Merge pull request #87 from pharmaverse/85_ADAE_example

closes #85 adae example

Author: bms63

adam/adae.R

@@ -0,0 +1,162 @@
+## ----r setup, message=FALSE, warning=FALSE, results='hold'--------------------
+library(metacore)
+library(metatools)
+library(pharmaversesdtm)
+library(pharmaverseadam)
+library(admiral)
+library(xportr)
+library(dplyr)
+library(lubridate)
+library(stringr)
+library(reactable)
+
+# Read in input data
+adsl <- pharmaverseadam::adsl
+ae <- pharmaversesdtm::ae
+ex <- pharmaversesdtm::ex
+
+# When SAS datasets are imported into R using haven::read_sas(), missing
+# character values from SAS appear as "" characters in R, instead of appearing
+# as NA values. Further details can be obtained via the following link:
+# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values
+ae <- convert_blanks_to_na(ae)
+ex <- convert_blanks_to_na(ex)
+
+## ----r echo=TRUE--------------------------------------------------------------
+# ---- Load Specs for Metacore ----
+metacore <- spec_to_metacore(
+  path = "./metadata/safety_specs.xlsx",
+  # All datasets are described in the same sheet
+  where_sep_sheet = FALSE
+) %>%
+  select_dataset("ADAE")
+
+## ----r------------------------------------------------------------------------
+# Select required ADSL variables
+adsl_vars <- exprs(TRTSDT, TRTEDT, DTHDT)
+
+# Join ADSL variables with VS
+adae <- ae %>%
+  derive_vars_merged(
+    dataset_add = adsl,
+    new_vars = adsl_vars,
+    by_vars = exprs(STUDYID, USUBJID)
+  )
+
+## ----r------------------------------------------------------------------------
+# Derive ASTDT/ASTDTF/ASTDY and AENDT/AENDTF/AENDY
+adae <- adae %>%
+  derive_vars_dt(
+    new_vars_prefix = "AEN",
+    dtc = AEENDTC,
+    date_imputation = "last",
+    highest_imputation = "M", # imputation is performed on missing days or months
+    flag_imputation = "auto" # to automatically create AENDTF variable
+  ) %>%
+  derive_vars_dt(
+    new_vars_prefix = "AST",
+    dtc = AESTDTC,
+    highest_imputation = "M", # imputation is performed on missing days or months
+    flag_imputation = "auto", # to automatically create ASTDTF variable
+    min_dates = exprs(TRTSDT), # apply a minimum date for the imputation
+    max_dates = exprs(AENDT) # apply a maximum date for the imputation
+  ) %>%
+  derive_vars_dy(
+    reference_date = TRTSDT,
+    source_vars = exprs(ASTDT, AENDT)
+  )
+
+## ----r------------------------------------------------------------------------
+# Derive ADURN/ADURU
+adae <- adae %>%
+  derive_vars_duration(
+    new_var = ADURN,
+    new_var_unit = ADURU,
+    start_date = ASTDT,
+    end_date = AENDT
+  )
+
+## ----r------------------------------------------------------------------------
+# Derive LDOSEDT
+# In our ex data the EXDOSFRQ (frequency) is "QD" which stands for once daily
+# If this was not the case then we would need to use the admiral::create_single_dose_dataset() function
+# to generate single doses from aggregate dose information
+# Refer to https://pharmaverse.github.io/admiral/reference/create_single_dose_dataset.html
+ex <- ex %>%
+  derive_vars_dt(
+    dtc = EXENDTC,
+    new_vars_prefix = "EXEN"
+  )
+
+adae <- adae %>%
+  derive_vars_joined(
+    dataset_add = ex,
+    by_vars = exprs(STUDYID, USUBJID),
+    order = exprs(EXENDT),
+    new_vars = exprs(LDOSEDT = EXENDT),
+    join_vars = exprs(EXENDT),
+    join_type = "all",
+    filter_add = (EXDOSE > 0 | (EXDOSE == 0 & str_detect(EXTRT, "PLACEBO"))) & !is.na(EXENDT),
+    filter_join = EXENDT <= ASTDT,
+    mode = "last"
+  )
+
+## ----r------------------------------------------------------------------------
+# Derive TRTEMFL and ONTRTFL
+adae <- adae %>%
+  derive_var_trtemfl(
+    start_date = ASTDT,
+    end_date = AENDT,
+    trt_start_date = TRTSDT,
+    trt_end_date = TRTEDT
+  ) %>%
+  derive_var_ontrtfl(
+    start_date = ASTDT,
+    ref_start_date = TRTSDT,
+    ref_end_date = TRTEDT,
+    ref_end_window = 30
+  )
+
+## ----r------------------------------------------------------------------------
+# Derive AOCCIFL
+adae <- adae %>%
+  # create temporary numeric ASEVN for sorting purpose
+  mutate(TEMP_AESEVN = as.integer(factor(AESEV, levels = c("SEVERE", "MODERATE", "MILD")))) %>%
+  derive_var_extreme_flag(
+    new_var = AOCCIFL,
+    by_vars = exprs(STUDYID, USUBJID),
+    order = exprs(TEMP_AESEVN, ASTDT, AESEQ),
+    mode = "first"
+  )
+
+## ----r------------------------------------------------------------------------
+queries <- admiral::queries %>%
+  filter(PREFIX %in% c("CQ01", "SMQ02"))
+
+## ----r------------------------------------------------------------------------
+# Derive CQ01NAM and SMQ02NAM
+adae <- adae %>%
+  derive_vars_query(dataset_queries = queries)
+
+## ----r eval=TRUE--------------------------------------------------------------
+adae <- adae %>%
+  derive_vars_merged(
+    dataset_add = select(adsl, !!!negate_vars(adsl_vars)),
+    by_vars = exprs(STUDYID, USUBJID)
+  )
+
+## ----r checks, warning=FALSE, message=FALSE-----------------------------------
+dir <- tempdir() # Specify the directory for saving the XPT file
+
+adae %>%
+  drop_unspec_vars(metacore) %>% # Drop unspecified variables from specs
+  check_variables(metacore) %>% # Check all variables specified are present and no more
+  check_ct_data(metacore, na_acceptable = TRUE) %>% # Checks all variables with CT only contain values within the CT
+  order_cols(metacore) %>% # Orders the columns according to the spec
+  sort_by_key(metacore) %>% # Sorts the rows by the sort keys
+  xportr_type(metacore, domain = "ADAE") %>% # Coerce variable type to match spec
+  xportr_length(metacore) %>% # Assigns SAS length from a variable level metadata
+  xportr_label(metacore) %>% # Assigns variable label from metacore specifications
+  xportr_df_label(metacore) %>%  # Assigns dataset label from metacore specifications
+  xportr_write(file.path(dir, "adae.xpt"), metadata = metacore, domain = "ADAE")
+