merge main into branch

Author: jeffreyad

DESCRIPTION

@@ -9,14 +9,19 @@ Authors@R:
     person("Jeffrey", "Dickinson", role = "aut"),
     person("Ege Can", "Taşlıçukur", role = "aut"),
     person("Vedha", "Viyash", role = "aut"),
-    person("David", "Blair", role = "aut")
+    person("David", "Blair", role = "aut"),
+    person("Daniel D.", "Sjoberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-0862-2018"))
 Description: This is not a package, but we just use this file to declare
     the dependencies of the site.
 URL: https://github.com/pharmaverse/examples
 Imports:
+    admiralonco,
     admiral,
+    cards,
     dplyr,
+    gtsummary,
     lubridate,
+    labelled,
     magrittr,
     metacore,
     metatools,

README.md

@@ -1,9 +1,3 @@
----
-editor:
-  markdown:
-    wrap: 72
----
-
 # Pharmaverse Examples
 
 The true beauty of pharmaverse (and open source in general) is when

adam/adrs.R

@@ -0,0 +1,174 @@
+## ----r setup, message=FALSE, warning=FALSE, results='hold'--------------------
+library(admiral)
+library(admiralonco)
+library(metacore)
+library(metatools)
+library(xportr)
+library(pharmaversesdtm)
+library(pharmaverseadam)
+library(dplyr)
+library(lubridate)
+library(stringr)
+
+## ----r read-specs-------------------------------------------------------------
+metacore <- spec_to_metacore("./metadata/onco_spec.xlsx") %>%
+  select_dataset("ADRS")
+
+## ----r load-data--------------------------------------------------------------
+data("adsl")
+data("rs_onco_recist")
+data("tu_onco_recist")
+
+rs <- rs_onco_recist
+tu <- tu_onco_recist
+
+# Convert blanks to NA
+rs <- convert_blanks_to_na(rs)
+tu <- convert_blanks_to_na(tu)
+
+## ----r merge-adsl-rs----------------------------------------------------------
+adsl_vars <- exprs(RANDDT)
+adrs_merged <- derive_vars_merged(
+  rs,
+  dataset_add = adsl,
+  new_vars = adsl_vars,
+  by_vars = exprs(STUDYID, USUBJID)
+)
+
+## ----r set-param-details------------------------------------------------------
+adrs_ovr <- adrs_merged %>%
+  filter(RSEVAL == "INVESTIGATOR" & RSTESTCD == "OVRLRESP") %>%
+  mutate(
+    PARAMCD = "OVR",
+    PARAM = "Overall Response by Investigator",
+    PARCAT1 = "Tumor Response",
+    PARCAT2 = "Investigator",
+    PARCAT3 = "RECIST 1.1"
+  )
+
+## ----r impute-dates-----------------------------------------------------------
+adrs_imputed <- adrs_ovr %>%
+  derive_vars_dt(
+    dtc = RSDTC,
+    new_vars_prefix = "A",
+    highest_imputation = "D",
+    date_imputation = "last"
+  ) %>%
+  mutate(AVISIT = VISIT)
+
+## ----r derive-aval------------------------------------------------------------
+adrs_aval <- adrs_imputed %>%
+  mutate(
+    AVALC = RSSTRESC,
+    AVAL = aval_resp(AVALC)
+  )
+
+## ----r flag-worst-assessment--------------------------------------------------
+worst_resp <- function(arg) {
+  case_when(
+    arg == "NE" ~ 1,
+    arg == "CR" ~ 2,
+    arg == "PR" ~ 3,
+    arg == "SD" ~ 4,
+    arg == "NON-CR/NON-PD" ~ 5,
+    arg == "PD" ~ 6,
+    TRUE ~ 0
+  )
+}
+
+adrs_anl01fl <- adrs_aval %>%
+  restrict_derivation(
+    derivation = derive_var_extreme_flag,
+    args = params(
+      by_vars = exprs(STUDYID, USUBJID, ADT),
+      order = exprs(worst_resp(AVALC), RSSEQ),
+      new_var = ANL01FL,
+      mode = "last"
+    ),
+    filter = !is.na(AVAL) & ADT >= RANDDT
+  )
+
+## ----r derive-pd--------------------------------------------------------------
+adrs_pd <- adrs_anl01fl %>%
+  derive_extreme_records(
+    dataset_ref = adsl,
+    dataset_add = adrs_anl01fl,
+    by_vars = exprs(STUDYID, USUBJID),
+    filter_add = PARAMCD == "OVR" & AVALC == "PD" & ANL01FL == "Y",
+    order = exprs(ADT, RSSEQ),
+    mode = "first",
+    exist_flag = AVALC,
+    false_value = "N",
+    set_values_to = exprs(
+      PARAMCD = "PD",
+      PARAM = "Disease Progression by Investigator",
+      PARCAT1 = "Tumor Response",
+      PARCAT2 = "Investigator",
+      PARCAT3 = "RECIST 1.1",
+      AVAL = yn_to_numeric(AVALC),
+      ANL01FL = "Y"
+    )
+  )
+
+## ----r derive-death-----------------------------------------------------------
+adsldth <- adsl %>%
+  select(STUDYID, USUBJID, DTHDT, !!!adsl_vars)
+
+adrs_death <- adrs_pd %>%
+  derive_extreme_records(
+    dataset_ref = adsldth,
+    dataset_add = adsldth,
+    by_vars = exprs(STUDYID, USUBJID),
+    filter_add = !is.na(DTHDT),
+    exist_flag = AVALC,
+    false_value = "N",
+    set_values_to = exprs(
+      PARAMCD = "DEATH",
+      PARAM = "Death",
+      PARCAT1 = "Reference Event",
+      AVAL = yn_to_numeric(AVALC),
+      ANL01FL = "Y",
+      ADT = DTHDT
+    )
+  ) %>%
+  select(-DTHDT)
+
+## ----r derive-lsta------------------------------------------------------------
+adrs_lsta <- adrs_death %>%
+  derive_extreme_records(
+    dataset_ref = adsl,
+    dataset_add = adrs_death,
+    by_vars = exprs(STUDYID, USUBJID),
+    filter_add = PARAMCD == "OVR" & ANL01FL == "Y",
+    order = exprs(ADT, RSSEQ),
+    mode = "last",
+    set_values_to = exprs(
+      PARAMCD = "LSTA",
+      PARAM = "Last Disease Assessment by Investigator",
+      PARCAT1 = "Tumor Response",
+      PARCAT2 = "Investigator",
+      PARCAT3 = "RECIST 1.1",
+      ANL01FL = "Y"
+    )
+  )
+
+## ----r apply-metadata-check, message=FALSE, warning=FALSE---------------------
+adrs_checked <- adrs_lsta %>%
+  add_variables(metacore) %>% # Add variables specified in the metadata
+  drop_unspec_vars(metacore) %>% # Drop variables not specified in metadata
+  check_variables(metacore) %>% # Check all variables specified are present and no more
+  check_ct_data(metacore) %>% # Check controlled terminology
+  order_cols(metacore) %>% # Order columns according to metadata
+  sort_by_key(metacore) # Sort rows by sort keys
+
+## ----r xportr-----------------------------------------------------------------
+dir <- tempdir() # Specify the directory for saving the XPT file
+
+adrs_xpt <- adrs_checked %>%
+  xportr_type(metacore, domain = "ADRS") %>% # Coerce variable types to match metadata
+  xportr_length(metacore) %>% # Assign variable lengths from metadata
+  xportr_label(metacore) %>% # Assign variable labels from metadata
+  xportr_format(metacore) %>% # Assign variable formats from metadata
+  xportr_df_label(metacore) %>% # Assign dataset labels from metadata
+  xportr_write(file.path(dir, "adrs.xpt")) # Write the XPT file
+