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pawelrudependabot-preview[bot]
pawelru
and
dependabot-preview[bot]
authored
use of roxy.shinylive (#1230)
similar to insightsengineering/teal.modules.general#775 - add "Examples in Shinylive" section where appropriate - modify examples code to use `teal_data()` everywhere - add a new "Playground" section in the README with links to the shinylive - include shinylive iframe in the getting started vignette --------- Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
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‎.gitignore‎

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@@ -29,3 +29,5 @@ vignettes/*.R
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coverage.*
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tests/testthat/_snaps/**/*.new.md
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tests/testthat/_snaps/**/*.new.svg
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/doc/
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/Meta/

‎DESCRIPTION‎

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@@ -71,6 +71,7 @@ Suggests:
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lubridate (>= 1.7.9),
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nestcolor (>= 0.1.0),
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pkgload,
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roxy.shinylive,
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rvest,
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shinytest2,
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styler,
@@ -90,12 +91,12 @@ Config/Needs/verdepcheck: insightsengineering/teal,
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insightsengineering/teal.widgets, insightsengineering/tern.gee,
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insightsengineering/tern.mmrm, shosaco/vistime, tidyverse/forcats,
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yihui/knitr, tidyverse/lubridate, insightsengineering/nestcolor,
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r-lib/pkgload, tidyverse/rvest, rstudio/shinytest2, r-lib/styler,
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r-lib/pkgload, insightsengineering/roxy.shinylive, tidyverse/rvest, rstudio/shinytest2, r-lib/styler,
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r-lib/testthat, r-lib/withr
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Config/Needs/website: insightsengineering/nesttemplate
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Config/testthat/edition: 3
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Encoding: UTF-8
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Language: en-US
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LazyData: true
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Roxygen: list(markdown = TRUE)
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Roxygen: list(markdown = TRUE, packages = c("roxy.shinylive"))
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RoxygenNote: 7.3.2

‎R/tm_a_gee.R‎

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@@ -135,8 +135,14 @@ template_a_gee <- function(output_table,
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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(dplyr)
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#'
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#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl
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#' ) %>%
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#' droplevels()
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#' })
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#' datanames <- c("ADSL", "ADQS")
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#' datanames(data) <- datanames
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#' join_keys(data) <- default_cdisc_join_keys[datanames]
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#' datanames(data) <- c("ADSL", "ADQS")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' app <- init(
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#' data = data,

‎R/tm_a_mmrm.R‎

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@@ -462,8 +462,14 @@ template_mmrm_plots <- function(fit_name,
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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(dplyr)
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#'
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#' arm_ref_comp <- list(
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#' ARMCD = list(
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#' ref = "ARM B",
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#' as.factor() #' making consecutive numeric factor
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#' )
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#' })
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#' datanames(data) <- c("ADSL", "ADQS")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' datanames <- c("ADSL", "ADQS")
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#' datanames(data) <- datanames
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#' join_keys(data) <- default_cdisc_join_keys[datanames]
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#' app <- init(
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#' data = data,
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#' modules = modules(

‎R/tm_g_barchart_simple.R‎

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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(nestcolor)
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#' library(dplyr)
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#'
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#' ADSL <- tmc_ex_adsl %>%
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#' mutate(ITTFL = factor("Y") %>%
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#' with_label("Intent-To-Treat Population Flag"))
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#' ADAE <- tmc_ex_adae %>%
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#' filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
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#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl %>%
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#' mutate(ITTFL = factor("Y") %>%
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#' with_label("Intent-To-Treat Population Flag"))
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#' ADAE <- tmc_ex_adae %>%
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#' filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
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#' })
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#' datanames(data) <- c("ADSL", "ADAE")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' ADSL <- data[["ADSL"]]
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#' ADAE <- data[["ADAE"]]
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#'
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#' app <- init(
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#' data = cdisc_data(
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#' ADSL = ADSL,
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#' ADAE = ADAE,
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#' code = "ADSL <- tmc_ex_adsl %>%
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#' mutate(ITTFL = factor(\"Y\") %>%
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#' with_label(\"Intent-To-Treat Population Flag\"))
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#' ADAE <- tmc_ex_adae %>%
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#' filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
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#' ),
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#' data = data,
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#' modules = modules(
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#' tm_g_barchart_simple(
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#' label = "ADAE Analysis",

‎R/tm_g_ci.R‎

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@@ -189,21 +189,27 @@ template_g_ci <- function(dataname,
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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(nestcolor)
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#'
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#' ADSL <- tmc_ex_adsl
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#' ADLB <- tmc_ex_adlb
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#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl
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#' ADLB <- tmc_ex_adlb
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#' })
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#' datanames(data) <- c("ADSL", "ADLB")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' ADSL <- data[["ADSL"]]
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#' ADLB <- data[["ADLB"]]
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#'
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#' app <- init(
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#' data = cdisc_data(
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#' ADSL = ADSL,
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#' ADLB = ADLB,
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#' code = "
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#' ADSL <- tmc_ex_adsl
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#' ADLB <- tmc_ex_adlb
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#' "
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#' ),
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#' data = data,
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#' modules = modules(
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#' tm_g_ci(
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#' label = "Confidence Interval Plot",
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#' )
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#' )
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#' )
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#' ),
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#' header = "Example of Confidence Interval Plot",
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#' footer = tags$p(
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#' class = "text-muted", "Source: `teal.modules.clinical::tm_g_ci`"
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#' )
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#' )
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#' if (interactive()) {

‎R/tm_g_forest_rsp.R‎

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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(nestcolor)
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#' library(dplyr)
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#'
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#' ADSL <- tmc_ex_adsl
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#' ADRS <- tmc_ex_adrs %>%
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#' mutate(AVALC = d_onco_rsp_label(AVALC) %>%
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#' with_label("Character Result/Finding")) %>%
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#' filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
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#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl
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#' ADRS <- tmc_ex_adrs %>%
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#' mutate(AVALC = d_onco_rsp_label(AVALC) %>%
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#' with_label("Character Result/Finding")) %>%
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#' filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
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#' })
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#' datanames(data) <- c("ADSL", "ADRS")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' ADSL <- data[["ADSL"]]
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#' ADRS <- data[["ADRS"]]
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#'
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#' arm_ref_comp <- list(
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#' ARM = list(
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#' )
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#'
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#' app <- init(
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#' data = cdisc_data(
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#' ADSL = ADSL,
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#' ADRS = ADRS,
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#' code = "
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#' ADSL <- tmc_ex_adsl
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#' ADRS <- tmc_ex_adrs %>%
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#' mutate(AVALC = d_onco_rsp_label(AVALC) %>%
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#' with_label(\"Character Result/Finding\")) %>%
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#' filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")
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#' "
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#' ),
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#' data = data,
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#' modules = modules(
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#' tm_g_forest_rsp(
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#' label = "Forest Response",

‎R/tm_g_forest_tte.R‎

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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(nestcolor)
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#' library(dplyr)
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#'
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#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl
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#' ADTTE <- tmc_ex_adtte
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#' ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
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#' })
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#' datanames(data) <- c("ADSL", "ADTTE")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' ADSL <- tmc_ex_adsl
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#' ADTTE <- tmc_ex_adtte
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#' ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
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#' ADSL <- data[["ADSL"]]
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#' ADTTE <- data[["ADTTE"]]
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#'
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#' arm_ref_comp <- list(
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#' ARM = list(
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#' )
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#'
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#' app <- init(
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#' data = cdisc_data(
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#' ADSL = ADSL,
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#' ADTTE = ADTTE,
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#' code = "
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#' ADSL <- tmc_ex_adsl
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#' ADTTE <- tmc_ex_adtte
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#' ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\"Race\")
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#' "
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#' ),
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#' data = data,
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#' modules = modules(
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#' tm_g_forest_tte(
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#' label = "Forest Survival",

‎R/tm_g_ipp.R‎

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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(nestcolor)
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#' library(dplyr)
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#'
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#' ADSL <- tmc_ex_adsl %>%
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#' slice(1:20) %>%
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#' df_explicit_na()
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#' ADLB <- tmc_ex_adlb %>%
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#' filter(USUBJID %in% ADSL$USUBJID) %>%
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#' df_explicit_na() %>%
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#' filter(AVISIT != "SCREENING")
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#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl %>%
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#' slice(1:20) %>%
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#' df_explicit_na()
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#' ADLB <- tmc_ex_adlb %>%
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#' filter(USUBJID %in% ADSL$USUBJID) %>%
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#' df_explicit_na() %>%
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#' filter(AVISIT != "SCREENING")
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#' })
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#' datanames(data) <- c("ADSL", "ADLB")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
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#' ADSL <- data[["ADSL"]]
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#' ADLB <- data[["ADLB"]]
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#'
194207
#' app <- init(
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#' data = cdisc_data(
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#' ADSL = ADSL,
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#' ADLB = ADLB,
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#' code = "
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#' ADSL <- tmc_ex_adsl %>% slice(1:20) %>% df_explicit_na()
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#' ADLB <- tmc_ex_adlb %>% filter(USUBJID %in% ADSL$USUBJID) %>%
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#' df_explicit_na() %>% filter(AVISIT != \"SCREENING\")
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#' "
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#' ),
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#' data = data,
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#' modules = modules(
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#' tm_g_ipp(
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#' label = "Individual Patient Plot",

‎R/tm_g_km.R‎

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#'
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#' @inherit module_arguments return seealso
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#'
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#' @examplesShinylive
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#' library(teal.modules.clinical)
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#' interactive <- function() TRUE
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#' {{ next_example }}
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#'
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#' @examples
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#' library(nestcolor)
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#'
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#' ADSL <- tmc_ex_adsl
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#' ADTTE <- tmc_ex_adtte
282+
#' data <- teal_data()
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#' data <- within(data, {
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#' ADSL <- tmc_ex_adsl
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#' ADTTE <- tmc_ex_adtte
286+
#' })
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#' datanames(data) <- c("ADSL", "ADTTE")
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#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
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#'
290+
#' ADSL <- data[["ADSL"]]
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#' ADTTE <- data[["ADTTE"]]
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#'
280293
#' arm_ref_comp <- list(
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#' ACTARMCD = list(
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#' )
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#'
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#' app <- init(
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#' data = cdisc_data(
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#' ADSL = ADSL,
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#' ADTTE = ADTTE,
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#' code = "
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#' ADSL <- tmc_ex_adsl
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#' ADTTE <- tmc_ex_adtte
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#' "
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#' ),
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#' data = data,
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#' modules = modules(
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#' tm_g_km(
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#' label = "Kaplan-Meier Plot",

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