GNU bug report logs - #66899
[PATCH 0/2] *** r-nestedcv and r-matrixtests ***

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

From: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
Subject: [PATCH 0/2] *** r-nestedcv and r-matrixtests ***
Date: Thu, 2 Nov 2023 16:51:51 +0000

*** The main package is r-nestedcv and r-matrixtests is the dependency. Thanks ***

Afkhami, Navid (2):
  gnu: Add r-nestedcv.
  gnu: Add r-matrixtests.

 gnu/packages/cran.scm | 58 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)


base-commit: f5346094f0365a2c04ca00111ff06e17dac832e2
-- 
2.41.0

Message #8 received at 66899 <at> debbugs.gnu.org (full text, mbox):

From: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
To: <66899 <at> debbugs.gnu.org>
Cc: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
Subject: [PATCH 1/2] gnu: Add r-nestedcv.
Date: Thu, 2 Nov 2023 17:13:49 +0000

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

Change-Id: Id998b4192565c220f8d238963ef61217aed12bd3
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e82b027052..5aff1a2dd5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10007,6 +10007,43 @@ (define-public r-n2r
 @acronym{NSW, Navigable Small World} graphs.")
     (license license:asl2.0)))
 
+(define-public r-nestedcv
+  (package
+    (name "r-nestedcv")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nestedcv" version))
+       (sha256
+        (base32 "0jpg4il1niyizfq8kkk391x7anhp2s38mrfypa86skr08ca46zss"))))
+    (properties `((upstream-name . "nestedcv")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-caret
+                             r-data-table
+                             r-doparallel
+                             r-foreach
+                             r-ggplot2
+                             r-glmnet
+                             r-matrixstats
+                             r-matrixtests
+                             r-proc
+                             r-rfast
+                             r-rlang))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/myles-lewis/nestedcv")
+    (synopsis "Nested cross-validation with 'glmnet' and 'caret'")
+    (description
+     "Nested cross-validation applied to the glmnet and caret packages.
+With glmnet this includes cross-validation of elastic net alpha
+parameter.  A number of feature selection filter functions
+(t-test, Wilcoxon test, ANOVA, Pearson/Spearman correlation,
+random forest, ReliefF) for feature selection are provided and
+can be embedded within the outer loop of the nested CV.  Nested
+CV can be also be performed with the caret package giving access
+to the large number of prediction methods available in caret.")
+    (license license:expat)))
+
 (define-public r-network
   (package
     (name "r-network")

base-commit: f5346094f0365a2c04ca00111ff06e17dac832e2
-- 
2.34.1

Message #11 received at 66899 <at> debbugs.gnu.org (full text, mbox):

From: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
To: <66899 <at> debbugs.gnu.org>
Cc: "Afkhami, Navid" <Navid.Afkhami <at> mdc-berlin.de>
Subject: [PATCH 2/2] gnu: Add r-matrixtests.
Date: Thu, 2 Nov 2023 17:13:50 +0000

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

Change-Id: I62f7bd760fc8603425906c304ef4293da1c0cf61
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5aff1a2dd5..6ff4c9324a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3125,6 +3125,27 @@ (define-public r-grr
 functions are simplified but can be faster or have other advantages.")
     (license license:gpl3)))
 
+(define-public r-matrixtests
+  (package
+    (name "r-matrixtests")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "matrixTests" version))
+       (sha256
+        (base32 "0d7i00cxzszfdnjm8q5b72ildic8nig6fbw7rba6acdnllpp7sza"))))
+    (properties `((upstream-name . "matrixTests")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-matrixstats))
+    (home-page "https://github.com/karoliskoncevicius/matrixTests")
+    (synopsis "Statistical hypothesis tests on rows and columns of matrices")
+    (description
+     "This package offers quick statistical hypothesis testing for matrix rows/columns.
+The main goals are speed through vectorization, detailed and user-friendly
+output, and compatibility with tests implemented in R.")
+    (license license:gpl2)))
+
 (define-public r-matrix-utils
   (package
     (name "r-matrix-utils")
-- 
2.34.1

Message #16 received at 66899-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 66899-done <at> debbugs.gnu.org 
Subject: [PATCH 0/2] *** r-nestedcv and r-matrixtests ***
Date: Thu, 02 Nov 2023 18:35:45 +0100

Thanks for the patches!  I applied them with minor changes to the
descriptions.

-- 
Ricardo

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