Closes #226 updated subject keys across package (#239)

* #226 updated subject keys across package * #226 chore: lint * #226 more lints
pharmaverse · Jun 11, 2024 · 50e4149 · 50e4149
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diff --git a/NEWS.md b/NEWS.md
@@ -7,6 +7,12 @@
   * The argument `dataset_occ`
   * The argument `lat_vals`
 
+## Various
+
+- All vignettes and templates in `{admiralophtha}` have been updated to use the `{admiral}` subject keys option rather than
+  explicitly quoting key variables such as `STUYDID` and `USUBJID`. For instance, a line such as `by_vars = exprs(STUDYID, USUBJID)`
+  would be replaced by `by_vars = get_admiral_option("subject_keys")` (#226).
+
 # admiralophtha 1.0.0
 
 ## Updates to Templates

diff --git a/R/derive_var_bcvacritxfl.R b/R/derive_var_bcvacritxfl.R
@@ -161,7 +161,7 @@ derive_var_bcvacritxfl <- function(dataset,
                                    critxfl_index = NULL) {
   # Input checks
   assert_vars(crit_var)
-  assert_data_frame(dataset, required_vars = c(exprs(STUDYID, USUBJID), crit_var))
+  assert_data_frame(dataset, required_vars = crit_var)
   assert_character_scalar(additional_text)
   assert_integer_scalar(critxfl_index, optional = TRUE)
   if (!is.null(bcva_ranges)) lapply(bcva_ranges, assert_numeric_vector)

diff --git a/R/derive_var_studyeye.R b/R/derive_var_studyeye.R
@@ -42,8 +42,8 @@
 #'
 #' derive_var_studyeye(adsl, sc)
 derive_var_studyeye <- function(dataset_adsl, dataset_sc, sctestcd_value = "FOCID") {
-  assert_data_frame(dataset_sc, required_vars = exprs(STUDYID, USUBJID, SCTESTCD, SCSTRESC))
-  assert_data_frame(dataset_adsl, required_vars = exprs(STUDYID, USUBJID))
+  assert_data_frame(dataset_sc, required_vars = exprs(SCTESTCD, SCSTRESC))
+  assert_data_frame(dataset_adsl)
 
   seye_cat <- function(seye) {
     case_when(

diff --git a/inst/templates/ad_adbcva.R b/inst/templates/ad_adbcva.R
@@ -112,7 +112,7 @@ adbcva_adslvar <- oe %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 adbcva_aval <- adbcva_adslvar %>%
@@ -137,7 +137,10 @@ adbcva_nlogparam <- adbcva_aval %>%
 adbcva_logparam <- adbcva_nlogparam %>%
   # Add derived log parameters
   derive_param_computed(
-    by_vars = c(exprs(STUDYID, USUBJID, VISIT, VISITNUM, OEDY, OEDTC, AFEYE), adsl_vars),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(VISIT, VISITNUM, OEDY, OEDTC, AFEYE, !!!adsl_vars)
+    ),
     parameters = c("SBCVA"),
     set_values_to = exprs(
       AVAL = convert_etdrs_to_logmar(AVAL.SBCVA),
@@ -148,7 +151,10 @@ adbcva_logparam <- adbcva_nlogparam %>%
     )
   ) %>%
   derive_param_computed(
-    by_vars = c(exprs(STUDYID, USUBJID, VISIT, OEDY, OEDTC, AFEYE), adsl_vars),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(VISIT, VISITNUM, OEDY, OEDTC, AFEYE, !!!adsl_vars)
+    ),
     parameters = c("FBCVA"),
     set_values_to = exprs(
       AVAL = convert_etdrs_to_logmar(AVAL.FBCVA),
@@ -195,7 +201,7 @@ adbcva_trtflag <- adbcva_visit %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ABLFL,
-      by_vars = exprs(STUDYID, USUBJID, BASETYPE, PARAMCD),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(BASETYPE, PARAMCD)),
       order = exprs(ADT, VISITNUM, OESEQ),
       mode = "last"
     ),
@@ -209,7 +215,7 @@ adbcva_vstflag <- adbcva_trtflag %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ANL01FL,
-      by_vars = exprs(USUBJID, PARAMCD, AVISIT, DTYPE),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, AVISIT, DTYPE)),
       order = exprs(ADT, AVAL),
       mode = "last"
     ),
@@ -220,7 +226,7 @@ adbcva_vstflag <- adbcva_trtflag %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ANL02FL,
-      by_vars = exprs(USUBJID, PARAMCD, ABLFL),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, ABLFL)),
       order = exprs(ADT),
       mode = "last"
     ),
@@ -231,7 +237,7 @@ adbcva_vstflag <- adbcva_trtflag %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
-      by_vars = exprs(USUBJID, PARAMCD),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD)),
       order = exprs(AVAL, ADT),
       new_var = WORS01FL,
       mode = "first"
@@ -243,13 +249,13 @@ adbcva_vstflag <- adbcva_trtflag %>%
 adbcva_change <- adbcva_vstflag %>%
   # Calculate BASE
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, BASETYPE),
+    by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, BASETYPE)),
     source_var = AVAL,
     new_var = BASE
   ) %>%
   # Calculate BASEC
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, BASETYPE),
+    by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, BASETYPE)),
     source_var = AVALC,
     new_var = BASEC
   ) %>%
@@ -262,7 +268,7 @@ adbcva_change <- adbcva_vstflag %>%
 adbcva_aseq <- adbcva_change %>%
   derive_var_obs_number(
     new_var = ASEQ,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(PARAMCD, ADT, AVISITN, VISITNUM, ATPTN),
     check_type = "error"
   )
@@ -271,7 +277,7 @@ adbcva_aseq <- adbcva_change %>%
 adbcva_adsl <- adbcva_aseq %>%
   derive_vars_merged(
     dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 adbcva_crtflag <- adbcva_adsl %>%

diff --git a/inst/templates/ad_adoe.R b/inst/templates/ad_adoe.R
@@ -54,7 +54,7 @@ adoe_adslvar <- oe %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 adoe_aval <- adoe_adslvar %>%
@@ -111,7 +111,7 @@ adoe_trtflag <- adoe_visit %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ABLFL,
-      by_vars = exprs(STUDYID, USUBJID, BASETYPE, PARAMCD),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(BASETYPE, PARAMCD)),
       order = exprs(ADT, VISITNUM, OESEQ),
       mode = "last"
     ),
@@ -125,7 +125,7 @@ adoe_vstflag <- adoe_trtflag %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ANL01FL,
-      by_vars = exprs(USUBJID, PARAMCD, AVISIT, DTYPE),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, AVISIT, DTYPE)),
       order = exprs(ADT, AVAL),
       mode = "last"
     ),
@@ -136,7 +136,7 @@ adoe_vstflag <- adoe_trtflag %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ANL02FL,
-      by_vars = exprs(USUBJID, PARAMCD, ABLFL),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, ABLFL)),
       order = exprs(ADT),
       mode = "last"
     ),
@@ -147,7 +147,7 @@ adoe_vstflag <- adoe_trtflag %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
-      by_vars = exprs(USUBJID, PARAMCD),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD)),
       order = exprs(AVAL, ADT),
       new_var = WORS01FL,
       mode = "last"
@@ -159,13 +159,13 @@ adoe_vstflag <- adoe_trtflag %>%
 adoe_change <- adoe_vstflag %>%
   # Calculate BASE
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, BASETYPE),
+    by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, BASETYPE)),
     source_var = AVAL,
     new_var = BASE
   ) %>%
   # Calculate BASEC
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, BASETYPE),
+    by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, BASETYPE)),
     source_var = AVALC,
     new_var = BASEC
   ) %>%
@@ -178,7 +178,7 @@ adoe_change <- adoe_vstflag %>%
 adoe_aseq <- adoe_change %>%
   derive_var_obs_number(
     new_var = ASEQ,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(PARAMCD, ADT, AVISITN, VISITNUM, ATPTN),
     check_type = "error"
   )
@@ -187,7 +187,7 @@ adoe_aseq <- adoe_change %>%
 adoe_adsl <- adoe_aseq %>%
   derive_vars_merged(
     dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 # Final Steps, Select final variables and Add labels

diff --git a/inst/templates/ad_advfq.R b/inst/templates/ad_advfq.R
@@ -43,7 +43,7 @@ advfq_dtdy <- derive_vars_merged(
   ungroup(qs),
   dataset_add = adsl,
   new_vars = adsl_vars,
-  by_vars = exprs(STUDYID, USUBJID)
+  by_vars = get_admiral_option("subject_keys")
 ) %>%
   ## Calculate ADT, ADY ----
   derive_vars_dt(
@@ -76,7 +76,10 @@ advfq_aval <- advfq_dtdy %>%
 advfq_qr01 <- advfq_aval %>%
   derive_summary_records(
     dataset_add = advfq_aval,
-    by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, PARAMCD, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(!!!adsl_vars, PARAMCD, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = QSTESTCD == "VFQ1" & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = identity(AVAL),
@@ -104,7 +107,10 @@ advfq_qr01 <- advfq_aval %>%
 advfq_qr02 <- advfq_qr01 %>%
   derive_summary_records(
     dataset_add = advfq_qr01,
-    by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, PARAMCD, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(!!!adsl_vars, PARAMCD, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = QSTESTCD == "VFQ2" & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = identity(AVAL),
@@ -132,7 +138,10 @@ advfq_qr02 <- advfq_qr01 %>%
 advfq_qr03 <- advfq_qr02 %>%
   derive_summary_records(
     dataset_add = advfq_qr02,
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(PARAMCD, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = QSTESTCD == "VFQ3" & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = identity(AVAL),
@@ -160,7 +169,10 @@ advfq_qr03 <- advfq_qr02 %>%
 advfq_qr04 <- advfq_qr03 %>%
   derive_summary_records(
     dataset_add = advfq_qr03,
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(PARAMCD, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = QSTESTCD == "VFQ4" & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = identity(AVAL),
@@ -184,7 +196,10 @@ advfq_qr04 <- advfq_qr03 %>%
 advfq_qsg01 <- advfq_qr04 %>%
   derive_summary_records(
     dataset_add = advfq_qr04,
-    by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(!!!adsl_vars, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = PARAMCD %in% c("QR01", "QR02") & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = mean(AVAL),
@@ -198,7 +213,10 @@ advfq_qsg01 <- advfq_qr04 %>%
 advfq_qsg02 <- advfq_qsg01 %>%
   derive_summary_records(
     dataset_add = advfq_qsg01,
-    by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(!!!adsl_vars, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = PARAMCD %in% c("QR03", "QR04") & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = mean(AVAL),
@@ -213,7 +231,10 @@ advfq_qsg02 <- advfq_qsg01 %>%
 advfq_qbcs <- advfq_qsg02 %>%
   derive_summary_records(
     dataset_add = advfq_qsg02,
-    by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(!!!adsl_vars, VISITNUM, VISIT, ADT, ADY)
+    ),
     filter_add = PARAMCD %in% c("QSG01", "QSG02") & !is.na(AVAL),
     set_values_to = exprs(
       AVAL = sum(AVAL),
@@ -259,7 +280,7 @@ advfq_blfl <- advfq_ontrt %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
-      by_vars = exprs(STUDYID, USUBJID, PARAMCD),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD)),
       order = exprs(ADT, VISITNUM, QSSEQ),
       new_var = ABLFL,
       mode = "last"
@@ -271,7 +292,7 @@ advfq_blfl <- advfq_ontrt %>%
 advfq_change <- advfq_blfl %>%
   # Calculate BASE
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD),
+    by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD)),
     source_var = AVAL,
     new_var = BASE
   ) %>%
@@ -287,7 +308,7 @@ advfq_anlflag <- advfq_change %>%
     derivation = derive_var_extreme_flag,
     args = params(
       new_var = ANL01FL,
-      by_vars = exprs(USUBJID, PARAMCD, AVISIT),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(PARAMCD, AVISIT)),
       order = exprs(ADT, AVAL),
       mode = "last"
     ),
@@ -299,7 +320,7 @@ advfq_aseq <- advfq_anlflag %>%
   # Calculate ASEQ
   derive_var_obs_number(
     new_var = ASEQ,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(PARAMCD, ADT, AVISITN, VISITNUM),
     check_type = "error"
   ) %>%
@@ -311,7 +332,7 @@ advfq_aseq <- advfq_anlflag %>%
 advfq_adsl <- advfq_aseq %>%
   derive_vars_merged(
     dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 # Final Steps, Select final variables and Add labels

diff --git a/vignettes/adbcva.Rmd b/vignettes/adbcva.Rmd
@@ -88,7 +88,7 @@ adbcva <- oe %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 ```
 
@@ -123,7 +123,10 @@ Often ADBCVA datasets contain derived records for BCVA in LogMAR units. This can
 ```{r}
 adbcva <- adbcva %>%
   derive_param_computed(
-    by_vars = c(exprs(STUDYID, USUBJID, VISIT, VISITNUM, OEDY, OEDTC, AFEYE), adsl_vars),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(VISIT, VISITNUM, OEDY, OEDTC, AFEYE, !!!adsl_vars)
+    ),
     parameters = c("SBCVA"),
     set_values_to = exprs(
       AVAL = convert_etdrs_to_logmar(AVAL.SBCVA),
@@ -134,7 +137,10 @@ adbcva <- adbcva %>%
     )
   ) %>%
   derive_param_computed(
-    by_vars = c(exprs(STUDYID, USUBJID, VISIT, OEDY, OEDTC, AFEYE), adsl_vars),
+    by_vars = c(
+      get_admiral_option("subject_keys"),
+      exprs(VISIT, VISITNUM, OEDY, OEDTC, AFEYE, !!!adsl_vars)
+    ),
     parameters = c("FBCVA"),
     set_values_to = exprs(
       AVAL = convert_etdrs_to_logmar(AVAL.FBCVA),

diff --git a/vignettes/adoe.Rmd b/vignettes/adoe.Rmd
@@ -90,7 +90,7 @@ adoe <- oe %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 ```