diff --git a/DESCRIPTION b/DESCRIPTION index 545c207de9..d176212f7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,13 +1,15 @@ Type: Package Package: teal Title: Exploratory Web Apps for Analyzing Clinical Trials Data -Version: 0.14.0.9046 -Date: 2024-02-09 +Version: 0.15.0 +Date: 2024-02-07 Authors@R: c( - person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")), + person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9533-457X")), person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"), - person("Aleksander", "Chlebowski", , "aleksander.chlebowski@contractors.roche.com", role = "aut"), + person("Aleksander", "Chlebowski", , "aleksander.chlebowski@contractors.roche.com", role = "aut", comment = c(ORCID = "0000-0001-5018-6294")), + person("Andre", "Verissimo", , "andre.verissimo@roche.com", role = "aut", comment = c(ORCID = "0000-0002-2212-339X")), person("Kartikeya", "Kirar", , "kartikeya.kirar@businesspartner.roche.com", role = "aut"), + person("Vedha", "Viyash", , "vedha.viyash@roche.com", role = "aut"), person("Marcin", "Kosinski", , "marcin.kosinski.mk1@roche.com", role = "aut"), person("Adrian", "Waddell", , "adrian.waddell@gene.com", role = "aut"), person("Chendi", "Liao", , "chendi.liao@roche.com", role = "rev"), @@ -31,8 +33,8 @@ BugReports: https://github.com/insightsengineering/teal/issues Depends: R (>= 4.0), shiny (>= 1.7.0), - teal.data (>= 0.3.0.9017), - teal.slice (>= 0.4.0.9027) + teal.data (>= 0.4.0), + teal.slice (>= 0.5.0) Imports: checkmate (>= 2.1.0), jsonlite, @@ -43,7 +45,7 @@ Imports: rlang (>= 1.0.0), shinyjs, stats, - teal.code (>= 0.3.0.9009), + teal.code (>= 0.5.0), teal.logger (>= 0.1.1), teal.reporter (>= 0.2.0), teal.widgets (>= 0.4.0), diff --git a/NEWS.md b/NEWS.md index c7c54e2238..17f3021cdf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal 0.14.0.9046 +# teal 0.15.0 ### New features diff --git a/R/init.R b/R/init.R index 01af3c0eea..2967290780 100644 --- a/R/init.R +++ b/R/init.R @@ -105,7 +105,7 @@ init <- function(data, ## `data` if (inherits(data, "TealData")) { lifecycle::deprecate_stop( - when = "0.99.0", + when = "0.15.0", what = "init(data)", paste( "TealData is no longer supported. Use teal_data() instead.", diff --git a/R/tdata.R b/R/tdata.R index d079b57eb6..b0c6d298d3 100644 --- a/R/tdata.R +++ b/R/tdata.R @@ -46,7 +46,7 @@ #' @export new_tdata <- function(data, code = "", join_keys = NULL, metadata = NULL) { lifecycle::deprecate_soft( - when = "0.99.0", + when = "0.15.0", what = "tdata()", details = paste( "tdata is deprecated and will be removed in the next release. Use `teal_data` instead.\n", diff --git a/README.md b/README.md index 6c5ec4d8e7..a7509a363a 100644 --- a/README.md +++ b/README.md @@ -78,13 +78,13 @@ library(teal) app <- init( data = teal_data(iris = iris), modules = list( - module( + module( label = "iris histogram", server = function(input, output, session, data) { updateSelectInput(session = session, inputId = "var", choices = names(data()[["iris"]])[1:4]) - + output$hist <- renderPlot({ req(input$var) hist(x = data()[["iris"]][[input$var]]) @@ -108,7 +108,7 @@ shinyApp(app$ui, app$server) ![App recording](man/figures/readme_app.webp) -Please see [`teal.gallery`](https://insightsengineering.github.io/teal.gallery) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog) to see examples of `teal` apps. +Please see [`teal.gallery`](https://insightsengineering.github.io/teal.gallery/) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog/) to see examples of `teal` apps. Please start with the ["Technical Blueprint" article](https://insightsengineering.github.io/teal/latest-tag/articles/blueprint/index.html), ["Getting Started" article](https://insightsengineering.github.io/teal/latest-tag/articles/teal.html), and then other [package vignettes](https://insightsengineering.github.io/teal/latest-tag/articles/index.html) for more detailed guide. diff --git a/inst/WORDLIST b/inst/WORDLIST index e1ada3e7b6..143e7a954f 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -23,3 +23,4 @@ tabsetted themer theming uncheck +ORCID diff --git a/man/teal-package.Rd b/man/teal-package.Rd index 027c900c47..e62434e0ca 100644 --- a/man/teal-package.Rd +++ b/man/teal-package.Rd @@ -23,13 +23,15 @@ Useful links: } \author{ -\strong{Maintainer}: Dawid Kaledkowski \email{dawid.kaledkowski@roche.com} +\strong{Maintainer}: Dawid Kaledkowski \email{dawid.kaledkowski@roche.com} (\href{https://orcid.org/0000-0001-9533-457X}{ORCID}) Authors: \itemize{ \item Pawel Rucki \email{pawel.rucki@roche.com} - \item Aleksander Chlebowski \email{aleksander.chlebowski@contractors.roche.com} + \item Aleksander Chlebowski \email{aleksander.chlebowski@contractors.roche.com} (\href{https://orcid.org/0000-0001-5018-6294}{ORCID}) + \item Andre Verissimo \email{andre.verissimo@roche.com} (\href{https://orcid.org/0000-0002-2212-339X}{ORCID}) \item Kartikeya Kirar \email{kartikeya.kirar@businesspartner.roche.com} + \item Vedha Viyash \email{vedha.viyash@roche.com} \item Marcin Kosinski \email{marcin.kosinski.mk1@roche.com} \item Adrian Waddell \email{adrian.waddell@gene.com} \item Nikolas Burkoff diff --git a/tests/testthat/test-tdata.R b/tests/testthat/test-tdata.R index ada4ebae18..faef6351d3 100644 --- a/tests/testthat/test-tdata.R +++ b/tests/testthat/test-tdata.R @@ -2,6 +2,7 @@ withr::local_options(lifecycle_verbosity = "quiet") # ---- constructor ---- testthat::test_that("new_tdata accepts reactive and not reactive MAE and data.frames", { + testthat::skip_if_not_installed("MultiAssayExperiment") utils::data(miniACC, package = "MultiAssayExperiment") testthat::expect_no_error( @@ -179,6 +180,7 @@ testthat::test_that("get_code_tdata returns character code", { # ---- tdata2env ---- testthat::test_that("tdata2env returns environment containing tdata contents ", { + testthat::skip_if_not_installed("MultiAssayExperiment") utils::data(miniACC, package = "MultiAssayExperiment") my_tdata <- new_tdata(data = list(iris = iris, mae = reactive(miniACC))) diff --git a/vignettes/getting-started-with-teal.Rmd b/vignettes/getting-started-with-teal.Rmd index f1947a53fb..89187a0d77 100644 --- a/vignettes/getting-started-with-teal.Rmd +++ b/vignettes/getting-started-with-teal.Rmd @@ -10,7 +10,7 @@ vignette: > ## Introduction -`teal` is a shiny-based interactive exploration framework for analyzing data, with particular emphasis on CDISC clinical trial data. +`teal` is a shiny-based interactive exploration framework for analyzing data, with particular emphasis on CDISC clinical trial data. `teal` applications allow their users to: * "Pull" in data from external data sources @@ -92,7 +92,7 @@ It is also possible to specify relationships between the datasets using the `joi If data is not available and has to be pulled from a remote source, `init` must receive a `teal_data_module` that specifies how to obtain the desired datasets and put them into a `teal_data` object. See [this vignette](data-as-shiny-module.html) for details. -In order to use CDISC clinical trial data in a `teal` application the `cdisc_data` function is used instead. +In order to use CDISC clinical trial data in a `teal` application the `cdisc_data` function is used instead. Custom `SDTM` standards can be handled with `teal_data` and `join_keys`. For further details, we recommend exploring the [`teal.data`](https://insightsengineering.github.io/teal.data/) package documentation. @@ -120,7 +120,7 @@ This report can then be downloaded and a special _Report Previewer_ module will `teal` hands over data with reproducible code to every module included in the application. Note that `teal` does not display the code, that is the modules' responsibility. For example, the `example_module` function used above shows the code in the main panel together with other outputs. -For more details see [this vignette](reproducible-code.html). +For more details see [this vignette](including-data-in-teal-applications.html). ## Where to go next