[bug#40779] Acknowledgement (Submission of CRAN Package Descriptions r-dcv r-stam r-grouped r-sgloptim r-awsmethods r-aws r-tea r-rcdd r-rxnat)

[Naga Malleswari <nagamalli@riseup.net>]

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Submitting Patches for CRAN PACKAGES

r-dcv

r-stam

r-grouped

r-sgloptim

r-awsmethods

r-aws

r-tea

r-rcdd

r-rxnat

I have done these patches earlier while practice. Submitting them to the
guix system.

On 23/04/20 1:11 am, GNU bug Tracking System wrote:
> Thank you for filing a new bug report with debbugs.gnu.org.
>
> This is an automatically generated reply to let you know your message
> has been received.
>
> Your message is being forwarded to the package maintainers and other
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>
> Your message has been sent to the package maintainer(s):
>  guix-patches@gnu.org
>
> If you wish to submit further information on this problem, please
> send it to 40779@debbugs.gnu.org.
>
> Please do not send mail to help-debbugs@gnu.org unless you wish
> to report a problem with the Bug-tracking system.
>
-- 
Regards
NagaMalli


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From 4812d174a235f5f545f5d7109df427fee341813a Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:29:26 +0530
Subject: [PATCH 9/9] gnu: Add r-rxnat.

* gnu/packages/cran.scm (r-rxnat): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b6a9a88067..09a561e219 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21375,3 +21375,29 @@ as convex hull of set of points and rays. Also does linear programming and
 redundant generator elimination. All functions can use exact
 infinite-precision rational arithmetic.")
     (license license:gpl2)))
+
+(define-public r-rxnat
+  (package
+    (name "r-rxnat")
+    (version "1.0.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "Rxnat" version))
+        (sha256
+          (base32
+            "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
+    (properties
+     `((upstream-name . "Rxnat")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-httr" ,r-httr)
+        ("r-rcurl" ,r-rcurl)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/web/packages/Rxnat")
+    (synopsis "Queries and extracts Images from Extensible Neuroimaging Archive Toolkit")
+    (description
+      "Allows communication with Extensible Neuroimaging Archive Toolkit.
+Rxnat uses the XNAT REST API to perform data queries and download images.")
+    (license license:gpl2)))
-- 
2.25.1


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From 3fae8711be15ff332d5378a33de34b5fd70bb2af Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:28:31 +0530
Subject: [PATCH 8/9] gnu: Add r-rcdd.

* gnu/packages/cran.scm (r-rcdd): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e4efa402d5..b6a9a88067 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21349,3 +21349,29 @@ methods for climate-growth model in the climate reconstruction from
 tree rings, including Sign Test statistic, Reduction of Error statistic,
 Product Mean Test, Durbin-Watson statistic etc.")
     (license license:gpl2)))
+
+(define-public r-rcdd
+  (package
+    (name "r-rcdd")
+    (version "1.2-2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "rcdd" version))
+        (sha256
+          (base32
+            "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
+    (properties
+     `((upstream-name . "rcdd")))
+    (build-system r-build-system)
+    (inputs
+     `(("gmp" ,gmp)))
+    (home-page "http://www.stat.umn.edu/geyer/rcdd/")
+    (synopsis "Computational Geometry")
+    (description
+      "Converts back and forth between two representations of a convex
+polytope: as solution of a set of linear equalities and inequalities and
+as convex hull of set of points and rays. Also does linear programming and
+redundant generator elimination. All functions can use exact
+infinite-precision rational arithmetic.")
+    (license license:gpl2)))
-- 
2.25.1


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From b1bb80e24748cf63f075dcf1e749f2b7ae559478 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:24:04 +0530
Subject: [PATCH 7/9] gnu: Add r-dcv.

* gnu/packages/cran.scm (r-dcv): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a2949d9d6e..e4efa402d5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21324,3 +21324,28 @@ at Random assumption.")
 to conduct Spatio-Temporal Analysis and Modelling,including Exploratory
 Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling.")
     (license license:gpl2+)))
+    
+(define-public r-dcv
+  (package
+    (name "r-dcv")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "dcv" version))
+        (sha256
+          (base32
+            "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
+    (properties
+     `((upstream-name . "dcv")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lmtest" ,r-lmtest)))
+    (home-page "https://cran.r-project.org/web/packages/dcv")
+    (synopsis "Conventional Cross-validation statistics for climate-growth model")
+    (description
+      "This package performs several conventional Cross-validation statistical
+methods for climate-growth model in the climate reconstruction from
+tree rings, including Sign Test statistic, Reduction of Error statistic,
+Product Mean Test, Durbin-Watson statistic etc.")
+    (license license:gpl2)))
-- 
2.25.1


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From 9906a033dfae2e4a7e5c482d4719166f8e3d3730 Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:22:22 +0530
Subject: [PATCH 5/9] gnu: Add r-grouped.

* gnu/packages/cran.scm (r-grouped): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2f4d53c970..93e691a26b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21276,3 +21276,26 @@ applicable to a broad class of loss functions. Use of parallel computing for
 cross validation and subsampling is supported through the foreach and
 doParallel packages.")
     (license license:gpl2+)))
+    
+(define-public r-grouped
+  (package
+    (name "r-grouped")
+    (version "0.6-0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "grouped" version))
+        (sha256
+          (base32
+            "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
+    (properties
+     `((upstream-name . "grouped")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/grouped")
+    (synopsis "Regression Analysis of Grouped and Coarse Data")
+    (description
+      "Regression models for grouped and coarse data, under the Coarsened
+at Random assumption.")
+    (license license:gpl2+)))
-- 
2.25.1


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From 574f7921578ef96a2d1fbe82a73c1164f6fb746f Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:23:07 +0530
Subject: [PATCH 6/9] gnu: Add r-stam.

* gnu/packages/cran.scm (r-stam): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 93e691a26b..a2949d9d6e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21299,3 +21299,28 @@ doParallel packages.")
       "Regression models for grouped and coarse data, under the Coarsened
 at Random assumption.")
     (license license:gpl2+)))
+    
+(define-public r-stam
+  (package
+    (name "r-stam")
+    (version "0.0-1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "stam" version))
+        (sha256
+          (base32
+            "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
+    (properties
+     `((upstream-name . "stam")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-np" ,r-np)
+        ("r-sp" ,r-sp)))
+    (home-page "https://cran.r-project.org/web/packages/stam")
+    (synopsis "Spatio-Temporal Analysis and Modelling")
+    (description
+      "Stam is an evolving package that target on the various methods
+to conduct Spatio-Temporal Analysis and Modelling,including Exploratory
+Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling.")
+    (license license:gpl2+)))
-- 
2.25.1


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From e45c000e1ac6c4c73358f2a32aa7f8ca3c92178d Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:21:19 +0530
Subject: [PATCH 4/9] gnu: Add r-sgloptim.

* gnu/packages/cran.scm (r-sgloptim): New variable.
---
 gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5f55fd62d4..2f4d53c970 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21240,3 +21240,39 @@ procedures in 1D, 2D and 3D. This includes the Propagation-Separation Approach
 to adaptive smoothing, the Intersecting Confidence Intervals (@dfn{ICI}),
 variational approaches and a non-local means filter.")
     (license license:gpl2+)))
+    
+(define-public r-sgloptim
+  (package
+    (name "r-sgloptim")
+    (version "1.3.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "sglOptim" version))
+        (sha256
+          (base32
+            "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
+    (properties
+     `((upstream-name . "sglOptim")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-bh" ,r-bh)
+        ("r-doparallel" ,r-doparallel)
+        ("r-foreach" ,r-foreach)
+        ("r-matrix" ,r-matrix)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcpparmadillo" ,r-rcpparmadillo)
+        ("r-rcppprogress" ,r-rcppprogress)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/nielsrhansen/sglOptim")
+    (synopsis "Generic Sparse Group Lasso Solver")
+    (description
+      "Fast generic solver for sparse group lasso optimization problems.
+The loss (objective) function must be defined in a C++ module. The
+optimization problem is solved using a coordinate gradient descent
+algorithm. Convergence of the algorithm is established and the algorithm is
+applicable to a broad class of loss functions. Use of parallel computing for
+cross validation and subsampling is supported through the foreach and
+doParallel packages.")
+    (license license:gpl2+)))
-- 
2.25.1


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From 4fa46cd6fd5fd00b0c81a302d61d72bfd293cccc Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:20:01 +0530
Subject: [PATCH 3/9] gnu: Add r-aws.

* gnu/packages/cran.scm (r-aws): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c856d133b7..5f55fd62d4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21212,3 +21212,31 @@ GPD-GoF-tests is also implemented here.")
       "Defines the method extract and provides @code{openMP} support as needed
 in several packages like @code{aws},@code{adimpro},@code{fmri},@code{dwi}.")
     (license license:gpl2+)))
+    
+(define-public r-aws
+  (package
+    (name "r-aws")
+    (version "2.4-2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "aws" version))
+        (sha256
+          (base32
+            "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
+    (properties
+     `((upstream-name . "aws")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-awsmethods" ,r-awsmethods)
+        ("r-gsl" ,r-gsl)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://www.wias-berlin.de/people/polzehl/")
+    (synopsis "Adaptive Weights Smoothing")
+    (description
+      "We provide a collection of R-functions implementing adaptive smoothing
+procedures in 1D, 2D and 3D. This includes the Propagation-Separation Approach
+to adaptive smoothing, the Intersecting Confidence Intervals (@dfn{ICI}),
+variational approaches and a non-local means filter.")
+    (license license:gpl2+)))
-- 
2.25.1


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From 0de70a861633665a4e971901f2ae4ea38c104b3e Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:15:40 +0530
Subject: [PATCH 2/9] gnu: Add r-awsmethods.

* gnu/packages/cran.scm (r-awsmethods): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ac55916964..c856d133b7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21191,3 +21191,24 @@ which is the number of data in the tail. The third class is motivated by
 graphical inspection.In addition, a sequential testing procedure for
 GPD-GoF-tests is also implemented here.")
     (license license:gpl3)))
+    
+(define-public r-awsmethods
+  (package
+    (name "r-awsmethods")
+    (version "1.1-1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "awsMethods" version))
+        (sha256
+          (base32
+            "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
+    (properties
+     `((upstream-name . "awsMethods")))
+    (build-system r-build-system)
+    (home-page "http://www.wias-berlin.de/software/imaging/")
+    (synopsis "Class and Methods Definitions")
+    (description
+      "Defines the method extract and provides @code{openMP} support as needed
+in several packages like @code{aws},@code{adimpro},@code{fmri},@code{dwi}.")
+    (license license:gpl2+)))
-- 
2.25.1


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From de01c0bceaee3062d32fdca209bc35280695d1cd Mon Sep 17 00:00:00 2001
From: Naga Malleswari <nagamalli@riseup.net>
Date: Thu, 23 Apr 2020 01:13:12 +0530
Subject: [PATCH 1/9] gnu: Add r-tea.

* gnu/packages/cran.scm (r-tea): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 70cb7cc700..ac55916964 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21162,3 +21162,32 @@ evaluated interactively.")
 Bayes factors, posterior model probabilities, and normalizing constants in
 general, via different versions of bridge sampling.")
     (license license:gpl2+)))
+
+(define-public r-tea
+  (package
+    (name "r-tea")
+    (version "1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "tea" version))
+        (sha256
+          (base32
+            "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
+    (properties
+     `((upstream-name . "tea")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)))
+    (home-page "https://cran.r-project.org/web/packages/tea")
+    (synopsis "Threshold Estimation Approaches")
+    (description
+      "Different approaches for selecting the threshold in generalized Pareto
+distributions.Most of them are based on minimizing the AMSE-criterion or
+atleast by reducing the bias of the assumed GPD-model. Others are
+heuristically motivated by searching for stable sample paths, i.e.  a
+nearly constant region of the tail index estimator with respect to k,
+which is the number of data in the tail. The third class is motivated by
+graphical inspection.In addition, a sequential testing procedure for
+GPD-GoF-tests is also implemented here.")
+    (license license:gpl3)))
-- 
2.25.1