[bug#67229] [PATCH] gnu: Add r-gtsummary and dependencies

[bug#67229] [PATCH] gnu: Add r-gtsummary and dependencies

[Sebastian Gibb via Guix-patches via]

Change-Id: I8925668063ca53b91bec49788fbed3df5eb2c2fc
---
 gnu/packages/cran.scm | 211 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 211 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 221a81612c..711308d36c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1061,6 +1061,159 @@ (define-public r-googlevis
 the output locally.")
     (license license:gpl2+)))
 
+(define-public r-reactr
+  (package
+    (name "r-reactr")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "reactR" version))
+       (sha256
+        (base32 "14pi2wc25qa9q0hp8jby07798l53phyj1zifj46fg2pjq8vkz7p7"))))
+    (properties `((upstream-name . "reactR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-htmltools))
+    (native-inputs (list esbuild r-knitr))
+    (home-page "https://github.com/react-R/reactR")
+    (synopsis "React Helpers")
+    (description
+     "Make it easy to use React in R with htmlwidget scaffolds, helper dependency
+functions, an embedded Babel transpiler', and examples.")
+    (license license:expat)))
+
+(define-public r-reactable
+  (package
+    (name "r-reactable")
+    (version "0.4.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "reactable" version))
+       (sha256
+        (base32 "1wkamzyyl3k3772n5g4rjklkkhdb07jiax064r9alnnq5nzfdaml"))))
+    (properties `((upstream-name . "reactable")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-digest r-htmltools r-htmlwidgets r-jsonlite
+                             r-reactr))
+    (home-page "https://glin.github.io/reactable/")
+    (synopsis "Interactive Data Tables for R")
+    (description
+     "Interactive data tables for R, based on the React Table @code{JavaScript}
+library.  Provides an HTML widget that can be used in R Markdown or Quarto
+documents, Shiny applications, or viewed from an R console.")
+    (license license:expat)))
+
+(define-public r-juicyjuice
+  (package
+    (name "r-juicyjuice")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "juicyjuice" version))
+       (sha256
+        (base32 "0ap1nsyihlagc1yqvwr2x9s16kzb3c8azfi50mzv95275a5l3xb4"))))
+    (properties `((upstream-name . "juicyjuice")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-v8))
+    (home-page "https://github.com/rich-iannone/juicyjuice")
+    (synopsis "Inline CSS Properties into HTML Tags Using 'juice'")
+    (description
+     "There are occasions where you need a piece of HTML with integrated styles.  A
+prime example of this is HTML email.  This transformation involves moving the
+CSS and associated formatting instructions from the style block in the head of
+your document into the body of the HTML. Many prominent email clients require
+integrated styles in HTML email; otherwise a received HTML email will be
+displayed without any styling.  This package will quickly and precisely perform
+these CSS transformations when given HTML text and it does so by using the
+@code{JavaScript} juice library.")
+    (license license:expat)))
+
+(define-public r-gt
+  (package
+    (name "r-gt")
+    (version "0.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gt" version))
+       (sha256
+        (base32 "0gkfqy7n0pv1cz4vrshl2w07c0ykipi5rvp46nyvlcd17qq5z2kh"))))
+    (properties `((upstream-name . "gt")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-base64enc
+                             r-bigd
+                             r-bitops
+                             r-cli
+                             r-commonmark
+                             r-dplyr
+                             r-fs
+                             r-glue
+                             r-htmltools
+                             r-htmlwidgets
+                             r-juicyjuice
+                             r-magrittr
+                             r-markdown
+                             r-reactable
+                             r-rlang
+                             r-sass
+                             r-scales
+                             r-tibble
+                             r-tidyselect
+                             r-xml2))
+    (home-page "https://gt.rstudio.com")
+    (synopsis "Easily Create Presentation-Ready Display Tables")
+    (description
+     "Build display tables from tabular data with an easy-to-use set of functions.
+With its progressive approach, we can construct display tables with a cohesive
+set of table parts.  Table values can be formatted using any of the included
+formatting functions.  Footnotes and cell styles can be precisely added through
+a location targeting system.  The way in which gt handles things for you means
+that you don't often have to worry about the fine details.")
+    (license license:expat)))
+
+(define-public r-gtsummary
+  (package
+    (name "r-gtsummary")
+    (version "1.7.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gtsummary" version))
+       (sha256
+        (base32 "02jbsdv8wwncnrmqmf12pz3ld759s8ll5dl5rrxv8ad6qgqjbhnx"))))
+    (properties `((upstream-name . "gtsummary")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-broom
+                             r-broom-helpers
+                             r-cli
+                             r-dplyr
+                             r-forcats
+                             r-glue
+                             r-gt
+                             r-knitr
+                             r-lifecycle
+                             r-purrr
+                             r-rlang
+                             r-stringr
+                             r-tibble
+                             r-tidyr
+                             r-vctrs))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ddsjoberg/gtsummary")
+    (synopsis "Presentation-Ready Data Summary and Analytic Result Tables")
+    (description
+     "This package creates presentation-ready tables summarizing data sets, regression
+models, and more.  The code to create the tables is concise and highly
+customizable.  Data frames can be summarized with any function, e.g. mean(),
+median(), even user-written functions.  Regression models are summarized and
+include the reference rows for categorical variables.  Common regression models,
+such as logistic regression and Cox proportional hazards regression, are
+automatically identified and the tables are pre-filled with appropriate column
+headers.")
+    (license license:expat)))
+
 (define-public r-gson
   (package
     (name "r-gson")
@@ -1973,6 +2126,32 @@ (define-public r-clipr
 the system clipboards.")
     (license license:gpl3)))
 
+(define-public r-bigd
+  (package
+    (name "r-bigd")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bigD" version))
+       (sha256
+        (base32 "0pzzqqazn1nv2b613vzdyhxvr454lyqq8235jydia6r3k86fpadw"))))
+    (properties `((upstream-name . "bigD")))
+    (build-system r-build-system)
+    (home-page "https://github.com/rich-iannone/bigD")
+    (synopsis "Flexibly Format Dates and Times to a Given Locale")
+    (description
+     "Format dates and times flexibly and to whichever locales make sense.  Parses
+dates, times, and date-times in various formats (including string-based ISO 8601
+constructions).  The formatting syntax gives the user many options for
+formatting the date and time output in a precise manner.  Time zones in the
+input can be expressed in multiple ways and there are many options for
+formatting time zones in the output as well.  Several of the provided helper
+functions allow for automatic generation of locale-aware formatting patterns
+based on date/time skeleton formats and standardized date/time formats with
+varying specificity.")
+    (license license:expat)))
+
 (define-public r-clock
   (package
     (name "r-clock")
@@ -8512,6 +8691,38 @@ (define-public r-broom
 provides a one-row summary of model-level statistics.")
     (license license:expat)))
 
+(define-public r-broom-helpers
+  (package
+    (name "r-broom-helpers")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "broom.helpers" version))
+       (sha256
+        (base32 "14vaqxv12yrvqllp8552nx68wk2qfjcy1iy7bajkspgdpwsjzhfd"))))
+    (properties `((upstream-name . "broom.helpers")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-broom
+                             r-cli
+                             r-dplyr
+                             r-labelled
+                             r-lifecycle
+                             r-purrr
+                             r-rlang
+                             r-stringr
+                             r-tibble
+                             r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://larmarange.github.io/broom.helpers/")
+    (synopsis "Helpers for Model Coefficients Tibbles")
+    (description
+     "This package provides suite of functions to work with regression model
+broom::tidy() tibbles.  The suite includes functions to group regression model
+terms by variable, insert reference and header rows for categorical variables,
+add variable labels, and more.")
+    (license license:gpl3+)))
+
 (define-public r-recipes
   (package
     (name "r-recipes")

base-commit: 23627b1706af25a0a30b96b9169a3495279aff1b
-- 
2.39.2

[bug#67229] [PATCH] gnu: Add r-gtsummary and dependencies

[Simon Tournier]

Hi,

(Sorry for the late reply.)

On Thu, 16 Nov 2023 at 15:07, Sebastian Gibb via Guix-patches via <guix-patches@gnu.org> wrote:
> Change-Id: I8925668063ca53b91bec49788fbed3df5eb2c2fc
> ---
>  gnu/packages/cran.scm | 211 ++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 211 insertions(+)

Thanks for your contributions.  From a first look, they look good to me
but it would help if you could:

 1. Split all the additions to atomic commits – one package per commit:

        +(define-public r-reactr
        +(define-public r-reactable
        +(define-public r-juicyjuice
        +(define-public r-gt
        +(define-public r-gtsummary
        +(define-public r-bigd
        +(define-public r-broom-helpers

    Hence 7 commits; :-)

 2. Write compliant commit messages, as:

--8<---------------cut here---------------start------------->8---
gnu: Add r-reactr.

* gnu/packages/cran.scm (r-reactr): New variable.
--8<---------------cut here---------------end--------------->8---

Could you send v2 (reroll-count=2)? 

Cheers,
simon

[bug#67229] [PATCH] gnu: Add r-gtsummary and dependencies

[Ricardo Wurmus]

Hi,

the r-reactr and r-reactable packages contain a lot of minified
JavaScript, which is why we don’t have them in the default Guix channel.
We do have these packages in the guix-science channel[1].

You could add r-gtsummary there until someone makes the effort to find
matching source code for all the bundled minified JavaScript in those
packages.

[1]: https://github.com/guix-science/guix-science

-- 
Ricardo

bug#67229: [PATCH] gnu: Add r-gtsummary and dependencies

[Ricardo Wurmus]

I'm closing this due to a lack of activity.

-- 
Ricardo