GNU bug report logs - #70827
[PATCH] gnu: Add r-mlr3cluster r-mlr3data r-mlr3filters r-mlr3fselect r-mlr3hyperband r-mlr3mbo, r-mlr3tuningspaces r-mlr3viz and r-mlr3verse.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-mlr3cluster r-mlr3data r-mlr3filters r-mlr3fselect
 r-mlr3hyperband r-mlr3mbo,
 r-mlr3tuningspaces r-mlr3viz and r-mlr3verse.
Date: Wed, 8 May 2024 01:50:30 +0200

* gnu/packages/cran.scm (r-mlr3cluster r-mlr3data r-mlr3filters 
r-mlr3fselect
r-mlr3hyperband r-mlr3mbo r-mlr3tuningspaces r-mlr3viz, r-mlr3verse): New
variables.

Message #8 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 3/9] gnu: Add r-mlr3filters.
Date: Wed, 8 May 2024 03:02:46 +0200

* gnu/packages/cran.scm (r-mlr3filters): New variable.

Change-Id: I94bd79843f5f35eeacb1ea788a76b63e9028f548
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 26ee9bca3e..123d792da7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -37799,6 +37799,33 @@ (define-public r-mlr3data
 mlr3 is loaded.")
     (license license:lgpl3)))
 
+(define-public r-mlr3filters
+  (package
+    (name "r-mlr3filters")
+    (version "0.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3filters" version))
+       (sha256
+        (base32 "16z359bc2li7f35xk4g08np3r2a3127avv0ak6bn9bywcs13z6bl"))))
+    (properties `((upstream-name . "mlr3filters")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-backports
+                             r-checkmate
+                             r-data-table
+                             r-mlr3
+                             r-mlr3misc
+                             r-paradox
+                             r-r6))
+    (home-page "https://mlr3filters.mlr-org.com")
+    (synopsis "Filter based feature selection for mlr3")
+    (description
+     "This package extends mlr3 with filter methods for feature selection.  Besides
+standalone filter methods built-in methods of any machine-learning algorithm are
+supported.  Partial scoring of multivariate filter methods is supported.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.41.0

Message #11 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 2/9] gnu: Add r-mlr3data.
Date: Wed, 8 May 2024 03:02:45 +0200

* gnu/packages/cran.scm (r-mlr3data): New variable.

Change-Id: I93bee828d1ac26da1146c853b4d88fbdec42905f
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0fd94e8cf1..26ee9bca3e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -37775,6 +37775,30 @@ (define-public r-mlr3cluster
      "This package extends the mlr3 package with cluster analysis.")
     (license license:lgpl3)))
 
+(define-public r-mlr3data
+  (package
+    (name "r-mlr3data")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3data" version))
+       (sha256
+        (base32 "04hwmj8cdszwgd845va26pgzdw0k4cm025zjrmp3fr7ypp73mirg"))))
+    (properties `((upstream-name . "mlr3data")))
+    (build-system r-build-system)
+    (home-page "https://github.com/mlr-org/mlr3data")
+    (synopsis "Collection of machine learning data Sets for mlr3")
+    (description
+     "This package provides a small collection of interesting and educational
+machine learning data sets which are used as examples in the mlr3 book Applied
+machine learning using mlr3 in R @url{https://mlr3book.mlr-org.com}, the use case
+gallery  @url{https://mlr3gallery.mlr-org.com}, or in other examples.  All data
+sets are properly preprocessed and ready to be analyzed by most machine learning
+algorithms.  Data sets are automatically added to the dictionary of tasks if
+mlr3 is loaded.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.41.0

Message #14 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 4/9] gnu: Add r-mlr3fselect.
Date: Wed, 8 May 2024 03:02:47 +0200

* gnu/packages/cran.scm (r-mlr3fselect): New variable.

Change-Id: I28ced76c34d99c864c09cbf7b92658fb7676b22c
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 123d792da7..459ad63c23 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -37826,6 +37826,36 @@ (define-public r-mlr3filters
 supported.  Partial scoring of multivariate filter methods is supported.")
     (license license:lgpl3)))
 
+(define-public r-mlr3fselect
+  (package
+    (name "r-mlr3fselect")
+    (version "0.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3fselect" version))
+       (sha256
+        (base32 "1f18y4ahnjzlwk9pfs87i80kb6z84hgyc5cdlj3mafawq790hg1h"))))
+    (properties `((upstream-name . "mlr3fselect")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bbotk
+                             r-checkmate
+                             r-data-table
+                             r-lgr
+                             r-mlr3
+                             r-mlr3misc
+                             r-paradox
+                             r-r6))
+    (home-page "https://mlr3fselect.mlr-org.com")
+    (synopsis "Feature selection for mlr3")
+    (description
+     "This package is a feature selection package of the mlr3 ecosystem.  It
+selects the optimal feature set for any mlr3 learner.  The package works with
+several optimization algorithms e.g. random search, Recursive feature elimination,
+and genetic search.  Moreover, it can automatically optimize learners and estimate
+the performance of optimized feature sets with nested resampling.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.41.0

Message #17 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 5/9] gnu: Add r-mlr3hyperband.
Date: Wed, 8 May 2024 03:02:48 +0200

* gnu/packages/cran.scm (r-mlr3hyperband): New variable.

Change-Id: I3e7a829da1f7687ef0bb201f6333bdd519cfa025
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 459ad63c23..399225445b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -37856,6 +37856,37 @@ (define-public r-mlr3fselect
 the performance of optimized feature sets with nested resampling.")
     (license license:lgpl3)))
 
+(define-public r-mlr3hyperband
+  (package
+    (name "r-mlr3hyperband")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3hyperband" version))
+       (sha256
+        (base32 "1x6vfhadxlb4c9q61d5qv957mkyfwdwchzbg3flfd0j28b4bck1p"))))
+    (properties `((upstream-name . "mlr3hyperband")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bbotk
+                             r-checkmate
+                             r-data-table
+                             r-lgr
+                             r-mlr3
+                             r-mlr3misc
+                             r-mlr3tuning
+                             r-paradox
+                             r-r6))
+    (home-page "https://mlr3hyperband.mlr-org.com")
+    (synopsis "Hyperband for mlr3")
+    (description
+     "This package implements a successive halving and hyperband optimization
+algorithm for the mlr3 ecosystem.  The implementation in mlr3hyperband features
+improved scheduling and parallelizes the evaluation of configurations.  The package
+includes tuners for hyperparameter optimization in mlr3tuning and optimizers for
+black-box optimization in bbotk.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.41.0

Message #20 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 1/9] gnu: Add r-mlr3cluster.
Date: Wed, 8 May 2024 03:02:44 +0200

* gnu/packages/cran.scm (r-mlr3cluster): New variable.

Change-Id: I3d970afeeaf4de1793974177bcf5abf64c957d6b
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 65e48e3445..0fd94e8cf1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -37747,6 +37747,34 @@ (define-public r-mlrmbo
 customization by the user.")
     (license license:bsd-2)))
 
+(define-public r-mlr3cluster
+  (package
+    (name "r-mlr3cluster")
+    (version "0.1.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3cluster" version))
+       (sha256
+        (base32 "09fsw2b43f9m7clv1qwylimyz622snhn9ykq3xwbiric7zr4ca91"))))
+    (properties `((upstream-name . "mlr3cluster")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-backports
+                             r-checkmate
+                             r-clue
+                             r-cluster
+                             r-data-table
+                             r-fpc
+                             r-mlr3
+                             r-mlr3misc
+                             r-paradox
+                             r-r6))
+    (home-page "https://mlr3cluster.mlr-org.com")
+    (synopsis "Cluster extension for mlr3")
+    (description
+     "This package extends the mlr3 package with cluster analysis.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")

base-commit: 00aa6b5a3c1505b033d19c6d3a3021d6d6ecb31b
-- 
2.41.0

Message #23 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 6/9] gnu: Add r-mlr3mbo.
Date: Wed, 8 May 2024 03:02:49 +0200

* gnu/packages/cran.scm (r-mlr3mbo): New variable.

Change-Id: I23d7af239f7ab55599faf99d5136621cc45c973f
---
 gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 399225445b..d1fc4cbb2f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -37887,6 +37887,42 @@ (define-public r-mlr3hyperband
 black-box optimization in bbotk.")
     (license license:lgpl3)))
 
+(define-public r-mlr3mbo
+  (package
+    (name "r-mlr3mbo")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3mbo" version))
+       (sha256
+        (base32 "0jdj5dx6jb7n0g950h0j8jhafdj5mcalv5vxfiyf07myr6mjipri"))))
+    (properties `((upstream-name . "mlr3mbo")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bbotk
+                             r-checkmate
+                             r-data-table
+                             r-lgr
+                             r-mlr3
+                             r-mlr3misc
+                             r-mlr3tuning
+                             r-paradox
+                             r-r6
+                             r-spacefillr))
+    (native-inputs (list r-knitr))
+    (home-page "https://mlr3mbo.mlr-org.com")
+    (synopsis "Flexible Bayesian optimization")
+    (description
+     "This package provides a flexible approach to Bayesian optimization / model
+based optimization building on the bbotk package.  The mlr3mbo is a toolbox
+providing both ready-to-use optimization algorithms as well as their fundamental
+building blocks allowing for straightforward implementation of custom algorithms.
+Single- and multi-objective optimization is supported as well as mixed continuous,
+categorical and conditional search spaces.  Moreover, using mlr3mbo for
+hyperparameter optimization of machine learning models within the mlr3 ecosystem
+is straightforward via mlr3tuning.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.41.0

Message #26 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 7/9] gnu: Add r-mlr3tuningspaces.
Date: Wed, 8 May 2024 03:02:50 +0200

* gnu/packages/cran.scm (r-mlr3tuningspaces): New variable.

Change-Id: Ifb35e78dab862921f000b055d3fa1eee3ef79309
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d1fc4cbb2f..6fcf0eb10d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -38031,6 +38031,34 @@ (define-public r-mlr3ordinal
 performing ordinal regression.")
       (license license:expat))))
 
+(define-public r-mlr3tuningspaces
+  (package
+    (name "r-mlr3tuningspaces")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3tuningspaces" version))
+       (sha256
+        (base32 "1snrd7xq388mvqh0ydaxvx8k9iwp40g06c3irp0m718jw3wsz5vm"))))
+    (properties `((upstream-name . "mlr3tuningspaces")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-checkmate
+                             r-data-table
+                             r-mlr3
+                             r-mlr3misc
+                             r-mlr3tuning
+                             r-paradox
+                             r-r6))
+    (home-page "https://mlr3tuningspaces.mlr-org.com")
+    (synopsis "Search spaces for mlr3")
+    (description
+     "This package is a collection of search spaces for hyperparameter optimization
+in the mlr3 ecosystem.  It features ready-to-use search spaces for many popular
+machine learning algorithms.  The search spaces are from scientific articles and
+work for a wide range of data sets.")
+    (license license:lgpl3)))
+
 (define-public r-paradox
   (package
     (name "r-paradox")
-- 
2.41.0

Message #29 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 8/9] gnu: Add r-mlr3viz.
Date: Wed, 8 May 2024 03:02:51 +0200

* gnu/packages/cran.scm (r-mlr3viz): New variable.

Change-Id: Iedca442886ebeb09d26cfa44290192c582aeeef3
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6fcf0eb10d..74c741d754 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -38059,6 +38059,34 @@ (define-public r-mlr3tuningspaces
 work for a wide range of data sets.")
     (license license:lgpl3)))
 
+(define-public r-mlr3viz
+  (package
+    (name "r-mlr3viz")
+    (version "0.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3viz" version))
+       (sha256
+        (base32 "1m2f54yqhk1bd4c30vd1z509yblz6y4i8qkwhg73aa1sflnsycvf"))))
+    (properties `((upstream-name . "mlr3viz")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-checkmate
+                             r-data-table
+                             r-ggplot2
+                             r-mlr3misc
+                             r-scales
+                             r-viridis))
+    (home-page "https://mlr3viz.mlr-org.com")
+    (synopsis "Visualizations for mlr3")
+    (description
+     "This package offers features plots for mlr3 objects such as tasks, learners,
+predictions, benchmark results, tuning instances and filters via the
+@code{autoplot()} generic of ggplot2.  The mlr3viz package draws plots with
+the viridis color palette and applies the minimal theme.  Visualizations include
+barplots, boxplots, histograms, ROC curves, and precision-recall curves.")
+    (license license:lgpl3)))
+
 (define-public r-paradox
   (package
     (name "r-paradox")
-- 
2.41.0

Message #32 received at 70827 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <70827 <at> debbugs.gnu.org>
Subject: [PATCH 9/9] gnu: Add r-mlr3verse.
Date: Wed, 8 May 2024 03:02:52 +0200

* gnu/packages/cran.scm (r-mlr3verse): New variable.

Change-Id: I52c01fffd13c72b599ae5bc9ff809daea11eaa59
---
 gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 74c741d754..a9db22589a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -38059,6 +38059,42 @@ (define-public r-mlr3tuningspaces
 work for a wide range of data sets.")
     (license license:lgpl3)))
 
+(define-public r-mlr3verse
+  (package
+    (name "r-mlr3verse")
+    (version "0.2.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mlr3verse" version))
+       (sha256
+        (base32 "0ld4vch1qdq3gh8vhj38s2wz7acn5z7f8hxmnwnrq22g44gckd8s"))))
+    (properties `((upstream-name . "mlr3verse")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bbotk
+                             r-data-table
+                             r-mlr3
+                             r-mlr3cluster
+                             r-mlr3data
+                             r-mlr3filters
+                             r-mlr3fselect
+                             r-mlr3hyperband
+                             r-mlr3learners
+                             r-mlr3mbo
+                             r-mlr3misc
+                             r-mlr3pipelines
+                             r-mlr3tuning
+                             r-mlr3tuningspaces
+                             r-mlr3viz
+                             r-paradox))
+    (home-page "https://mlr3verse.mlr-org.com")
+    (synopsis "Easily install and load of the mlr3 package family")
+    (description
+     "The mlr3 package family is a set of packages for machine-learning purposes
+built in a modular fashion.  This wrapper package is aimed to simplify the
+installation and loading of the core mlr3 packages.")
+    (license license:lgpl3)))
+
 (define-public r-mlr3viz
   (package
     (name "r-mlr3viz")
-- 
2.41.0

Message #37 received at 70827-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 70827-done <at> debbugs.gnu.org
Subject: Re: [bug#70827] [PATCH 1/9] gnu: Add r-mlr3cluster.
Date: Wed, 08 May 2024 15:30:14 +0200

Applied all, thank you!

-- 
Ricardo

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