R/toxpiR-package.R

In toxpiR: Create ToxPi Prioritization Models

#' @keywords internal
"_PACKAGE"

## usethis namespace: start
## usethis namespace: end
NULL

# TXP_FILLS = c("dodgerblue",
#               "bisque",
#               "darkolivegreen3",
#               "darkorchid3",
#               "mistyrose2",
#               "darkgoldenrod1")
TXP_FILLS = c(
  "#f3622d",
  "#fba71b",
  "#57b757",
  "#41a9c9",
  "#4258c9",
  "#9a42c8",
  "#c84164",
  "#888888"
)

#' @name toxpiR-datasets
#' @title toxpiR data objects
#' @description Objects included in the toxpiR package, loaded with
#' [utils::data]
#' @aliases txp_example_input txp_example_model
#'
#' @usage data(txp_example_input, package = "toxpiR")
#' @usage data(txp_example_model, package = "toxpiR")
#'
#' @section txp_example_input:
#'
#' Small example input data to be used with [txpCalculateScores] in creating
#' [TxpResult] objects. A [base::data.frame] with 10 rows and 9 variables
#' \describe{
#'   \item{name}{Observation names}
#'   \item{metric#}{Input data for ToxPi models}
#' }
#'
#' @source <https://github.com/ToxPi/ToxPi-example-files>
#'
#' @section txp_example_model:
#'
#' Example [TxpModel] object intended for `txp_example_data`; model with 4
#' slices.
#'
#' @examples
#' data(txp_example_input, package = "toxpiR")
#' data(txp_example_model, package = "toxpiR")
#' txp_example_input
#' txp_example_model
#'
#' ## Code to create txp_example_model
#' tf1 <- TxpTransFuncList(linear = function(x) x)
#' sl <- TxpSliceList(s1 = TxpSlice(sprintf("metric%d", 1:2)),
#'                    s2 = TxpSlice("metric3"),
#'                    s3 = TxpSlice(sprintf("metric%d", 4:7),
#'                                  tf1[rep("linear", 4)]),
#'                    s4 = TxpSlice("metric8", tf1))
#' tf2 <- TxpTransFuncList(NULL, linear = function(x) x, NULL, NULL)
#' TxpModel(txpSlices = sl, txpWeights = c(2, 1, 3, 2), txpTransFuncs = tf2)
#'
#' @importFrom utils data

NULL