## ----knitr-config, include = FALSE--------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----load-gdr-libraries, echo = FALSE-----------------------------------------
library(gDRtestData)
library(gDRcore)
log_level <- futile.logger::flog.threshold("ERROR")

## ----fetch-import-test-data---------------------------------------------------
td <- gDRimport::get_test_data()

## ----merge-manifest-templates-results, include=FALSE--------------------------
loaded_data <-
  suppressMessages(
    gDRimport::load_data(
      gDRimport::manifest_path(td),
      gDRimport::template_path(td),
      gDRimport::result_path(td)
    )
  )
input_df <- merge_data(loaded_data$manifest, loaded_data$treatments, loaded_data$data)
head(input_df)

## ----execute-processing-pipeline, message = FALSE, results = FALSE, warning = FALSE----
mae <- runDrugResponseProcessingPipeline(input_df)

## ----inspect-mae-output-------------------------------------------------------
mae

## ----subset-single-agent-experiment-------------------------------------------
mae[["single-agent"]]

## ----session-info-------------------------------------------------------------
sessionInfo()