Derive disease progression by investigator,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs_basic.R
ADRS,BDS,RSP,Adds a parameter indicating if a subject had a response before progressive disease,admiralonco,derive_param_response,https://pharmaverse.github.io/admiralonco/reference/derive_param_response.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs_basic.R
ADRS,BDS,RSP,Adds a parameter indicating if a subject had a response before progressive disease,admiral,derive_extreme_event,https://pharmaverse.github.io/admiral/reference/derive_extreme_event.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adrs_basic.R
ADTR,BDS,TULOC,Derive location of tumor,admiral,derive_vars_merged,https://pharmaverse.github.io/admiral/reference/derive_vars_merged.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
ADTR,BDS,ADT,Derive analysis date ,admiral,derive_vars_dt,https://pharmaverse.github.io/admiral/reference/derive_vars_dt.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
ADTR,BDS,SDIAM,Derive target lesions sum of diameters by investigator,admiral,get_summary_records,https://pharmaverse.github.io/admiral/reference/get_summary_records.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
ADTR,BDS,SDIAM,Derive target lesions sum of diameters by investigator,admiral,derive_summary_records,https://pharmaverse.github.io/admiral/reference/derive_summary_records.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
ADTR,BDS,LSEXP,Derive lesion ID expected from flag,admiral,derive_var_merged_summary,https://pharmaverse.github.io/admiral/reference/derive_var_merged_summary.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
ADTR,BDS,LSASS,Derive lesion ID assessed from flag ,admiral,derive_var_merged_summary,https://pharmaverse.github.io/admiral/reference/derive_var_merged_summary.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
ADTR,BDS,ADY,Derive analysis relative day,admiral,derive_var_merged_summary,https://pharmaverse.github.io/admiral/reference/derive_var_merged_summary.html,Template Example,https://github.com/pharmaverse/admiralonco/blob/main/inst/templates/ad_adtr.R
Expand All @@ -264,34 +263,34 @@ ADFACE,ADSL,ADTM,Derive a datetime object from a date character ,admiral,derive_
ADFACE,ADSL,ADY,Derive relative day variable,admiral,derive_vars_dy,https://pharmaverse.github.io/admiral/reference/derive_vars_dy.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,APERSDT,Derive period start date,admiral,create_period_dataset,https://pharmaverse.github.io/admiral/reference/create_period_dataset.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,APEREDT,Derive period end date,admiral,create_period_dataset,https://pharmaverse.github.io/admiral/reference/create_period_dataset.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,SEV,"Derive severity records from diameter for redness, swelling, etc",admiralvaccine,derive_diam_to_sev_records,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_diam_to_sev_records.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,SEV,"Derive severity records from diameter for redness, swelling, etc",admiralvaccine,derive_diam_to_sev_records,https://pharmaverse.github.io/admiralvaccine/reference/derive_diam_to_sev_records.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,MAXSEV,Deriving maximum severity for local and systemic events,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,MAXDIAM,Deriving maximum diameter for administrative site reactions,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,MAXTEMP,Deriving maximum temperature,admiral,derive_extreme_records,https://pharmaverse.github.io/admiral/reference/derive_extreme_records.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,ANL01FL,Derive flags for the maximum record per subject per event per vaccination,admiralvaccine,derive_vars_max_flag,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_max_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,ANL02FL,Derive flags for the maximum record per subject per event for overall,admiralvaccine,derive_vars_max_flag,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_max_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,EVENTFL,Derive flags the record if at least one of the event occurred within the observation period,admiralvaccine,derive_vars_event_flag,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_max_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,EVENTDFL,Derive flags the record if the event is occurred,admiralvaccine,derive_vars_event_flag,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_max_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,ANL01FL,Derive flags for the maximum record per subject per event per vaccination,admiralvaccine,derive_vars_max_flag,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_max_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,ANL02FL,Derive flags for the maximum record per subject per event for overall,admiralvaccine,derive_vars_max_flag,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_max_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,EVENTFL,Derive flags the record if at least one of the event occurred within the observation period,admiralvaccine,derive_vars_event_flag,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_event_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADFACE,ADSL,EVENTDFL,Derive flags the record if the event is occurred,admiralvaccine,derive_vars_event_flag,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_event_flag.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adface.R
ADIS,BDS,ADT,Derive analysis date ,admiral,derive_vars_dt,https://pharmaverse.github.io/admiral/reference/derive_vars_dt.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,ADY,Derive relative day variable,admiral,derive_vars_dy,https://pharmaverse.github.io/admiral/reference/derive_vars_dy.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,PARAM,Derive a list of parameter ,admiral,derive_vars_merged_lookup,https://pharmaverse.github.io/admiral/reference/derive_vars_merged_lookup.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,ORIG,Derive original AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,LOG10,Derive log 10 of AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,4FOLD,Derive 4 fold AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,LOG10 4FOLD,Derive log 10 of 4 fold AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,ORIG,Derive original AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,LOG10,Derive log 10 of AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,4FOLD,Derive 4 fold AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,LOG10 4FOLD,Derive log 10 of 4 fold AVAL variable for Laboratory Immunology Data ADaM domain ,admiralvaccine,derive_var_aval_adis,https://pharmaverse.github.io/admiralvaccine/reference/derive_var_aval_adis.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,SERCAT1N,Derive SERCAT1N variable,admiral,derive_vars_merged_lookup,https://pharmaverse.github.io/admiral/reference/derive_vars_merged_lookup.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,BASE,Calculate BASE,admiral,derive_var_base,https://pharmaverse.github.io/admiral/reference/derive_var_base.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,ABLFL,Derive analysis baseline flag,admiral,restrict_derivation,https://pharmaverse.github.io/admiral/reference/restrict_derivation.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,CHG,Derive change from baseline,admiral,restrict_derivation,https://pharmaverse.github.io/admiral/reference/restrict_derivation.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,R2BASE,Derive ratio to baseline,admiral,restrict_derivation,https://pharmaverse.github.io/admiral/reference/restrict_derivation.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,CRIT1FL,Derive criterion 1 evaluation result flag as character,admiralvaccine,derive_vars_crit,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_crit.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,CRIT1FN,Derive criterion 1 evaluation result flag as numeric,admiralvaccine,derive_vars_crit,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_crit.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,CRIT1FL,Derive criterion 1 evaluation result flag as character,admiralvaccine,derive_vars_crit,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_crit.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,CRIT1FN,Derive criterion 1 evaluation result flag as numeric,admiralvaccine,derive_vars_crit,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_crit.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,APERSDT,Derive period start date,admiral,create_period_dataset,https://pharmaverse.github.io/admiral/reference/create_period_dataset.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,TRTA,Derive treatment analysis ,admiral,create_period_dataset,https://pharmaverse.github.io/admiral/reference/create_period_dataset.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADIS,BDS,TRTP,Derive period start date,admiral,create_period_dataset,https://pharmaverse.github.io/admiral/reference/create_period_dataset.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adis.R
ADSL,ADSL,TRT01A,Derive actual treatment for period 1 ,admiral,derive_vars_merged,https://pharmaverse.github.io/admiral/reference/derive_vars_merged.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,TRT02A,Derive actual treatment for period 2,admiral,derive_vars_merged,https://pharmaverse.github.io/admiral/reference/derive_vars_merged.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,VAX01DT,"Derive vaccination date from from EX domain, i.e. variable EXSTDTC domain",admiralvaccine,derive_vars_vaxdt,https://pharmaverse.github.io/admiralvaccine/main/reference/derive_vars_vaxdt.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adsl.R
ADSL,ADSL,VAX01DT,"Derive vaccination date from from EX domain, i.e. variable EXSTDTC domain",admiralvaccine,derive_vars_vaxdt,https://pharmaverse.github.io/admiralvaccine/reference/derive_vars_vaxdt.html,Template Example,https://github.com/pharmaverse/admiralvaccine/blob/main/inst/templates/ad_adsl.R
ADBCVA,OCCDS,PARAM,Derive a list of parameter ,admiral,derive_vars_merged,https://pharmaverse.github.io/admiral/reference/derive_vars_merged.html,Template Example,https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adbcva.R
ADBCVA,OCCDS,SBCVALOG,Derive study eye visual acuity log MAR Score,admiral,derive_param_computed,https://pharmaverse.github.io/admiral/reference/derive_param_computed.html,Template Example,https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adbcva.R
ADBCVA,OCCDS,FBCVALOG,Derive fellow eye visual acuity log MAR Score,admiral,derive_param_computed,https://pharmaverse.github.io/admiral/reference/derive_param_computed.html,Template Example,https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adbcva.R
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2 changes: 1 addition & 1 deletion tests/testthat/test-discovery.R
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Expand Up @@ -40,7 +40,7 @@ test_that("discovery DATASET is consistent", {
)
})

test_that("Warn for Deprecated/Supersded Functions", {
test_that("Warn for Deprecated/Superseded Functions", {
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expect_output({
df_superseded <-
dplyr::inner_join(
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