diff --git a/DESCRIPTION b/DESCRIPTION index 39d6e19..b8dd510 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,7 +4,7 @@ Version: 0.1.0.9000 Authors@R: c( person("Daniel D.", "Sjoberg", , "danield.sjoberg@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0862-2018")), - person("Amelia", "Tran", , "tran.amelia@gene.com", role = "aut", + person("Amelia H.", "Tran", , "tran.amelia@gene.com", role = "aut", comment = c(ORCID = "0000-0002-9472-0302")) ) Description: Package exports a function that creates an interactive gt or @@ -43,4 +43,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.0 diff --git a/_pkgdown.yml b/_pkgdown.yml index 2a9ea9f..2281c14 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -9,6 +9,8 @@ development: authors: Daniel D. Sjoberg: href: https://www.danieldsjoberg.com/ + Amelia H. Tran: + href: https://athenamelia.github.io/ navbar: structure: diff --git a/data/discovery.rda b/data/discovery.rda index 07cf11d..068931b 100644 Binary files a/data/discovery.rda and b/data/discovery.rda differ diff --git a/inst/admiral-lookup-book.csv b/inst/admiral-lookup-book.csv index 3a00d29..19cbdbb 100644 --- a/inst/admiral-lookup-book.csv +++ b/inst/admiral-lookup-book.csv @@ -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 @@ -236,10 +236,10 @@ ADRS,BDS,DEATH,Derive death,admiral,derive_extreme_records,https://pharmaverse.g 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 @@ -264,34 +264,34 @@ 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 diff --git a/man/admiraldiscovery-package.Rd b/man/admiraldiscovery-package.Rd index 6d76a2c..d00c877 100644 --- a/man/admiraldiscovery-package.Rd +++ b/man/admiraldiscovery-package.Rd @@ -20,7 +20,7 @@ Useful links: Authors: \itemize{ - \item Amelia Tran \email{tran.amelia@gene.com} (\href{https://orcid.org/0000-0002-9472-0302}{ORCID}) + \item Amelia H. Tran \email{tran.amelia@gene.com} (\href{https://orcid.org/0000-0002-9472-0302}{ORCID}) } } diff --git a/tests/testthat/test-discovery.R b/tests/testthat/test-discovery.R index bacf55e..4bf3a4e 100644 --- a/tests/testthat/test-discovery.R +++ b/tests/testthat/test-discovery.R @@ -40,7 +40,7 @@ test_that("discovery DATASET is consistent", { ) }) -test_that("Warn for Deprecated/Supersded Functions", { +test_that("Warn for Deprecated/Superseded Functions", { expect_output({ df_superseded <- dplyr::inner_join(