Closes #143 add exposure response data

adam/ader.R

@@ -0,0 +1,187 @@
+## ----r echo=TRUE, message=FALSE-----------------------------------------------
+# Load Packages
+library(admiral)
+library(admiralonco)
+# pharmaverseadam contains example datasets generated from the CDISC pilot
+# project SDTM ran through admiral templates
+library(pharmaverseadam)
+library(dplyr)
+library(lubridate)
+library(stringr)
+library(metacore)
+library(metatools)
+library(xportr)
+
+## ----r echo=TRUE, message=FALSE-----------------------------------------------
+# ---- Load Specs for Metacore ----
+metacore <- spec_to_metacore("./metadata/pk_spec.xlsx") %>%
+  select_dataset("ADER")
+
+## ----r------------------------------------------------------------------------
+# ---- Load source datasets ----
+# Load ADRS, ADTTE, ADSL, ADLB, ADVS and ADEX
+adrs <- pharmaverseadam::adrs_onco
+adtte <- pharmaverseadam::adtte_onco
+
+adsl <- pharmaverseadam::adsl
+adlb <- pharmaverseadam::adlb
+advs <- pharmaverseadam::advs
+adex <- pharmaverseadam::adex %>%
+  filter(PARCAT1 == "INDIVIDUAL")
+adpp <- pharmaverseadam::adpp
+
+## ----r------------------------------------------------------------------------
+# ---- Derivations ----
+# For ADTTE censor variables add "IND" to PARAMCD
+adttei <- adtte %>%
+  mutate(PARAMCD = paste0(PARAMCD, "IND"))
+
+ader_tte <- adsl %>%
+  select(!!!get_admiral_option("subject_keys")) %>%
+  # Create OS and PFS variables from ADTTE
+  derive_vars_transposed(
+    dataset_merge = adtte,
+    by_vars = get_admiral_option("subject_keys"),
+    key_var = PARAMCD,
+    value_var = AVAL
+  ) %>%
+  # Create OS and PFS censor variables
+  derive_vars_transposed(
+    dataset_merge = adttei,
+    by_vars = get_admiral_option("subject_keys"),
+    key_var = PARAMCD,
+    value_var = CNSR
+  )
+
+## ----r------------------------------------------------------------------------
+# ---- Add ADRS data ----
+# Add response date to ADSL for duration of response calculation
+ader_bor <- ader_tte %>%
+  derive_vars_merged(
+    dataset_add = adrs,
+    filter_add = PARAMCD == "BOR" & ANL01FL == "Y",
+    by_vars = get_admiral_option("subject_keys"),
+    new_vars = exprs(BOR = AVAL, BORC = AVALC)
+  )
+
+## ----r------------------------------------------------------------------------
+# ---- Add Exposure Metrics  ----
+ader_auc <- ader_bor %>%
+  derive_vars_transposed(
+    dataset_merge = adpp,
+    filter = PARAMCD %in% c("AUCLST", "CMAX"),
+    by_vars = get_admiral_option("subject_keys"),
+    key_var = PARAMCD,
+    value_var = AVAL
+  ) %>%
+  rename(AUCSS = AUCLST, CMAXSS = CMAX)
+
+## ----r------------------------------------------------------------------------
+# ---- Add Sequence Number ----
+ader_aseq <- ader_auc %>%
+  derive_var_obs_number(
+    by_vars = get_admiral_option("subject_keys"),
+    check_type = "error"
+  )
+
+## ----r------------------------------------------------------------------------
+# ---- Derive Covariates ----
+# Include numeric values for STUDYIDN, USUBJIDN, SEXN, RACEN etc.
+
+covar <- adsl %>%
+  create_var_from_codelist(metacore, input_var = STUDYID, out_var = STUDYIDN) %>%
+  create_var_from_codelist(metacore, input_var = SEX, out_var = SEXN) %>%
+  create_var_from_codelist(metacore, input_var = RACE, out_var = RACEN) %>%
+  create_var_from_codelist(metacore, input_var = ETHNIC, out_var = ETHNICN) %>%
+  create_var_from_codelist(metacore, input_var = ARMCD, out_var = COHORT) %>%
+  create_var_from_codelist(metacore, input_var = ARMCD, out_var = COHORTC) %>%
+  create_var_from_codelist(metacore, input_var = ARM, out_var = ARMN) %>%
+  create_var_from_codelist(metacore, input_var = ACTARM, out_var = ACTARMN) %>%
+  create_var_from_codelist(metacore, input_var = COUNTRY, out_var = COUNTRYN) %>%
+  create_var_from_codelist(metacore, input_var = COUNTRY, out_var = COUNTRYL) %>%
+  mutate(
+    STUDYIDN = as.numeric(word(USUBJID, 1, sep = fixed("-"))),
+    SITEIDN = as.numeric(word(USUBJID, 2, sep = fixed("-"))),
+    USUBJIDN = as.numeric(word(USUBJID, 3, sep = fixed("-"))),
+    SUBJIDN = as.numeric(SUBJID),
+    ROUTE = unique(adex$EXROUTE)[1],
+    FORM = unique(adex$EXDOSFRM)[1],
+    REGION1 = COUNTRY,
+    REGION1N = COUNTRYN,
+  ) %>%
+  create_var_from_codelist(metacore, input_var = FORM, out_var = FORMN) %>%
+  create_var_from_codelist(metacore, input_var = ROUTE, out_var = ROUTEN)
+
+## ----r------------------------------------------------------------------------
+# ---- Derive additional baselines from ADVS and ADLB ----
+
+labsbl <- adlb %>%
+  filter(ABLFL == "Y" & PARAMCD %in% c("CREAT", "ALT", "AST", "BILI")) %>%
+  mutate(PARAMCDB = paste0(PARAMCD, "BL")) %>%
+  select(STUDYID, USUBJID, PARAMCDB, AVAL)
+
+covar_vslb <- covar %>%
+  derive_vars_merged(
+    dataset_add = advs,
+    filter_add = PARAMCD == "HEIGHT" & ABLFL == "Y",
+    by_vars = exprs(STUDYID, USUBJID),
+    new_vars = exprs(HTBL = AVAL)
+  ) %>%
+  derive_vars_merged(
+    dataset_add = advs,
+    filter_add = PARAMCD == "WEIGHT" & ABLFL == "Y",
+    by_vars = exprs(STUDYID, USUBJID),
+    new_vars = exprs(WTBL = AVAL)
+  ) %>%
+  derive_vars_transposed(
+    dataset_merge = labsbl,
+    by_vars = exprs(STUDYID, USUBJID),
+    key_var = PARAMCDB,
+    value_var = AVAL
+  ) %>%
+  mutate(
+    BMIBL = compute_bmi(height = HTBL, weight = WTBL),
+    BSABL = compute_bsa(
+      height = HTBL,
+      weight = WTBL,
+      method = "Mosteller"
+    ),
+    CRCLBL = compute_egfr(
+      creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
+      method = "CRCL"
+    ),
+    EGFRBL = compute_egfr(
+      creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
+      method = "CKD-EPI"
+    )
+  ) %>%
+  rename(TBILBL = BILIBL)
+
+## ----r------------------------------------------------------------------------
+# Combine covariates with APPPK data
+# Combine covariates with ADER data
+
+ader_prefinal <- ader_aseq %>%
+  derive_vars_merged(
+    dataset_add = covar_vslb,
+    by_vars = exprs(STUDYID, USUBJID)
+  )
+
+## ----r------------------------------------------------------------------------
+ader <- ader_prefinal %>%
+  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) %>% # 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
+
+## ----r------------------------------------------------------------------------
+dir <- tempdir() # Change to whichever directory you want to save the dataset in
+
+ader_xpt <- ader %>%
+  xportr_type(metacore, domain = "ADER") %>% # 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_format(metacore) %>% # Assigns variable format from metacore specifications
+  xportr_df_label(metacore) %>% # Assigns dataset label from metacore specifications
+  xportr_write(file.path(dir, "ader.xpt")) # Write xpt v5 transport file