204 admiral updates

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiralophtha
 Type: Package
 Title: ADaM in R Asset Library - Ophthalmology
-Version: 0.3.0.9002
+Version: 0.3.0.9003
 Authors@R: c(
     person("Edoardo", "Mancini", email = "[email protected]", role = c("aut", "cre")),
     person("Ritika", "Aggarwal", email = "[email protected]", role = c("aut")),

NEWS.md

@@ -4,11 +4,16 @@
 
 - Removed `analysis_value` argument in the calls to `derive_param_computed()` in ADBCVA template in line with the deprecation of this argument in the new version of `{admiral}`. Variable values for parameters of interest are now all populated through the `set_values_to` argument (#207). 
 
+- Modified calls to `derive_summary_records()` in ADVFQ template in line with the updates to this function in the new version of the `{admiral}` package. The `filter` argument is now renamed to `filter_add`, the argument `dataset_add` is now always specified and the variable values are now all populated through the `set_values_to` argument (#204).
+
 ## Updates to Documentation
 
 - Added release date for `{admiralophtha}` 1.0 to the front page (#203).
+
 - Removed `analysis_value` argument in the calls to `derive_param_computed()` in ADBCVA vignette in line with the deprecation of this argument in the new version of `{admiral}`. Variable values for parameters of interest are now all populated through the `set_values_to` argument (#207). 
 
+- Modified calls to `derive_summary_records()` in ADVFQ vignette in line with the updates to this function in the new version of the `{admiral}` package. The `filter` argument is now renamed to `filter_add`, the argument `dataset_add` is now always specified and the variable values are now all populated through the `set_values_to` argument (#204).
+
 ## Various
 
 - Website now has button/links to Slack channel and GitHub Issues (#206).

inst/templates/ad_advfq.R

@@ -75,11 +75,13 @@ advfq_aval <- advfq_dtdy %>%
 # else set to 0 if [advfq.AVAL] = 5
 advfq_qr01 <- advfq_aval %>%
   derive_summary_records(
+    dataset_add = advfq_aval,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, PARAMCD, VISITNUM, VISIT, ADT, ADY),
-    filter = QSTESTCD == "VFQ1" & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = identity,
-    set_values_to = exprs(PARAMCD = "QR01")
+    filter_add = QSTESTCD == "VFQ1" & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = identity(AVAL),
+      PARAMCD = "QR01"
+    )
   ) %>%
   mutate(AVAL = ifelse(PARAMCD == "QR01",
     case_when(
@@ -101,11 +103,13 @@ advfq_qr01 <- advfq_aval %>%
 # else set to 0 if [advfq.AVAL] = 6
 advfq_qr02 <- advfq_qr01 %>%
   derive_summary_records(
+    dataset_add = advfq_qr01,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, PARAMCD, VISITNUM, VISIT, ADT, ADY),
-    filter = QSTESTCD == "VFQ2" & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = identity,
-    set_values_to = exprs(PARAMCD = "QR02")
+    filter_add = QSTESTCD == "VFQ2" & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = identity(AVAL),
+      PARAMCD = "QR02"
+    )
   ) %>%
   mutate(AVAL = ifelse(PARAMCD == "QR02",
     case_when(
@@ -127,11 +131,13 @@ advfq_qr02 <- advfq_qr01 %>%
 # else set to 0 if [advfq.AVAL] = 1
 advfq_qr03 <- advfq_qr02 %>%
   derive_summary_records(
+    dataset_add = advfq_qr02,
     by_vars = exprs(STUDYID, USUBJID, PARAMCD, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
-    filter = QSTESTCD == "VFQ3" & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = identity,
-    set_values_to = exprs(PARAMCD = "QR03")
+    filter_add = QSTESTCD == "VFQ3" & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = identity(AVAL),
+      PARAMCD = "QR03"
+    )
   ) %>%
   mutate(AVAL = ifelse(PARAMCD == "QR03",
     case_when(
@@ -153,11 +159,13 @@ advfq_qr03 <- advfq_qr02 %>%
 # else set to 0 if [advfq.AVAL] = 1
 advfq_qr04 <- advfq_qr03 %>%
   derive_summary_records(
+    dataset_add = advfq_qr03,
     by_vars = exprs(STUDYID, USUBJID, PARAMCD, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
-    filter = QSTESTCD == "VFQ4" & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = identity,
-    set_values_to = exprs(PARAMCD = "QR04")
+    filter_add = QSTESTCD == "VFQ4" & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = identity(AVAL),
+      PARAMCD = "QR04"
+    )
   ) %>%
   mutate(AVAL = ifelse(PARAMCD == "QR04",
     case_when(
@@ -175,23 +183,27 @@ advfq_qr04 <- advfq_qr03 %>%
 # Average of QR01 and QR02 records
 advfq_qsg01 <- advfq_qr04 %>%
   derive_summary_records(
+    dataset_add = advfq_qr04,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
-    filter = PARAMCD %in% c("QR01", "QR02") & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = mean,
-    set_values_to = exprs(PARAMCD = "QSG01")
+    filter_add = PARAMCD %in% c("QR01", "QR02") & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = mean(AVAL),
+      PARAMCD = "QSG01"
+    )
   )
 
 ## Derive a new record as a summary record  ----
 ## QSG02 General Score 02
 # Average of QR03 and QR04 records
 advfq_qsg02 <- advfq_qsg01 %>%
   derive_summary_records(
+    dataset_add = advfq_qsg01,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
-    filter = PARAMCD %in% c("QR03", "QR04") & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = mean,
-    set_values_to = exprs(PARAMCD = "QSG02")
+    filter_add = PARAMCD %in% c("QR03", "QR04") & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = mean(AVAL),
+      PARAMCD = "QSG02"
+    )
   )
 
 
@@ -200,11 +212,13 @@ advfq_qsg02 <- advfq_qsg01 %>%
 # Average of QSG01 and QSG02 records
 advfq_qbcs <- advfq_qsg02 %>%
   derive_summary_records(
+    dataset_add = advfq_qsg02,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
-    filter = PARAMCD %in% c("QSG01", "QSG02") & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = sum,
-    set_values_to = exprs(PARAMCD = "QBCSCORE")
+    filter_add = PARAMCD %in% c("QSG01", "QSG02") & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = sum(AVAL),
+      PARAMCD = "QBCSCORE"
+    )
   )
 
 ## Get visit info ----
@@ -220,11 +234,14 @@ advfq_visit <- advfq_qbcs %>%
       !is.na(VISIT) ~ str_to_title(VISIT),
       TRUE ~ NA_character_
     ),
-    AVISITN = as.numeric(case_when(
+    AVISITN = case_when(
       VISIT == "BASELINE" ~ "0",
-      str_detect(VISIT, "WEEK") ~ str_trim(str_replace(VISIT, "WEEK", "")),
-      TRUE ~ NA_character_
-    ))
+      str_detect(VISIT, "WEEK") ~ VISIT %>%
+        str_replace("WEEK", "") %>%
+        str_replace("\\(T\\)", "") %>%
+        str_trim(),
+      TRUE ~ NA
+    ),
   )
 
 advfq_ontrt <- advfq_visit %>%

vignettes/advfq.Rmd

@@ -126,11 +126,13 @@ Run this section of code for every question that you need recoding. This gives a
 # else set to 0 if [advfq.AVAL] = 5
 advfq <- advfq %>%
   derive_summary_records(
+    dataset_add = advfq,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, PARAMCD, VISITNUM, VISIT),
-    filter = QSTESTCD == "VFQ1" & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = identity,
-    set_values_to = exprs(PARAMCD = "QR01")
+    filter_add = QSTESTCD == "VFQ1" & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = identity(AVAL),
+      PARAMCD = "QR01"
+    )
   ) %>%
   mutate(AVAL = ifelse(PARAMCD == "QR01",
     case_when(
@@ -152,11 +154,13 @@ Next, the programmer should create summary records as average of recoded questio
 # Average of QR01 and QR02 records
 advfq <- advfq %>%
   derive_summary_records(
+    dataset_add = advfq,
     by_vars = exprs(STUDYID, USUBJID, !!!adsl_vars, VISITNUM, VISIT, ADT, ADY),
-    filter = PARAMCD %in% c("QR01", "QR02") & !is.na(AVAL),
-    analysis_var = AVAL,
-    summary_fun = mean,
-    set_values_to = exprs(PARAMCD = "QSG01")
+    filter_add = PARAMCD %in% c("QR01", "QR02") & !is.na(AVAL),
+    set_values_to = exprs(
+      AVAL = mean(AVAL),
+      PARAMCD = "QSG01"
+    )
   )
 ```