Closes #244 Used derive_vars_cat() to derive AVALCA1N and AVALCAT1, r…

…eplacing look-up table with derive_vars_merged() (#256) * feat: #244 Used derive_vars_cat() to derive AVALCA1N and AVALCAT1, replacing look-up table with derive_vars_merged() feat: #247 Used call_derivation with derive_vars_crit_flag() to generate CRITy conditions and CRITyFL flags, superseding derive_var_bcvacritxfl() * Closes #244 Used derive_vars_cat() to derive AVALCA1N and AVALCAT1, replacing look-up table with derive_vars_merged() * Closes #244 Used derive_vars_cat() to derive AVALCA1N and AVALCAT1, replacing look-up table with derive_vars_merged() * Closes 244 Updating admiralophtha documentation * Closes #244 Update header to include documentation on using derive_vars_merged() in adbcva_crtflag dataframe with derive_vars_cat() to derive AVALCA1N and AVALCAT1 in ADBCVA template * Closes #244 Used derive_vars_cat() to derive AVALCA1N and AVALCAT1, replacing look-up table with derive_vars_merged() * Closes #244 Add authorship * Closes #244 Added derive_vars_cat() used in ADBCVA template * Closes 244 Add authorship * Closes 244 Add derive_vars_cat used in ADBCVA template * Closes 244 Added email * Closes 244 Added email * #244 try adding cli to imports to fix failing checks * Closes 244 Added get_admiral_option to admiral package * Closes 244 Used `derive_vars_cat` to derive AVALCA1N and AVALCAT1, replacing look-up table with `derive_vars_merged` * Update NEWS.md Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Update vignettes/adbcva.Rmd Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Update vignettes/adbcva.Rmd Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Update vignettes/adbcva.Rmd Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Closes 244 Updated under admiralophtha 1.1.0.9007 on changes to ADBCVA template to use `admiral::derive_vars_cat()` to derive `AVALCA1N` and `AVALCAT1` * Closes 244 Updated for documentation under admiralophtha 1.1.0.9007 for use of new function `admiral::derive_vars_cat()` to derive `AVALCA1N` and `AVALCAT1` in ADBCVA template * Update NEWS.md --------- Co-authored-by: Edoardo Mancini <edoardo.mancini@roche.com> Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com>
pharmaverse · Nov 19, 2024 · 470a94c · 470a94c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,7 +15,8 @@ Authors@R: c(
     person("Rachel", "Linacre", , "rachel.linacre@roche.com", role = "aut"),
     person("Lucy", "Palmen", , "lucy.palmen@roche.com", role = "aut"),
     person("Nandini", "R Thampi", , "nandini.rajendhiran@novartis.com", role = "aut"),
-    person("Aldrich", "Salva", , "salva.aldrich@gene.com", role = "aut")
+    person("Aldrich", "Salva", , "salva.aldrich@gene.com", role = "aut"),
+    person("Steven", "Ting", , "steven.ting@cytel.com", role = "aut")    
   )
 Description: Aids the programming of Clinical Data Standards Interchange
     Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM)
@@ -34,6 +35,7 @@ Depends:
 Imports:
     admiral (>= 1.1.1),
     admiraldev (>= 1.1.0),
+    cli (>= 3.6.2),
     dplyr (>= 1.0.5),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(derive_var_afeye)
 export(derive_var_bcvacritxfl)
 export(derive_var_studyeye)
 importFrom(admiral,derive_param_computed)
+importFrom(admiral,derive_vars_cat)
 importFrom(admiral,derive_vars_merged)
 importFrom(admiral,get_admiral_option)
 importFrom(admiral,params)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,13 @@
 # admiralophtha 1.1.0.9007
 
+## Updates to Templates
+
+- Within the ADBCVA template, updated `AVALCA1N` and `AVALCAT1` derivations to use new function `admiral::derive_vars_cat()`. (#244)
+
+## Updates to Documentation
+
+- Within the ADBCVA vignette, updated `AVALCA1N` and `AVALCAT1` derivations to use new function `admiral::derive_vars_cat()`. (#244)
+
 ## Updates to Functions
 
 - The following function arguments of `derive_var_afeye()` are removed following the end of their deprecation cycle (#237):

diff --git a/R/admiralophtha-package.R b/R/admiralophtha-package.R
@@ -24,7 +24,7 @@
 #' @importFrom hms as_hms
 #' @importFrom lifecycle deprecate_warn deprecated deprecate_stop
 #' @importFrom admiral derive_vars_merged restrict_derivation params derive_param_computed
-#'             get_admiral_option
+#'             derive_vars_cat get_admiral_option
 #' @importFrom admiraldev assert_symbol assert_data_frame expect_dfs_equal assert_data_frame
 #'             assert_character_vector assert_character_scalar assert_integer_scalar
 #'             assert_numeric_vector assert_vars expr_c vars2chr

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,117 +1,51 @@
-ABLFL
 ADBCVA
+ADIOP
 ADOE
+ADQS
 ADSL
-AE
 ADVFQ
-ADXX
 ADaM
 ADaMs
-AFEYE
-ASEQ
-AVAL
-AVALC
-AVISIT
-AVISITN
+AE
+AVALCA
+AVALCAT
 BCVA
+BDS
 Biologics
 CDISC
-CRITx
-CRITxFL
 ETDRS
+FBCVA
 FOCID
 Laterality
-AVALCATx
-AVALCAxN
-CMD
-Changelog
-dataset
-datasets
-DM
+LogMAR
+ORCID
 QS
-VFQ
-Edoardo
-Farrugia
-Palmen
-Linacre
-GSK
-Hoch
-LinkedIn
-Onboarding
-README
+Recoded
+SBCVA
 SDTM
-TAs
-Template'
-USUBJIDs
-adae
-adam
-adamig
-admiraltemplate
-admiralxxx
-adsl
+Snellen
+Thampi
+VFQ
 adbcva
-anonymized
-cdisc
-dev
-github
+adoe
+advfq
+al
+basetypes
+categorisation
+crtflag
+doi
+eg
+et
 https
-onboarding
-paramcds
-pharmaverse
-repo
-studyeye
-tribble
-sc
-www
-xxLOC
-xxLAT
-laterality
-afeye
-logMAR
-LogMAR
-Nandini
-Occurence
-PARAMCD
-PCHG
-QSTESTCD
-SCTESTCD
-SDTM
-STUDYEYE
-Thampi
-USUBJID
+intraocular
 laterality
 logMAR
+masse
 pharmaverse
+programmatically
+recode
 recoded
 recoding
+scrutinise
 th
-v
-basetype
-basetypes
-BDS
-categorisation
-eg
-EXLAT
-EXLOC
-Snellen
 toolset
-lookup
-ADQS
-recode
-masse
-programmatically
-intraocular
-scrutinise
-DTYPE
-OEDTC
-OEDY
-ORCID
-VISITNUM
-NEI
-al
-doi
-et
-ADIOP
-OE
-adoe
-advfq
diff --git a/inst/templates/ad_adbcva.R b/inst/templates/ad_adbcva.R
@@ -38,66 +38,54 @@ param_lookup <- tibble::tribble(
   "VACSCORE", "BEST CORRECTED VISUAL ACUITY", "OVERALL EVALUATION", "Fellow Eye", "FBCVA", "Fellow Eye Visual Acuity Score (letters)", 2, # nolint
 )
 
-# Assign AVALCAT1
-avalcat_lookup <- tibble::tribble(
-  ~PARAMCD, ~AVALCA1N, ~AVALCAT1,
-  "SBCVA", 1000, "< 20/800",
-  "SBCVA", 800, "20/800",
-  "SBCVA", 640, "20/640",
-  "SBCVA", 500, "20/500",
-  "SBCVA", 400, "20/400",
-  "SBCVA", 320, "20/320",
-  "SBCVA", 250, "20/250",
-  "SBCVA", 200, "20/200",
-  "SBCVA", 160, "20/160",
-  "SBCVA", 125, "20/125",
-  "SBCVA", 100, "20/100",
-  "SBCVA", 80, "20/80",
-  "SBCVA", 63, "20/63",
-  "SBCVA", 50, "20/50",
-  "SBCVA", 40, "20/40",
-  "SBCVA", 32, "20/32",
-  "SBCVA", 25, "20/25",
-  "SBCVA", 20, "20/20",
-  "SBCVA", 16, "20/16",
-  "SBCVA", 12, "20/12",
-  "SBCVA", 1, "> 20/12",
+# SBCVA and FBCVA definition list
+# This can be sourced from a separate R script
+definition_bcva <- exprs(
+  ~PARAMCD, ~condition, ~AVALCA1N, ~AVALCAT1,
+  "SBCVA", AVAL >= 0 & AVAL <= 3, 1000, "< 20/800",
+  "FBCVA", AVAL >= 0 & AVAL <= 3, 1000, "< 20/800",
+  "SBCVA", AVAL >= 4 & AVAL <= 8, 800, "20/800",
+  "FBCVA", AVAL >= 4 & AVAL <= 8, 800, "20/800",
+  "SBCVA", AVAL >= 9 & AVAL <= 13, 640, "20/640",
+  "FBCVA", AVAL >= 9 & AVAL <= 13, 640, "20/640",
+  "SBCVA", AVAL >= 14 & AVAL <= 18, 500, "20/500",
+  "FBCVA", AVAL >= 14 & AVAL <= 18, 500, "20/500",
+  "SBCVA", AVAL >= 19 & AVAL <= 23, 400, "20/400",
+  "FBCVA", AVAL >= 19 & AVAL <= 23, 400, "20/400",
+  "SBCVA", AVAL >= 24 & AVAL <= 28, 320, "20/320",
+  "FBCVA", AVAL >= 24 & AVAL <= 28, 320, "20/320",
+  "SBCVA", AVAL >= 29 & AVAL <= 33, 250, "20/250",
+  "FBCVA", AVAL >= 29 & AVAL <= 33, 250, "20/250",
+  "SBCVA", AVAL >= 34 & AVAL <= 38, 200, "20/200",
+  "FBCVA", AVAL >= 34 & AVAL <= 38, 200, "20/200",
+  "SBCVA", AVAL >= 39 & AVAL <= 43, 160, "20/160",
+  "FBCVA", AVAL >= 39 & AVAL <= 43, 160, "20/160",
+  "SBCVA", AVAL >= 44 & AVAL <= 48, 125, "20/125",
+  "FBCVA", AVAL >= 44 & AVAL <= 48, 125, "20/125",
+  "SBCVA", AVAL >= 49 & AVAL <= 53, 100, "20/100",
+  "FBCVA", AVAL >= 49 & AVAL <= 53, 100, "20/100",
+  "SBCVA", AVAL >= 54 & AVAL <= 58, 80, "20/80",
+  "FBCVA", AVAL >= 54 & AVAL <= 58, 80, "20/80",
+  "SBCVA", AVAL >= 59 & AVAL <= 63, 63, "20/63",
+  "FBCVA", AVAL >= 59 & AVAL <= 63, 63, "20/63",
+  "SBCVA", AVAL >= 64 & AVAL <= 68, 50, "20/50",
+  "FBCVA", AVAL >= 64 & AVAL <= 68, 50, "20/50",
+  "SBCVA", AVAL >= 69 & AVAL <= 73, 40, "20/40",
+  "FBCVA", AVAL >= 69 & AVAL <= 73, 40, "20/40",
+  "SBCVA", AVAL >= 74 & AVAL <= 78, 32, "20/32",
+  "FBCVA", AVAL >= 74 & AVAL <= 78, 32, "20/32",
+  "SBCVA", AVAL >= 79 & AVAL <= 83, 25, "20/25",
+  "FBCVA", AVAL >= 79 & AVAL <= 83, 25, "20/25",
+  "SBCVA", AVAL >= 84 & AVAL <= 88, 20, "20/20",
+  "FBCVA", AVAL >= 84 & AVAL <= 88, 20, "20/20",
+  "SBCVA", AVAL >= 89 & AVAL <= 93, 16, "20/16",
+  "FBCVA", AVAL >= 89 & AVAL <= 93, 16, "20/16",
+  "SBCVA", AVAL >= 94 & AVAL <= 97, 12, "20/12",
+  "FBCVA", AVAL >= 94 & AVAL <= 97, 12, "20/12",
+  "SBCVA", AVAL >= 98, 1, "> 20/12",
+  "FBCVA", AVAL >= 98, 1, "> 20/12"
 )
 
-# add equivalent rows for PARAMCD = "FBCVA"
-avalcat_lookup <- avalcat_lookup %>%
-  mutate(PARAMCD = "FBCVA") %>%
-  rbind(avalcat_lookup)
-
-# ---- Utility functions ----
-
-# Format function for AVALCAT1
-format_avalcat1n <- function(param, aval) {
-  case_when(
-    param %in% c("SBCVA", "FBCVA") & aval >= 0 & aval <= 3 ~ 1000,
-    param %in% c("SBCVA", "FBCVA") & aval >= 4 & aval <= 8 ~ 800,
-    param %in% c("SBCVA", "FBCVA") & aval >= 9 & aval <= 13 ~ 640,
-    param %in% c("SBCVA", "FBCVA") & aval >= 14 & aval <= 18 ~ 500,
-    param %in% c("SBCVA", "FBCVA") & aval >= 19 & aval <= 23 ~ 400,
-    param %in% c("SBCVA", "FBCVA") & aval >= 24 & aval <= 28 ~ 320,
-    param %in% c("SBCVA", "FBCVA") & aval >= 29 & aval <= 33 ~ 250,
-    param %in% c("SBCVA", "FBCVA") & aval >= 34 & aval <= 38 ~ 200,
-    param %in% c("SBCVA", "FBCVA") & aval >= 39 & aval <= 43 ~ 160,
-    param %in% c("SBCVA", "FBCVA") & aval >= 44 & aval <= 48 ~ 125,
-    param %in% c("SBCVA", "FBCVA") & aval >= 49 & aval <= 53 ~ 100,
-    param %in% c("SBCVA", "FBCVA") & aval >= 54 & aval <= 58 ~ 80,
-    param %in% c("SBCVA", "FBCVA") & aval >= 59 & aval <= 63 ~ 63,
-    param %in% c("SBCVA", "FBCVA") & aval >= 64 & aval <= 68 ~ 50,
-    param %in% c("SBCVA", "FBCVA") & aval >= 69 & aval <= 73 ~ 40,
-    param %in% c("SBCVA", "FBCVA") & aval >= 74 & aval <= 78 ~ 32,
-    param %in% c("SBCVA", "FBCVA") & aval >= 79 & aval <= 83 ~ 25,
-    param %in% c("SBCVA", "FBCVA") & aval >= 84 & aval <= 88 ~ 20,
-    param %in% c("SBCVA", "FBCVA") & aval >= 89 & aval <= 93 ~ 16,
-    param %in% c("SBCVA", "FBCVA") & aval >= 94 & aval <= 97 ~ 12,
-    param %in% c("SBCVA", "FBCVA") & aval >= 98 ~ 1
-  )
-}
-
 # ---- Derivations ----
 
 # Get list of ADSL vars required for derivations
@@ -294,12 +282,12 @@ adbcva_crtflag <- adbcva_adsl %>%
     filter = PARAMCD %in% c("SBCVA", "FBCVA")
   ) %>%
   # Add AVALCATx variables
-  mutate(AVALCA1N = format_avalcat1n(param = PARAMCD, aval = AVAL)) %>%
-  derive_vars_merged(
-    avalcat_lookup,
-    by = exprs(PARAMCD, AVALCA1N)
+  derive_vars_cat(
+    definition = definition_bcva,
+    by_vars = exprs(PARAMCD)
   )
 
+
 # Final Steps, Select final variables and Add labels
 # This process will be based on your metadata, no example given for this reason
 # ...

diff --git a/man/admiralophtha-package.Rd b/man/admiralophtha-package.Rd