From 55973efe3d8ca6871005545d2fd70a230af798f2 Mon Sep 17 00:00:00 2001 From: Carson Date: Thu, 18 Feb 2021 09:55:23 -0600 Subject: [PATCH 1/6] Follow up to #1706: When runtime:shiny is used with bslib, call shiny::bootstrapLib() inside html_document_base()'s preprocessor (instead of at run()-time) The former time-point is too early -- it doesn't allow other output formats like flex_dashboard to modify the theme before passing it to html_document_base() --- R/html_document_base.R | 15 +++++++++++---- R/shiny.R | 17 +++++------------ R/shiny_prerendered.R | 20 +------------------- 3 files changed, 17 insertions(+), 35 deletions(-) diff --git a/R/html_document_base.R b/R/html_document_base.R index f89cb64e20..d2188e16dd 100644 --- a/R/html_document_base.R +++ b/R/html_document_base.R @@ -89,10 +89,17 @@ html_document_base <- function(theme = NULL, format_deps <- append(format_deps, html_dependency_header_attrs()) if (!is.null(theme)) { format_deps <- append(format_deps, list(html_dependency_jquery())) - format_deps <- append(format_deps, bootstrap_dependencies( - # If TRUE, an as_bs_theme(theme) has been set globally (so users may customize it) - if (is_bs_theme(theme)) bslib::bs_global_get() else theme - )) + # theme was set globally pre-knit, and it may be modified during knit + if (is_bs_theme(theme)) { + theme <- bslib::bs_global_get() + } + bootstrap_deps <- if (is_bs_theme(theme) && is_shiny(runtime)) { + if (!is_available("shiny", "1.6.0")) stop("Using a {bslib} theme with `runtime: shiny` requires shiny 1.6.0 or higher.") + list(shiny::bootstrapLib(theme)) + } else { + bootstrap_dependencies(theme) + } + format_deps <- append(format_deps, htmltools::resolveDependencies(bootstrap_deps)) } else if (isTRUE(bootstrap_compatible) && is_shiny(runtime)) { # If we can add bootstrap for Shiny, do it diff --git a/R/shiny.R b/R/shiny.R index c0c57fe9ef..a174d3e02c 100644 --- a/R/shiny.R +++ b/R/shiny.R @@ -131,19 +131,13 @@ run <- function(file = "index.Rmd", dir = dirname(file), default_file = NULL, # determine the runtime of the target file target_file <- file %||% file.path(dir, default_file) - yaml_front <- if (length(target_file)) yaml_front_matter(target_file) - runtime <- yaml_front$runtime - theme <- render_args$output_options$theme - if (length(target_file)) { - format <- output_format_from_yaml_front_matter(read_utf8(target_file)) - theme <- format$options$theme - } + runtime <- if (length(target_file)) yaml_front_matter(target_file) # run using the requested mode if (is_shiny_prerendered(runtime)) { # get the pre-rendered shiny app - app <- shiny_prerendered_app(target_file, render_args = render_args, theme = theme) + app <- shiny_prerendered_app(target_file, render_args = render_args) } else { # add rmd_resources handler on start @@ -158,7 +152,7 @@ run <- function(file = "index.Rmd", dir = dirname(file), default_file = NULL, # combine the user-supplied list of Shiny arguments with our own and start # the Shiny server; handle requests for the root (/) and any R markdown files # within - app <- shiny::shinyApp(ui = rmarkdown_shiny_ui(dir, default_file, theme), + app <- shiny::shinyApp(ui = rmarkdown_shiny_ui(dir, default_file), uiPattern = "^/$|^/index\\.html?$|^(/.*\\.[Rr][Mm][Dd])$", onStart = onStart, server = rmarkdown_shiny_server( @@ -317,7 +311,7 @@ rmarkdown_shiny_server <- function(dir, file, auto_reload, render_args) { } # create the Shiny UI function -rmarkdown_shiny_ui <- function(dir, file, theme) { +rmarkdown_shiny_ui <- function(dir, file) { function(req) { # map requests to / to requests for the default--index.Rmd, or another if # specified @@ -339,8 +333,7 @@ rmarkdown_shiny_ui <- function(dir, file, theme) { tags$div( tags$head( tags$script(src = "rmd_resources/rmd_loader.js"), - tags$link(href = "rmd_resources/rmd_loader.css", rel = "stylesheet"), - shiny_bootstrap_lib(theme) + tags$link(href = "rmd_resources/rmd_loader.css", rel = "stylesheet") ), # Shiny shows the outer conditionalPanel as long as the document hasn't diff --git a/R/shiny_prerendered.R b/R/shiny_prerendered.R index 2b22d8554b..855f01ce29 100644 --- a/R/shiny_prerendered.R +++ b/R/shiny_prerendered.R @@ -4,10 +4,7 @@ shiny_prerendered_app <- function(input_rmd, render_args, theme) { # get rendered html and capture dependencies html <- shiny_prerendered_html(input_rmd, render_args) - deps <- c( - htmltools::htmlDependencies(html), - shiny_bootstrap_lib(theme) - ) + deps <- htmltools::htmlDependencies(html) # create the server environment server_envir = new.env(parent = globalenv()) @@ -687,18 +684,3 @@ shiny_prerendered_data_file_name <- function(label, cache) { type <- ifelse(cache, ".cached", "") sprintf("%s%s.RData", label, type) } - -# Use me instead of html_dependency_bootstrap() in a shiny runtime to get -# dynamic theming (i.e., have it work with session$setCurrentTheme()) -shiny_bootstrap_lib <- function(theme) { - theme <- resolve_theme(theme) - if (!is_bs_theme(theme)) { - return(NULL) - } - if (!is_available("shiny", "1.5.0.9007")) { - stop( - "Using a {bslib} theme with `runtime: shiny` requires shiny 1.5.0.9007 or higher." - ) - } - shiny::bootstrapLib(theme) -} From 841f9f007476b647c5e369c13ad990ab45df5896 Mon Sep 17 00:00:00 2001 From: Carson Date: Fri, 19 Feb 2021 09:23:36 -0600 Subject: [PATCH 2/6] update news --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index cf4579bdfe..a832410b9c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,7 @@ rmarkdown 2.8 ================================================================================ +- Provided a `runtime: shiny` fix for output formats that pass a modified `bslib::bs_theme()` object to `html_document_base()`'s `theme` (thanks, @cpsievert, #2049). rmarkdown 2.7 ================================================================================ From 185182591ca92ec2eb83e131ef74cec0037af6cb Mon Sep 17 00:00:00 2001 From: Carson Date: Fri, 19 Feb 2021 12:13:00 -0600 Subject: [PATCH 3/6] bugfix --- R/shiny.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/shiny.R b/R/shiny.R index a174d3e02c..c460bdabdf 100644 --- a/R/shiny.R +++ b/R/shiny.R @@ -131,7 +131,7 @@ run <- function(file = "index.Rmd", dir = dirname(file), default_file = NULL, # determine the runtime of the target file target_file <- file %||% file.path(dir, default_file) - runtime <- if (length(target_file)) yaml_front_matter(target_file) + runtime <- if (length(target_file)) yaml_front_matter(target_file)$runtime # run using the requested mode if (is_shiny_prerendered(runtime)) { From de1edf743ae3f85351bbe1e31239bdb0e90a7494 Mon Sep 17 00:00:00 2001 From: Carson Date: Fri, 19 Feb 2021 13:20:59 -0600 Subject: [PATCH 4/6] Call setCurrentTheme() at run()-time so server code may be aware of it --- R/html_document_base.R | 3 +-- R/shiny.R | 20 +++++++++++++++++++- R/shiny_prerendered.R | 17 ++++++++++++++++- 3 files changed, 36 insertions(+), 4 deletions(-) diff --git a/R/html_document_base.R b/R/html_document_base.R index d2188e16dd..2009c16622 100644 --- a/R/html_document_base.R +++ b/R/html_document_base.R @@ -94,8 +94,7 @@ html_document_base <- function(theme = NULL, theme <- bslib::bs_global_get() } bootstrap_deps <- if (is_bs_theme(theme) && is_shiny(runtime)) { - if (!is_available("shiny", "1.6.0")) stop("Using a {bslib} theme with `runtime: shiny` requires shiny 1.6.0 or higher.") - list(shiny::bootstrapLib(theme)) + list(shiny_bootstrap_lib(theme)) } else { bootstrap_dependencies(theme) } diff --git a/R/shiny.R b/R/shiny.R index c460bdabdf..b666963e0e 100644 --- a/R/shiny.R +++ b/R/shiny.R @@ -131,7 +131,18 @@ run <- function(file = "index.Rmd", dir = dirname(file), default_file = NULL, # determine the runtime of the target file target_file <- file %||% file.path(dir, default_file) - runtime <- if (length(target_file)) yaml_front_matter(target_file)$runtime + yaml_front <- if (length(target_file)) yaml_front_matter(target_file) + runtime <- yaml_front$runtime + theme <- render_args$output_options$theme + # Let shiny::getCurrentTheme() know about the yaml's theme, so + # things like `bslib::bs_themer()` can work with prerendered documents. + # Also note that we add the actual shiny::bootstrapLib() dependency + # inside the document's pre-processing hook so the 'last' version of + # the theme wins out + if (length(target_file)) { + format <- output_format_from_yaml_front_matter(read_utf8(target_file)) + set_current_theme(resolve_theme(format$options$theme)) + } # run using the requested mode if (is_shiny_prerendered(runtime)) { @@ -579,3 +590,10 @@ read_shiny_deps <- function(files_dir) { list() } } + + +# shiny:::setCurrentTheme() was added in 1.6 (we may export in next version) +set_current_theme <- function(theme) { + set_theme <- asNamespace("shiny")$setCurrentTheme + if (is.function(set_theme)) set_theme(theme) +} diff --git a/R/shiny_prerendered.R b/R/shiny_prerendered.R index 855f01ce29..ffab81a103 100644 --- a/R/shiny_prerendered.R +++ b/R/shiny_prerendered.R @@ -1,6 +1,6 @@ # Create a shiny app object from an Rmd w/ runtime: shiny_prerendered -shiny_prerendered_app <- function(input_rmd, render_args, theme) { +shiny_prerendered_app <- function(input_rmd, render_args) { # get rendered html and capture dependencies html <- shiny_prerendered_html(input_rmd, render_args) @@ -684,3 +684,18 @@ shiny_prerendered_data_file_name <- function(label, cache) { type <- ifelse(cache, ".cached", "") sprintf("%s%s.RData", label, type) } + +# Use me instead of html_dependency_bootstrap() in a shiny runtime to get +# dynamic theming (i.e., have it work with session$setCurrentTheme()) +shiny_bootstrap_lib <- function(theme) { + theme <- resolve_theme(theme) + if (!is_bs_theme(theme)) { + return(NULL) + } + if (!is_available("shiny", "1.6.0")) { + stop( + "Using a {bslib} theme with `runtime: shiny` requires shiny 1.6.0 or higher." + ) + } + shiny::bootstrapLib(theme) +} From 5e6a9287b0d439b1286e8836ee96e844b3be9da0 Mon Sep 17 00:00:00 2001 From: Carson Date: Fri, 19 Feb 2021 13:29:24 -0600 Subject: [PATCH 5/6] Add a unit test for set_current_theme() --- tests/testthat/filee6521d8194fd.aux | 0 tests/testthat/filee6521d8194fd.log | 1073 +++++++++++++++++++++++++++ tests/testthat/filee6521d8194fd.pdf | Bin tests/testthat/packages.bib | 30 + tests/testthat/test-formats.knit.md | 86 +++ tests/testthat/test-formats.utf8.md | 86 +++ tests/testthat/test-shiny.R | 10 + 7 files changed, 1285 insertions(+) create mode 100644 tests/testthat/filee6521d8194fd.aux create mode 100644 tests/testthat/filee6521d8194fd.log create mode 100644 tests/testthat/filee6521d8194fd.pdf create mode 100644 tests/testthat/packages.bib create mode 100644 tests/testthat/test-formats.knit.md create mode 100644 tests/testthat/test-formats.utf8.md diff --git a/tests/testthat/filee6521d8194fd.aux b/tests/testthat/filee6521d8194fd.aux new file mode 100644 index 0000000000..e69de29bb2 diff --git 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for font family +(microtype) `lms \ No newline at end of file diff --git a/tests/testthat/filee6521d8194fd.pdf b/tests/testthat/filee6521d8194fd.pdf new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/tests/testthat/packages.bib b/tests/testthat/packages.bib new file mode 100644 index 0000000000..b19d0217ba --- /dev/null +++ b/tests/testthat/packages.bib @@ -0,0 +1,30 @@ +@Manual{R-knitr, + title = {knitr: A General-Purpose Package for Dynamic Report Generation in R}, + author = {Yihui Xie}, + year = {2021}, + note = {R package version 1.31}, + url = {https://yihui.org/knitr/}, +} + +@Book{knitr2015, + title = {Dynamic Documents with {R} and knitr}, + author = {Yihui Xie}, + publisher = {Chapman and Hall/CRC}, + address = {Boca Raton, Florida}, + year = {2015}, + edition = {2nd}, + note = {ISBN 978-1498716963}, + url = {https://yihui.org/knitr/}, +} + +@InCollection{knitr2014, + booktitle = {Implementing Reproducible Computational Research}, + editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng}, + title = {knitr: A Comprehensive Tool for Reproducible Research in {R}}, + author = {Yihui Xie}, + publisher = {Chapman and Hall/CRC}, + year = {2014}, + note = {ISBN 978-1466561595}, + url = {http://www.crcpress.com/product/isbn/9781466561595}, +} + diff --git a/tests/testthat/test-formats.knit.md b/tests/testthat/test-formats.knit.md new file mode 100644 index 0000000000..c6aa698312 --- /dev/null +++ b/tests/testthat/test-formats.knit.md @@ -0,0 +1,86 @@ +--- +title: "Untitled" +author: "John Doe" +output: + html_document: + md_extensions: -autolink_bare_uris +bibliography: packages.bib +--- + + +```r +knitr::opts_chunk$set(tidy = FALSE) +``` + +## Section One + + +```r +summary(cars) +``` + +``` +## speed dist +## Min. : 4.0 Min. : 2.00 +## 1st Qu.:12.0 1st Qu.: 26.00 +## Median :15.0 Median : 36.00 +## Mean :15.4 Mean : 42.98 +## 3rd Qu.:19.0 3rd Qu.: 56.00 +## Max. :25.0 Max. :120.00 +``` + +## Section Two + +You can also embed plots, for example: + +![](/var/folders/t8/jxw4bftj35g15fcb6m4mfbc80000gn/T//RtmpFbqVGl/filee6521d8194fd_files/figure-beamer/unnamed-chunk-2-1.pdf) + +Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot. + +## Section Three + +You can also print data frames + + +```r +mtcars +``` + +``` +## mpg cyl disp hp drat wt qsec vs am gear carb +## Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 +## Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 +## Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 +## Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 +## Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 +## Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 +## Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 +## Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 +## Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 +## Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 +## Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 +## Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 +## Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 +## Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 +## Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 +## Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 +## Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 +## Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 +## Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 +## Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 +## Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 +## Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 +## AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 +## Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 +## Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 +## Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 +## Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 +## Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 +## Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 +## Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 +## Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 +## Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 +``` + + + diff --git a/tests/testthat/test-formats.utf8.md b/tests/testthat/test-formats.utf8.md new file mode 100644 index 0000000000..c6aa698312 --- /dev/null +++ b/tests/testthat/test-formats.utf8.md @@ -0,0 +1,86 @@ +--- +title: "Untitled" +author: "John Doe" +output: + html_document: + md_extensions: -autolink_bare_uris +bibliography: packages.bib +--- + + +```r +knitr::opts_chunk$set(tidy = FALSE) +``` + +## Section One + + +```r +summary(cars) +``` + +``` +## speed dist +## Min. : 4.0 Min. : 2.00 +## 1st Qu.:12.0 1st Qu.: 26.00 +## Median :15.0 Median : 36.00 +## Mean :15.4 Mean : 42.98 +## 3rd Qu.:19.0 3rd Qu.: 56.00 +## Max. :25.0 Max. :120.00 +``` + +## Section Two + +You can also embed plots, for example: + +![](/var/folders/t8/jxw4bftj35g15fcb6m4mfbc80000gn/T//RtmpFbqVGl/filee6521d8194fd_files/figure-beamer/unnamed-chunk-2-1.pdf) + +Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot. + +## Section Three + +You can also print data frames + + +```r +mtcars +``` + +``` +## mpg cyl disp hp drat wt qsec vs am gear carb +## Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 +## Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 +## Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 +## Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 +## Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 +## Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 +## Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 +## Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 +## Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 +## Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 +## Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 +## Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 +## Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 +## Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 +## Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 +## Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 +## Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 +## Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 +## Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 +## Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 +## Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 +## Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 +## AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 +## Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 +## Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 +## Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 +## Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 +## Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 +## Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 +## Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 +## Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 +## Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 +``` + + + diff --git a/tests/testthat/test-shiny.R b/tests/testthat/test-shiny.R index a0b576deca..3b830140df 100644 --- a/tests/testthat/test-shiny.R +++ b/tests/testthat/test-shiny.R @@ -16,3 +16,13 @@ test_that("file.path.ci returns correctly no matter the case", { expect_equal_file("global.R", "donotexist") expect_equal_file("global.Rmd", tmp_dir, "global.R") }) + + +test_that("set_current_theme() informs shiny::getCurrentTheme()", { + expect_null(shiny::getCurrentTheme()) + theme <- bslib::bs_theme() + set_current_theme(theme) + expect_equal(theme, shiny::getCurrentTheme()) + set_current_theme(NULL) + expect_null(shiny::getCurrentTheme()) +}) From 1886417b64bfa8bbcda011705dd69c4be764fd74 Mon Sep 17 00:00:00 2001 From: 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100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/tests/testthat/packages.bib b/tests/testthat/packages.bib deleted file mode 100644 index b19d0217ba..0000000000 --- a/tests/testthat/packages.bib +++ /dev/null @@ -1,30 +0,0 @@ -@Manual{R-knitr, - title = {knitr: A General-Purpose Package for Dynamic Report Generation in R}, - author = {Yihui Xie}, - year = {2021}, - note = {R package version 1.31}, - url = {https://yihui.org/knitr/}, -} - -@Book{knitr2015, - title = {Dynamic Documents with {R} and knitr}, - author = {Yihui Xie}, - publisher = {Chapman and Hall/CRC}, - address = {Boca Raton, Florida}, - year = {2015}, - edition = {2nd}, - note = {ISBN 978-1498716963}, - url = {https://yihui.org/knitr/}, -} - -@InCollection{knitr2014, - booktitle = {Implementing Reproducible Computational Research}, - editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng}, - title = {knitr: A Comprehensive Tool for Reproducible Research in {R}}, - author = {Yihui Xie}, - publisher = {Chapman and Hall/CRC}, - year = {2014}, - note = {ISBN 978-1466561595}, - url = {http://www.crcpress.com/product/isbn/9781466561595}, -} - diff --git a/tests/testthat/test-formats.knit.md b/tests/testthat/test-formats.knit.md deleted file mode 100644 index c6aa698312..0000000000 --- a/tests/testthat/test-formats.knit.md +++ /dev/null @@ -1,86 +0,0 @@ ---- -title: "Untitled" -author: "John Doe" -output: - html_document: - md_extensions: -autolink_bare_uris -bibliography: packages.bib ---- - - -```r -knitr::opts_chunk$set(tidy = FALSE) -``` - -## Section One - - -```r -summary(cars) -``` - -``` -## speed dist -## Min. : 4.0 Min. : 2.00 -## 1st Qu.:12.0 1st Qu.: 26.00 -## Median :15.0 Median : 36.00 -## Mean :15.4 Mean : 42.98 -## 3rd Qu.:19.0 3rd Qu.: 56.00 -## Max. :25.0 Max. :120.00 -``` - -## Section Two - -You can also embed plots, for example: - -![](/var/folders/t8/jxw4bftj35g15fcb6m4mfbc80000gn/T//RtmpFbqVGl/filee6521d8194fd_files/figure-beamer/unnamed-chunk-2-1.pdf) - -Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot. - -## Section Three - -You can also print data frames - - -```r -mtcars -``` - -``` -## mpg cyl disp hp drat wt qsec vs am gear carb -## Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 -## Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 -## Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 -## Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 -## Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 -## Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 -## Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 -## Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 -## Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 -## Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 -## Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 -## Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 -## Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 -## Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 -## Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 -## Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 -## Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 -## Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 -## Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 -## Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 -## Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 -## Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 -## AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 -## Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 -## Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 -## Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 -## Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 -## Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 -## Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 -## Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 -## Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 -## Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 -``` - - - diff --git a/tests/testthat/test-formats.utf8.md b/tests/testthat/test-formats.utf8.md deleted file mode 100644 index c6aa698312..0000000000 --- a/tests/testthat/test-formats.utf8.md +++ /dev/null @@ -1,86 +0,0 @@ ---- -title: "Untitled" -author: "John Doe" -output: - html_document: - md_extensions: -autolink_bare_uris -bibliography: packages.bib ---- - - -```r -knitr::opts_chunk$set(tidy = FALSE) -``` - -## Section One - - -```r -summary(cars) -``` - -``` -## speed dist -## Min. : 4.0 Min. : 2.00 -## 1st Qu.:12.0 1st Qu.: 26.00 -## Median :15.0 Median : 36.00 -## Mean :15.4 Mean : 42.98 -## 3rd Qu.:19.0 3rd Qu.: 56.00 -## Max. :25.0 Max. :120.00 -``` - -## Section Two - -You can also embed plots, for example: - -![](/var/folders/t8/jxw4bftj35g15fcb6m4mfbc80000gn/T//RtmpFbqVGl/filee6521d8194fd_files/figure-beamer/unnamed-chunk-2-1.pdf) - -Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot. - -## Section Three - -You can also print data frames - - -```r -mtcars -``` - -``` -## mpg cyl disp hp drat wt qsec vs am gear carb -## Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 -## Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 -## Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 -## Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 -## Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 -## Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 -## Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 -## Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 -## Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 -## Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 -## Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 -## Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 -## Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 -## Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 -## Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 -## Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 -## Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 -## Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 -## Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 -## Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 -## Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 -## Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 -## AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 -## Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 -## Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 -## Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 -## Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 -## Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 -## Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 -## Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 -## Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 -## Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 -``` - - -