Update to handle urine records #2392

pharmaverse · Mar 29, 2024 · 62c91cd · 62c91cd
1 parent fc102b3
commit 62c91cd
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Showing 5 changed files with 22 additions and 14 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -7,6 +7,7 @@
 ## Updates of Existing Functions
 
 - Created three unit tests for `get_summary_records()`. (#2304)
+- Templates for ADPC, ADPPK and ADPP are updated to handle urine records. (#2392)
 
 ## Breaking Changes
 

diff --git a/inst/templates/ad_adpc.R b/inst/templates/ad_adpc.R
@@ -346,6 +346,7 @@ adpc_nrrlt <- adpc_arrlt %>%
 
 adpc_aval <- adpc_nrrlt %>%
   mutate(
+    PARCAT1 = PCSPEC,
     ATPTN = case_when(
       EVID == 1 ~ 0,
       TRUE ~ PCTPTNUM
@@ -444,7 +445,7 @@ adpc_dtype <- bind_rows(adpc_aval, dtype) %>%
 
 adpc_base <- adpc_dtype %>%
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, BASETYPE),
+    by_vars = exprs(STUDYID, USUBJID, PARAMCD, PARCAT1, BASETYPE),
     source_var = AVAL,
     new_var = BASE,
     filter = ABLFL == "Y"
@@ -459,7 +460,7 @@ adpc_aseq <- adpc_chg %>%
   derive_var_obs_number(
     new_var = ASEQ,
     by_vars = exprs(STUDYID, USUBJID),
-    order = exprs(ADTM, BASETYPE, EVID, AVISITN, ATPTN, DTYPE),
+    order = exprs(ADTM, BASETYPE, EVID, AVISITN, ATPTN, PARCAT1, DTYPE),
     check_type = "error"
   ) %>%
   # Remove temporary variables

diff --git a/inst/templates/ad_adpp.R b/inst/templates/ad_adpp.R
@@ -51,7 +51,9 @@ param_lookup <- tibble::tribble(
   "TCEND", "TCEND", "Time of CEND", 17, # non Cdisc Term
   "TLST", "TLST", "Time of Last Nonzero Conc", 18,
   "TMAX", "TMAX", "Time of CMAX", 19,
-  "VSSO", "VSSO", "Vol Dist Steady State Obs", 20
+  "VSSO", "VSSO", "Vol Dist Steady State Obs", 20,
+  "RCAMINT", "RCAMINT", "Ae", 21,
+  "RENALCL", "RENALCL", "CLR", 22
 )
 
 # ASSIGN AVALCAT1
@@ -100,8 +102,9 @@ adpp_aval <- adpp_pp %>%
     select(param_lookup, PPTESTCD, PARAMCD),
     by = "PPTESTCD"
   ) %>%
-  ## Calculate AVAL and AVALC ----
+  ## Calculate PARCAT1, AVAL and AVALC ----
   mutate(
+    PARCAT1 = PPCAT,
     AVAL = PPSTRESN,
     AVALC = PPSTRESC,
     AVALU = PPSTRESU,

diff --git a/inst/templates/ad_adppk.R b/inst/templates/ad_adppk.R
@@ -277,7 +277,8 @@ adppk_aval <- adppk_aprlt %>%
     # Derive CMT
     CMT = case_when(
       EVID == 1 ~ 1,
-      TRUE ~ 2
+      PCSPEC == "PLASMA" ~ 2,
+      TRUE ~ 3
     ),
     # Derive BLQFL/BLQFN
     BLQFL = case_when(
@@ -321,7 +322,7 @@ adppk_aseq <- adppk_aval %>%
   derive_var_obs_number(
     new_var = ASEQ,
     by_vars = exprs(STUDYID, USUBJID),
-    order = exprs(AFRLT, EVID),
+    order = exprs(AFRLT, EVID, CMT),
     check_type = "error"
   ) %>%
   # Derive PARAM and PARAMN
@@ -335,8 +336,8 @@ adppk_aseq <- adppk_aval %>%
     -DOMAIN, -starts_with("min"), -starts_with("max"), -starts_with("EX"),
     -starts_with("PC"), -ends_with("first"), -ends_with("prev"),
     -ends_with("DTM"), -ends_with("DT"), -ends_with("TM"), -starts_with("VISIT"),
-    -starts_with("AVISIT"), -starts_with("PARAM"),
-    -ends_with("TMF"), -starts_with("TRT"), -starts_with("ATPT"), -DRUG
+    -starts_with("AVISIT"), -ends_with("TMF"), -starts_with("TRT"),
+    -starts_with("ATPT"), -DRUG
   )
 
 #---- Derive Covariates ----

diff --git a/vignettes/pk_adnca.Rmd b/vignettes/pk_adnca.Rmd
@@ -652,6 +652,7 @@ variables.
 
 adpc_aval <- adpc_nrrlt %>%
   mutate(
+    PARCAT1 = PCSPEC,
     ATPTN = case_when(
       EVID == 1 ~ 0,
       TRUE ~ PCTPTNUM
@@ -827,7 +828,7 @@ Finally we derive `PARAM` and `PARAMN` from a lookup table.
 adpc_base <- adpc_dtype %>%
   # Derive BASE
   derive_var_base(
-    by_vars = exprs(STUDYID, USUBJID, PARAMCD, BASETYPE),
+    by_vars = exprs(STUDYID, USUBJID, PARAMCD, PARCAT1, BASETYPE),
     source_var = AVAL,
     new_var = BASE,
     filter = ABLFL == "Y"
@@ -842,7 +843,7 @@ adpc_aseq <- adpc_chg %>%
   derive_var_obs_number(
     new_var = ASEQ,
     by_vars = exprs(STUDYID, USUBJID),
-    order = exprs(ADTM, BASETYPE, EVID, AVISITN, ATPTN, DTYPE),
+    order = exprs(ADTM, BASETYPE, EVID, AVISITN, ATPTN, PARCAT1, DTYPE),
     check_type = "error"
   ) %>%
   # Remove temporary variables
@@ -1164,7 +1165,8 @@ adppk_aval <- adppk_aprlt %>%
     # Derive CMT
     CMT = case_when(
       EVID == 1 ~ 1,
-      TRUE ~ 2
+      PCSPEC == "PLASMA" ~ 2,
+      TRUE ~ 3
     ),
     # Derive BLQFL/BLQFN
     BLQFL = case_when(
@@ -1225,7 +1227,7 @@ adppk_aseq <- adppk_aval %>%
   derive_var_obs_number(
     new_var = ASEQ,
     by_vars = exprs(STUDYID, USUBJID),
-    order = exprs(AFRLT, EVID),
+    order = exprs(AFRLT, EVID, CMT),
     check_type = "error"
   ) %>%
   # Derive PARAM and PARAMN
@@ -1239,8 +1241,8 @@ adppk_aseq <- adppk_aval %>%
     -DOMAIN, -starts_with("min"), -starts_with("max"), -starts_with("EX"),
     -starts_with("PC"), -ends_with("first"), -ends_with("prev"),
     -ends_with("DTM"), -ends_with("DT"), -ends_with("TM"), -starts_with("VISIT"),
-    -starts_with("AVISIT"), -starts_with("PARAM"),
-    -ends_with("TMF"), -starts_with("TRT"), -starts_with("ATPT"), -DRUG
+    -starts_with("AVISIT"), -ends_with("TMF"), -starts_with("TRT"), 
+    -starts_with("ATPT"), -DRUG
   )
 ```