From b172b887e95e48d6792e4f0018053d53fb8cdebc Mon Sep 17 00:00:00 2001
From: Amelia Tran <tran26h@mtholyoke.edu>
Date: Fri, 19 Jan 2024 15:30:40 -0800
Subject: [PATCH] Superseded deprecated function (#36)

* update admiral look-up

* update admiral look-up

* update admiral lookup csv

* running documentation for the one row added
---
 DESCRIPTION                     |   4 ++--
 _pkgdown.yml                    |   2 ++
 data/discovery.rda              | Bin 6248 -> 6209 bytes
 inst/admiral-lookup-book.csv    |  30 +++++++++++++++---------------
 man/admiraldiscovery-package.Rd |   2 +-
 tests/testthat/test-discovery.R |   2 +-
 6 files changed, 21 insertions(+), 19 deletions(-)

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 07cf11dfb80ec6ef8b53d10d7991a905f15ef8f0..068931baa50ed2d7bc193d157dc5a2372bde0b65 100644
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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(