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87 remove datasets - decrease package size #396

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merged 2 commits into from
Dec 13, 2024
Merged

87 remove datasets - decrease package size #396

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868d25a
reause datasets from teal.data
m7pr Dec 13, 2024
be7d89e
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
github-actions[bot] Dec 13, 2024
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4 changes: 2 additions & 2 deletions R/adtteSpec.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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$CNSR == 0)
#' MAE <- hermes::multi_assay_experiment
#' })
Expand Down
12 changes: 0 additions & 12 deletions R/data.R
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4 changes: 2 additions & 2 deletions R/forestplot.R
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Expand Up @@ -15,7 +15,7 @@
#'
#' data <- teal_data()
#' data <- within(data, {
#' ADTTE <- teal.modules.hermes::rADTTE %>%
#' ADTTE <- teal.data::rADTTE %>%
#' dplyr::mutate(is_event = .data$CNSR == 0)
#' MAE <- hermes::multi_assay_experiment
#' })
Expand Down Expand Up @@ -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$CNSR == 0)
MAE <- hermes::multi_assay_experiment # nolint
})
Expand Down
4 changes: 2 additions & 2 deletions R/km.R
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Expand Up @@ -16,7 +16,7 @@
#'
#' data <- teal_data()
#' data <- within(data, {
#' ADTTE <- teal.modules.hermes::rADTTE %>%
#' ADTTE <- teal.data::rADTTE %>%
#' dplyr::mutate(is_event = .data$CNSR == 0)
#' MAE <- hermes::multi_assay_experiment
#' })
Expand Down Expand Up @@ -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
})
Expand Down
5 changes: 0 additions & 5 deletions data-raw/data.R
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2 changes: 1 addition & 1 deletion man/adtteSpecServer.Rd
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2 changes: 1 addition & 1 deletion man/h_km_mae_to_adtte.Rd
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20 changes: 0 additions & 20 deletions man/rADTTE.Rd
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2 changes: 1 addition & 1 deletion man/tm_g_forest_tte.Rd
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2 changes: 1 addition & 1 deletion man/tm_g_km.Rd
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4 changes: 2 additions & 2 deletions tests/testthat/adtteSpec/app.R
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Expand Up @@ -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))"
)

Expand Down
12 changes: 6 additions & 6 deletions tests/testthat/test-adtteSpec.R
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Expand Up @@ -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(
Expand All @@ -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(
Expand All @@ -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(
Expand All @@ -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(
Expand All @@ -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

Expand Down Expand Up @@ -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.
Expand Down
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