Devr 3487 forestlydata

data-raw/forestly_adae.R

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+
+library(arsenal)
+library(stringr)
+library(dplyr)
+
+
+
+adae <- r2rtf::r2rtf_adae
+
+
+
+# Derive AREL from existing AEREL
+adae <- adae %>% filter(TRTA!="Xanomeline High Dose") %>%
+  mutate(AREL = case_when(
+    AEREL %in% c("PROBABLE", "POSSIBLE") ~ "RELATED",
+    AEREL %in% c("NONE", "REMOTE", "") ~ "NOT RELATED",
+    TRUE ~ AEREL  # Keep original AREL if none of the conditions are met
+  ))
+
+
+freq <- adae %>% count(AREL, AEREL) %>%
+  arrange(desc(n))
+print(freq)
+
+freq2 <- forestly_adae %>% count(AREL, AEREL) %>%
+  arrange(desc(n))
+print(freq2)
+
+str(adae$TRTA)
+str(forestly_adae$TRTA)
+
+
+
+
+adae$AEACN <- sample(
+  x = c("DOSE NOT CHANGED", "DRUG INTERRUPTED", "DRUG WITHDRAWN", "NOT APPLICABLE", "UNKNOWN"),
+  size = length(adae$USUBJID),
+  prob = c(0.7, 0.1, 0.05, 0.1, 0.05), replace = TRUE
+)
+
+for (i in seq_along(adae$AEACN)) {
+  adae$action_taken[i] <- switch(adae$AEACN[i],
+                                 "DOSE NOT CHANGED" = "None",
+                                 "DRUG INTERRUPTED" = "Interrupted",
+                                 "DRUG WITHDRAWN" = "Discontinued",
+                                 "NOT APPLICABLE" = "N/A",
+                                 "UNKNOWN" = "Unknown",
+                                 "''" = "None",
+                                 tools::toTitleCase(tolower(adae$AEACN[i]))
+  )
+}
+
+#CHECKS
+# freq <- adae %>% count(AEACN) %>% arrange(desc(n))
+# print(freq)
+#
+#
+# adae %>%
+#   select(USUBJID, TRTAN, TRTA, TRTSDT, ASTDT, ADURN, AETERM, AEREL, AESEQ, TRTEMFL, AREL, AEACN) %>%
+#   slice(1) %>%
+#   print()
+# forestly_adae %>%
+#   select(USUBJID, TRTAN, TRTA, TRTSDT, ASTDT, ADURN, AETERM, AEREL, AESEQ, TRTEMFL, AREL, AEACN) %>%
+#   slice(1) %>%
+#   print()
+

data-raw/forestly_adae_3grp.R

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+
+library(arsenal)
+library(stringr)
+library(dplyr)
+
+
+
+adae <- r2rtf::r2rtf_adae
+
+
+
+# Derive AREL from existing AEREL
+adae <- adae %>%
+  mutate(AREL = case_when(
+    AEREL %in% c("PROBABLE", "POSSIBLE") ~ "RELATED",
+    AEREL %in% c("NONE", "REMOTE", "") ~ "NOT RELATED",
+    TRUE ~ AEREL  # Keep original AREL if none of the conditions are met
+  ),
+  TRTA = str_replace_all(as.character(TRTA), "Xanomeline ", "") %>% as.factor()  # Remove "Xanomeline " and convert to factor
+  )
+
+freq <- adae %>% count(AREL, AEREL) %>%
+  arrange(desc(n))
+print(freq)
+
+str(adae$TRTA)
+str(forestly_adae_3grp$TRTA)
+
+# Define the desired order of levels
+desired_levels <- c("Placebo", "Low Dose", "High Dose")
+
+# Standardize TRTA in adae
+adae$TRTA <- factor(adae$TRTA, levels = desired_levels)
+
+
+

data-raw/forestly_adsl.R

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+
+library(arsenal)
+library(stringr)
+
+
+adsl <- r2rtf::r2rtf_adsl
+
+
+
+
+load("~/forestly/data/forestly_adsl_3grp.rda")
+
+
+
+source("~/forestly/R/function_dataset0compare.R")
+
+
+#Compare ADSL dataset
+
+freq <- forestly_adsl_3grp %>% count(TRT01A, TRTA) %>%
+  arrange(desc(n))
+print(freq)
+
+# Derive TRTA from existing AEREL
+adsl <- adsl %>%
+  mutate(
+   TRTA = str_replace_all(as.character(TRT01A), "Xanomeline ", "") %>% as.factor()  # Remove "Xanomeline " and convert to factor
+  )
+
+# Define the desired order of levels
+desired_levels <- c("Placebo", "Low Dose", "High Dose")
+
+# Standardize TRTA in adae
+adsl$TRTA <- factor(adsl$TRTA, levels = desired_levels)
+
+
+# Save the adae  dataset as an .rda file
+save(adsl, file = "~/forestly/data-raw/forestly_adsl.rda")