339 migrate to teal data@78 simplify joinkeys@main

NEWS.md

@@ -4,6 +4,10 @@
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.
 * Disabled the select input for `assaySpec` and `adtteSpec` when there are no options available.
 
+### Enhancements
+
+* Updated the documentation and vignettes with the new way of specifying data for `teal::init()`. The `data` argument accepts `teal_data` object.
+
 # teal.modules.hermes 0.1.5
 
 ### Bug Fixes

design/design_km.Rmd

@@ -140,36 +140,32 @@ library(teal)
 library(hermes)
 library(random.cdisc.data)
 library(dplyr)
-adsl <- cdisc_dataset("ADSL", radsl(cached = TRUE, na_percentage = 0.2)) %>%
-  mutate_dataset(
-    "ADSL$SEX[1:20] <- NA
-     ADSL$AGE[21:30] <- Inf
-     ADSL$AGE[31:40] <- NaN
-     ADSL$EOSDT[51:60] <- NA
-     ADSL$EOSDT[71:70] <- NA
-     ADSL$all_na <- NA
-     ADSL$unknown <- as.list(ADSL$SEX)"
-  )
-adtte <- cdisc_dataset("ADTTE", radtte(cached = TRUE, seed = 1)) %>%
-  mutate_dataset(
-    "ADTTE$CNSR <- as.logical(ADTTE$CNSR)
-     ADTTE$CNSR[100:110] <- NA"
-  )
 
-mae <- multi_assay_experiment # from hermes
-mae <- dataset("MAE", mae)
+adsl = radsl(cached = TRUE, na_percentage = 0.2)
+adsl$SEX[1:20] <- NA
+adsl$AGE[21:30] <- Inf
+adsl$AGE[31:40] <- NaN
+adsl$EOSDT[51:60] <- NA
+adsl$EOSDT[71:70] <- NA
+adsl$all_na <- NA
+adsl$unknown <- as.list(ADSL$SEX)
+
+adtte = radtte(cached = TRUE, seed = 1)
+adtte$CNSR <- as.logical(ADTTE$CNSR)
+adtte$CNSR[100:110] <- NA
 
-adtte <- radtte(cached = TRUE, seed = 1) %>%
-  mutate(
-    "ADTTE$CNSR <- as.logical(ADTTE$CNSR)
-     ADTTE$CNSR[100:110] <- NA"
-  )
+mae <- multi_assay_experiment # from hermes
 
 choices_endpoints <- levels(adtte$PARAMCD)
 
+data <- teal_data(MAE = mae, ADSL = adsl, ADTTE = adtte)
+
+datanames <- datanames(data)
+data@join_keys <- cdisc_join_keys(!!!datanames)
+data@join_keys$mutate(
+  "MAE", "MAE", c("STUDYID", "USUBJID")
+)
 
-data <- teal_data(mae, adsl, adtte) %>%
-  mutate_join_keys("MAE", "MAE", c("STUDYID", "USUBJID"))
 ```
 
 ## App Launch

design/design_survival_forest.Rmd

@@ -24,17 +24,20 @@ We want to design a simple survival forest plot teal module.
 ## General module workflow
 
 ```{r}
-# Example ADSL data converted into a CDISCDataset object.
-adsl <- cdisc_dataset("ADSL", ex_adsl)
+# Example ADSL data
+adsl <- ex_adsl
 
-# Example ADTTE data converted into a CDISCDataset object.
-adtte <- cdisc_dataset("ADTTE", ex_adtte)
+# Example ADTTE data
+adtte <- ex_adtte
 
 # Example MAE data and merge datasets.
 MAE <- multi_assay_experiment
-mae <- dataset("MAE", MAE)
-data <- teal_data(mae, adsl, adtte) %>%
-  mutate_join_keys("MAE", "MAE", c("STUDYID", "USUBJID"))
+data <- teal_data(MAE = mae, ADSL = ex_adsl, ADTTE = ex_adtte)
+datanames <- datanames(data)
+data@join_keys <- cdisc_join_keys(!!!datanames)
+data@join_keys$mutate(
+  "MAE", "MAE", c("STUDYID", "USUBJID")
+)
 
 # Get raw ADTTE.
 adtte_raw <- get_raw_data(adtte)

design/mae_cdisc_example.R

@@ -95,27 +95,27 @@ srv_made_up_merge_pr <- function(input, output, session, datasets, dataname) {
 library(teal)
 library(hermes)
 library(random.cdisc.data)
-adsl <- cdisc_dataset("ADSL", radsl(cached = TRUE, na_percentage = 0.2)) %>%
-  mutate_dataset(
-    "ADSL$SEX[1:20] <- NA
-    ADSL$AGE[21:30] <- Inf
-    ADSL$AGE[31:40] <- NaN
-    ADSL$EOSDT[51:60] <- NA
-    ADSL$EOSDT[71:70] <- NA
-    ADSL$all_na <- NA
-    ADSL$unknown <- as.list(ADSL$SEX)"
-  )
-adtte <- cdisc_dataset("ADTTE", radtte(cached = TRUE)) %>%
-  mutate_dataset(
-    "ADTTE$CNSR <- as.logical(ADTTE$CNSR)
-    ADTTE$CNSR[100:110] <- NA"
-  )
+adsl = radsl(cached = TRUE, na_percentage = 0.2)
+adsl$SEX[1:20] <- NA
+adsl$AGE[21:30] <- Inf
+adsl$AGE[31:40] <- NaN
+adsl$EOSDT[51:60] <- NA
+adsl$EOSDT[71:70] <- NA
+adsl$all_na <- NA
+adsl$unknown <- as.list(ADSL$SEX)
 
+adtte = radtte(cached = TRUE)
+adtte$CNSR <- as.logical(ADTTE$CNSR)
+adtte$CNSR[100:110] <- NA
 
 mae <- multi_assay_experiment # from hermes
 
-data <- cdisc_data(dataset("MAE", mae), adsl, adtte) %>%
-  mutate_join_keys("MAE", "MAE", c("STUDYID", "USUBJID"))
+data <- cdisc_data(MAE = mae, ADSL = adsl, ADTTE = adtte)
+datanames <- datanames(data)
+data@join_keys <- cdisc_join_keys(!!!datanames)
+data@join_keys$mutate(
+  "MAE", "MAE", c("STUDYID", "USUBJID")
+)
 
 app <- init(
   data = data,