Merge pull request #285 from pharmaverse/281_subject_keys

closes #281 closes #284 subject keys and slack link
pharmaverse · Jun 18, 2024 · 6d4afe3 · 6d4afe3
2 parents 430574f + d696dcf
commit 6d4afe3
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# admiralonco (development version)
+
+## Updates of Existing Functions
+
+- Replaced hard coding of `expr(USUBJID, STUDYID)` and `expr(USUBJID)` with `get_admiral_option("subject_keys")` so the argument is flexible and can be changed from the default by the user. (#281)
+
 # admiralonco 1.0.0
 
 ## Updates of Existing Functions

diff --git a/README.md b/README.md
@@ -84,7 +84,7 @@ Here’s a summary of our strategy for this package related to R versions:
 We use the following for support and communications between user and
 developer community:
 
--   [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) - for
+-   [Slack](https://pharmaverse.slack.com/) - for
     informal discussions, Q&A and building our user community. If you
     don’t have access, use this
     [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A)

diff --git a/inst/templates/ad_adrs.R b/inst/templates/ad_adrs.R
@@ -39,7 +39,7 @@ adrs <- rs %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 # Company-specific pre-processing ----
@@ -93,15 +93,15 @@ adrs <- adrs %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
-      by_vars = exprs(STUDYID, USUBJID, ADT),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(ADT)),
       order = exprs(worst_resp(AVALC), RSSEQ),
       new_var = ANL01FL,
       mode = "last"
     ),
     filter = !is.na(AVAL) & ADT >= RANDDT
   ) %>%
   derive_var_relative_flag(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(ADT, RSSEQ),
     new_var = ANL02FL,
     condition = AVALC == "PD",
@@ -143,7 +143,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "OVR" & AVALC == "PD" & ANL01FL == "Y",
     order = exprs(ADT, RSSEQ),
     mode = "first",
@@ -163,7 +163,7 @@ adrs <- adrs %>%
 ## Response ----
 adrs <- adrs %>%
   derive_extreme_event(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(event_nr, ADT),
     tmp_event_nr_var = event_nr,
     mode = "first",
@@ -186,7 +186,7 @@ adrs <- adrs %>%
 ## Clinical benefit ----
 adrs <- adrs %>%
   derive_extreme_event(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(desc(AVALC), ADT, event_nr),
     tmp_event_nr_var = event_nr,
     mode = "first",
@@ -214,7 +214,7 @@ adrs <- adrs %>%
 # response for this subject.
 adrs <- adrs %>%
   derive_extreme_event(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(event_nr, ADT),
     tmp_event_nr_var = event_nr,
     mode = "first",
@@ -239,7 +239,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "BOR" & AVALC %in% c("CR", "PR"),
     exist_flag = AVALC,
     false_value = "N",
@@ -257,7 +257,7 @@ adrs <- adrs %>%
 ## Confirmed response versions of the above parameters ----
 adrs <- adrs %>%
   derive_extreme_event(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(desc(AVALC), ADT, event_nr),
     tmp_event_nr_var = event_nr,
     mode = "first",
@@ -279,7 +279,7 @@ adrs <- adrs %>%
 
 adrs <- adrs %>%
   derive_extreme_event(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(desc(AVALC), ADT, event_nr),
     tmp_event_nr_var = event_nr,
     mode = "first",
@@ -301,7 +301,7 @@ adrs <- adrs %>%
 
 adrs <- adrs %>%
   derive_extreme_event(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(event_nr, ADT),
     tmp_event_nr_var = event_nr,
     mode = "first",
@@ -323,7 +323,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "CBOR" & AVALC %in% c("CR", "PR"),
     exist_flag = AVALC,
     false_value = "N",
@@ -340,13 +340,13 @@ adrs <- adrs %>%
 
 ## Death ----
 adsldth <- adsl %>%
-  select(STUDYID, USUBJID, DTHDT, !!!adsl_vars)
+  select(!!!get_admiral_option("subject_keys"), DTHDT, !!!adsl_vars)
 
 adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsldth,
     dataset_add = adsldth,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = !is.na(DTHDT),
     exist_flag = AVALC,
     false_value = "N",
@@ -366,7 +366,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "OVR" & ANL01FL == "Y",
     order = exprs(ADT, RSSEQ),
     mode = "last",
@@ -382,7 +382,7 @@ adrs <- adrs %>%
 
 ## Measurable disease at baseline ----
 adslmdis <- adsl %>%
-  select(STUDYID, USUBJID, !!!adsl_vars)
+  select(!!!get_admiral_option("subject_keys"), !!!adsl_vars)
 
 adrs <- adrs %>%
   derive_param_exist_flag(
@@ -404,7 +404,7 @@ adrs <- adrs %>%
 # Derive analysis sequence
 adrs <- adrs %>%
   derive_var_obs_number(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(PARAMCD, ADT, VISITNUM, RSSEQ),
     check_type = "error"
   )
@@ -413,7 +413,7 @@ adrs <- adrs %>%
 adrs <- adrs %>%
   derive_vars_merged(
     dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 # Save output ----

diff --git a/inst/templates/ad_adrs_basic.R b/inst/templates/ad_adrs_basic.R
@@ -47,7 +47,7 @@ adrs <- rs %>%
   derive_vars_merged(
     dataset_add = adsl,
     new_vars = adsl_vars,
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 # ---- Company-specific pre-processing ----
@@ -101,7 +101,7 @@ adrs <- adrs %>%
   restrict_derivation(
     derivation = derive_var_extreme_flag,
     args = params(
-      by_vars = exprs(STUDYID, USUBJID, ADT),
+      by_vars = c(get_admiral_option("subject_keys"), exprs(ADT)),
       order = exprs(worst_resp(AVALC), RSSEQ),
       new_var = ANL01FL,
       mode = "last"
@@ -116,7 +116,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "OVR" & AVALC == "PD" & ANL01FL == "Y",
     order = exprs(ADT, RSSEQ),
     mode = "first",
@@ -211,7 +211,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "BOR" & AVALC %in% c("CR", "PR"),
     order = exprs(ADT, RSSEQ),
     mode = "first",
@@ -293,7 +293,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "CBOR" & AVALC %in% c("CR", "PR"),
     order = exprs(ADT, RSSEQ),
     mode = "first",
@@ -312,13 +312,13 @@ adrs <- adrs %>%
 
 # Death
 adsldth <- adsl %>%
-  select(STUDYID, USUBJID, DTHDT, !!!adsl_vars)
+  select(!!!get_admiral_option("subject_keys"), DTHDT, !!!adsl_vars)
 
 adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsldth,
     dataset_add = adsldth,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = !is.na(DTHDT),
     exist_flag = AVALC,
     false_value = "N",
@@ -338,7 +338,7 @@ adrs <- adrs %>%
   derive_extreme_records(
     dataset_ref = adsl,
     dataset_add = adrs,
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     filter_add = PARAMCD == "OVR" & ANL01FL == "Y",
     order = exprs(ADT, RSSEQ),
     mode = "last",
@@ -354,7 +354,7 @@ adrs <- adrs %>%
 
 # Measurable disease at baseline
 adslmdis <- adsl %>%
-  select(STUDYID, USUBJID, !!!adsl_vars)
+  select(!!!get_admiral_option("subject_keys"), !!!adsl_vars)
 
 adrs <- adrs %>%
   derive_param_exist_flag(
@@ -376,7 +376,7 @@ adrs <- adrs %>%
 # Derive analysis sequence
 adrs <- adrs %>%
   derive_var_obs_number(
-    by_vars = exprs(STUDYID, USUBJID),
+    by_vars = get_admiral_option("subject_keys"),
     order = exprs(PARAMCD, ADT, VISITNUM, RSSEQ),
     check_type = "error"
   )
@@ -385,7 +385,7 @@ adrs <- adrs %>%
 adrs <- adrs %>%
   derive_vars_merged(
     dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
-    by_vars = exprs(STUDYID, USUBJID)
+    by_vars = get_admiral_option("subject_keys")
   )
 
 # ---- Save output ----