diff --git a/R/adtteSpec.R b/R/adtteSpec.R index ea09b999..da48d12a 100644 --- a/R/adtteSpec.R +++ b/R/adtteSpec.R @@ -18,7 +18,7 @@ #' @examples #' library(dplyr) #' mae <- hermes::multi_assay_experiment -#' adtte <- teal.modules.hermes::rADTTE %>% +#' adtte <- teal.data::rADTTE %>% #' dplyr::mutate(CNSR = as.logical(CNSR)) #' #' new_adtte <- h_km_mae_to_adtte( @@ -218,7 +218,7 @@ adtteSpecInput <- function(inputId, # nolint #' data <- teal_data() #' data <- within(data, { #' ADSL <- teal.data::rADSL -#' ADTTE <- teal.modules.hermes::rADTTE %>% +#' ADTTE <- teal.data::rADTTE %>% #' dplyr::mutate(is_event = .data$CNSR == 0) #' MAE <- hermes::multi_assay_experiment #' }) diff --git a/R/data.R b/R/data.R deleted file mode 100644 index 59e400ff..00000000 --- a/R/data.R +++ /dev/null @@ -1,12 +0,0 @@ -#' Random Time to Event Analysis Dataset -#' -#' @description Random Time to Event Analysis Dataset -#' @docType data -#' -#' @usage rADTTE -#' -#' @keywords datasets internal -#' -#' @source internal -#' @name rADTTE -"rADTTE" diff --git a/R/forestplot.R b/R/forestplot.R index 293378cb..63f9f44c 100644 --- a/R/forestplot.R +++ b/R/forestplot.R @@ -15,7 +15,7 @@ #' #' data <- teal_data() #' data <- within(data, { -#' ADTTE <- teal.modules.hermes::rADTTE %>% +#' ADTTE <- teal.data::rADTTE %>% #' dplyr::mutate(is_event = .data$CNSR == 0) #' MAE <- hermes::multi_assay_experiment #' }) @@ -307,7 +307,7 @@ srv_g_forest_tte <- function(id, sample_tm_g_forest_tte <- function(.test = FALSE) { # nolint data <- teal_data() data <- within(data, { - ADTTE <- teal.modules.hermes::rADTTE %>% # nolint + ADTTE <- teal.data::rADTTE %>% # nolint dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment # nolint }) diff --git a/R/km.R b/R/km.R index f52eefc0..f88efcd0 100644 --- a/R/km.R +++ b/R/km.R @@ -16,7 +16,7 @@ #' #' data <- teal_data() #' data <- within(data, { -#' ADTTE <- teal.modules.hermes::rADTTE %>% +#' ADTTE <- teal.data::rADTTE %>% #' dplyr::mutate(is_event = .data$CNSR == 0) #' MAE <- hermes::multi_assay_experiment #' }) @@ -303,7 +303,7 @@ srv_g_km <- function(id, sample_tm_g_km <- function(.test = FALSE) { # nolint data <- teal_data() data <- within(data, { - ADTTE <- teal.modules.hermes::rADTTE %>% # nolint + ADTTE <- teal.data::rADTTE %>% # nolint dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment # nolint }) diff --git a/data-raw/data.R b/data-raw/data.R deleted file mode 100644 index 7d2fc0f3..00000000 --- a/data-raw/data.R +++ /dev/null @@ -1,5 +0,0 @@ -## code to prepare `data` for testing examples -library(random.cdisc.data) - -rADTTE <- random.cdisc.data::cadtte -usethis::use_data(rADTTE) diff --git a/data/rADTTE.rda b/data/rADTTE.rda deleted file mode 100644 index 08fb284e..00000000 Binary files a/data/rADTTE.rda and /dev/null differ diff --git a/man/adtteSpecServer.Rd b/man/adtteSpecServer.Rd index ebeb23dd..a22523ad 100644 --- a/man/adtteSpecServer.Rd +++ b/man/adtteSpecServer.Rd @@ -143,7 +143,7 @@ my_app <- function() { data <- teal_data() data <- within(data, { ADSL <- teal.data::rADSL - ADTTE <- teal.modules.hermes::rADTTE \%>\% + ADTTE <- teal.data::rADTTE \%>\% dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment }) diff --git a/man/h_km_mae_to_adtte.Rd b/man/h_km_mae_to_adtte.Rd index e80d32dd..9cc8e802 100644 --- a/man/h_km_mae_to_adtte.Rd +++ b/man/h_km_mae_to_adtte.Rd @@ -45,7 +45,7 @@ the original gene IDs (or labels), in particular white space and colons are remo \examples{ library(dplyr) mae <- hermes::multi_assay_experiment -adtte <- teal.modules.hermes::rADTTE \%>\% +adtte <- teal.data::rADTTE \%>\% dplyr::mutate(CNSR = as.logical(CNSR)) new_adtte <- h_km_mae_to_adtte( diff --git a/man/rADTTE.Rd b/man/rADTTE.Rd deleted file mode 100644 index 56d85983..00000000 --- a/man/rADTTE.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{rADTTE} -\alias{rADTTE} -\title{Random Time to Event Analysis Dataset} -\format{ -An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 2000 rows and 67 columns. -} -\source{ -internal -} -\usage{ -rADTTE -} -\description{ -Random Time to Event Analysis Dataset -} -\keyword{datasets} -\keyword{internal} diff --git a/man/sampleVarSpecServer.Rd b/man/sampleVarSpecServer.Rd index a5bbe24a..e218e58c 100644 --- a/man/sampleVarSpecServer.Rd +++ b/man/sampleVarSpecServer.Rd @@ -44,7 +44,7 @@ from.} \item{label_modal_title}{(\code{string})\cr title for the dialog that asks for the text input.} } \value{ -Reactive \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} which can be used as +Reactive \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} which can be used as input for the relevant \code{hermes} functions. } \description{ diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index c05f6d36..924c84fe 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -127,7 +127,7 @@ library(dplyr) data <- teal_data() data <- within(data, { - ADTTE <- teal.modules.hermes::rADTTE \%>\% + ADTTE <- teal.data::rADTTE \%>\% dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment }) diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd index cb0d9c29..a45d2826 100644 --- a/man/tm_g_km.Rd +++ b/man/tm_g_km.Rd @@ -118,7 +118,7 @@ library(dplyr) data <- teal_data() data <- within(data, { - ADTTE <- teal.modules.hermes::rADTTE \%>\% + ADTTE <- teal.data::rADTTE \%>\% dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment }) diff --git a/tests/testthat/adtteSpec/app.R b/tests/testthat/adtteSpec/app.R index 9c56af07..97694c2a 100644 --- a/tests/testthat/adtteSpec/app.R +++ b/tests/testthat/adtteSpec/app.R @@ -65,14 +65,14 @@ server <- function(id, } my_app <- function() { - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(is_event = (.data$CNSR == 0)) data <- teal_data( ADTTE = adtte, MAE = hermes::multi_assay_experiment, code = - "adtte <- teal.modules.hermes::rADTTE %>% + "adtte <- teal.data::rADTTE %>% dplyr::mutate(is_event = (.data$CNSR == 0))" ) diff --git a/tests/testthat/test-adtteSpec.R b/tests/testthat/test-adtteSpec.R index e74a8406..55447fb2 100644 --- a/tests/testthat/test-adtteSpec.R +++ b/tests/testthat/test-adtteSpec.R @@ -2,7 +2,7 @@ test_that("h_km_mae_to_adtte function works as expected with a single gene", { mae <- hermes::multi_assay_experiment - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(CNSR = as.logical(.data$CNSR)) result <- h_km_mae_to_adtte( @@ -19,7 +19,7 @@ test_that("h_km_mae_to_adtte function also works when some ID variables are fact mae <- hermes::multi_assay_experiment SummarizedExperiment::colData(mae)$USUBJID <- # nolint factor(SummarizedExperiment::colData(mae)$USUBJID) - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(USUBJID = factor(USUBJID)) result <- h_km_mae_to_adtte( @@ -34,7 +34,7 @@ test_that("h_km_mae_to_adtte function also works when some ID variables are fact test_that("h_km_mae_to_adtte function works as expected with multiple genes", { mae <- hermes::multi_assay_experiment - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(CNSR = as.logical(.data$CNSR)) result <- h_km_mae_to_adtte( @@ -49,7 +49,7 @@ test_that("h_km_mae_to_adtte function works as expected with multiple genes", { test_that("h_km_mae_to_adtte function works as expected with a gene signature", { mae <- hermes::multi_assay_experiment - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(CNSR = as.logical(.data$CNSR)) result <- h_km_mae_to_adtte( @@ -65,7 +65,7 @@ test_that("h_km_mae_to_adtte function works as expected with a gene signature", test_that("h_km_mae_to_adtte fails as expected with invalid settings", { mae <- hermes::multi_assay_experiment - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(CNSR = as.logical(.data$CNSR)) good_adtte <- adtte @@ -97,7 +97,7 @@ test_that("h_km_mae_to_adtte fails as expected with invalid settings", { test_that("h_km_mae_to_adtte warns when patients are not in ADTTE and therefore removed", { mae <- hermes::multi_assay_experiment - adtte <- teal.modules.hermes::rADTTE %>% + adtte <- teal.data::rADTTE %>% dplyr::mutate(CNSR = as.logical(.data$CNSR)) # Example with no matched patient IDs.