[bug#59870] [PATCH] gnu: Add r-animalcules, r-plotroc, r-gridsvg, r-gunifrac, r-dirmult, r-modeest, r-fbasics, r-timeseries, r-gss, r-stable, r-rmutil, r-statip.

[bug#59870] [PATCH] gnu: Add r-animalcules, r-plotroc, r-gridsvg, r-gunifrac, r-dirmult, r-modeest, r-fbasics, r-timeseries, r-gss, r-stable, r-rmutil, r-statip.

[MadalinIonel.Patrascu]

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* gnu/packages/bioconductor.scm (r-animalcules): New variable.
* gnu/packages/cran.scm (r-plotroc, r-gridsvg, r-gunifrac, r-dirmult, r-modeest,
r-fbasics, r-timeseries, r-gss, r-stable, r-rmutil, r-statip): New variables.


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[bug#59870] [PATCH 01/12] gnu: Add r-statip.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-statip): New variable.
---
 gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5c5258d6e0..d23265ad07 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6452,6 +6452,41 @@ (define-public r-corrplot
     ;; Any version of the GPL
     (license license:gpl2+)))
 
+(define-public r-statip
+  (package
+    (name "r-statip")
+    (version "0.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "statip" version))
+              (sha256
+               (base32
+                "0kymc3ds1nx0h11ffmm3vmqr1w34gd0k788vf72x2v45h8c1ma2n"))))
+    (properties `((upstream-name . "statip")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-clue
+           r-rpart))
+    (home-page "https://github.com/paulponcet/statip")
+    (synopsis
+     "Statistical functions for probability distributions and regression")
+    (description
+     "This package provides a collection of miscellaneous statistical functions for:
+@itemize
+@item probability distributions: @code{dbern()}, @code{pbern()}, @code{qbern()},
+@code{rbern()} for the Bernoulli distribution, and @code{distr2name()}, @code{
+name2distr()} for distribution names;
+@item probability density estimation: @code{densityfun()};
+@item most frequent value estimation: @code{mfv()}, @code{mfv1()};
+@item other statistical measures of location: @code{cv()} (coefficient of
+variation), @code{midhinge()}, @code{midrange()}, @code{trimean()};
+@item construction of histograms: @code{histo()}, @code{find_breaks()};
+@item calculation of the Hellinger distance: @code{hellinger()};
+@item use of classical kernels: @code{kernelfun()}, @code{kernel_properties()};
+@item univariate piecewise-constant regression: @code{picor()}.
+@end itemize")
+    (license license:gpl3)))
+
 (define-public r-stringdist
   (package
     (name "r-stringdist")

base-commit: b2a848d23d37f31496e1ff664f1dcf6abcdcc388
-- 
2.38.1

[bug#59870] [PATCH 02/12] gnu: Add r-rmutil.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-rmutil): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d23265ad07..792fcf1a7d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16231,6 +16231,28 @@ (define-public r-rmpfr
 Precision Floating-Point Reliable} (MPFR) library.")
     (license license:gpl2+)))
 
+(define-public r-rmutil
+  (package
+    (name "r-rmutil")
+    (version "1.1.10")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "rmutil" version))
+              (sha256
+               (base32
+                "1yd5gkg4jg3rvqrfl8c5r07lcr37n1p9h1a7b6s45iswd77dg7w1"))))
+    (properties `((upstream-name . "rmutil")))
+    (build-system r-build-system)
+    (native-inputs (list gfortran))
+    (home-page "https://www.commanster.eu/rcode.html")
+    (synopsis
+     "Utilities for nonlinear regression and repeated measurements models")
+    (description
+     "This package provides a toolkit of functions for nonlinear regression and
+repeated measurements.  It was designated to be imported by other packages such
+as @code{gnlm}, @code{stable}, @code{growth}, @code{repeated}, and @code{event}.")
+    (license license:gpl2+)))
+
 (define-public r-assertive-base
   (package
     (name "r-assertive-base")
-- 
2.38.1

[bug#59870] [PATCH 03/12] gnu: Add r-stable.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-stable): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 792fcf1a7d..b773c6aeb9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6452,6 +6452,28 @@ (define-public r-corrplot
     ;; Any version of the GPL
     (license license:gpl2+)))
 
+(define-public r-stable
+  (package
+    (name "r-stable")
+    (version "1.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "stable" version))
+              (sha256
+               (base32
+                "194xsa291v5f0jya1c3aigbclg8cci427ffpb8brxamm6n57hf12"))))
+    (properties `((upstream-name . "stable")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rmutil))
+    (home-page "https://www.commanster.eu/rcode.html")
+    (synopsis
+     "Probability functions and regression models for stable distributions")
+    (description
+     "This package provides density, distribution, quantile and hazard functions
+of a stable variate; generalized regression models for the parameters of a stable
+distribution.")
+    (license license:gpl2+)))
+
 (define-public r-statip
   (package
     (name "r-statip")
-- 
2.38.1

[bug#59870] [PATCH 04/12] gnu: Add r-gss.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-gss): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b773c6aeb9..bb163aa47a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7228,6 +7228,26 @@ (define-public r-ggjoy
 plots in @code{ggplot2}.")
     (license license:gpl2)))
 
+(define-public r-gss
+  (package
+    (name "r-gss")
+    (version "2.2-3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "gss" version))
+              (sha256
+               (base32
+                "0jr45lkpcndg5nynjsfnxn1wwkh4gkhsgv4hlvw6jn2frw0n8c14"))))
+    (properties `((upstream-name . "gss")))
+    (build-system r-build-system)
+    (native-inputs (list gfortran))
+    (home-page "https://cran.r-project.org/package=gss")
+    (synopsis "General smoothing splines")
+    (description
+     "This package provides a comprehensive collection for structural multivariate
+function estimation using smoothing splines.")
+    (license license:gpl2+)))
+
 (define-public r-cli
   (package
     (name "r-cli")
-- 
2.38.1

[bug#59870] [PATCH 05/12] gnu: Add r-timeseries.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-timeseries): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bb163aa47a..36c1d72a66 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7357,6 +7357,28 @@ (define-public r-processx
 timeout.  It can also poll several processes at once.")
     (license license:expat)))
 
+(define-public r-timeseries
+  (package
+    (name "r-timeseries")
+    (version "4021.105")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "timeSeries" version))
+              (sha256
+               (base32
+                "1k6vihbs20m7zjrxh13y9mmsvnia3844c7j13p0b7m5i9fb6rqxz"))))
+    (properties `((upstream-name . "timeSeries")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-timedate))
+    (home-page
+     "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics")
+    (synopsis "Metrics for financial time series objects")
+    (description
+     "This package implements S4 classes and various tools for financial time series.
+Basic functions such as scaling and sorting, subsetting, mathematical operations
+and statistical functions are provided.")
+    (license license:gpl2+)))
+
 (define-public r-tsp
   (package
     (name "r-tsp")
-- 
2.38.1

[bug#59870] [PATCH 06/12] gnu: Add r-fbasics.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-fbasics): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 36c1d72a66..6239a53d85 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8364,6 +8364,36 @@ (define-public r-extradistr
 multivariate distributions.")
     (license license:gpl2)))
 
+(define-public r-fbasics
+  (package
+    (name "r-fbasics")
+    (version "4021.93")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "fBasics" version))
+              (sha256
+               (base32
+                "1lmmdwzvqhggy6rr7yc9y5f8hxxgyzsgwm3ry0sz5ljbgfijl7g6"))))
+    (properties `((upstream-name . "fBasics")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-gss
+           r-mass
+           r-spatial
+           r-stabledist
+           r-timedate
+           r-timeseries))
+    (home-page
+     "https://r-forge.r-project.org/scm/viewvc.php/pkg/fBasics/?root=rmetrics")
+    (synopsis "Metrics for markets and basic statistics")
+    (description
+     "This package provides a collection of functions to explore and to investigate
+basic properties of financial returns and related quantities.  The covered fields
+include techniques of explorative data analysis and the investigation of
+distributional properties, including parameter estimation and hypothesis testing.
+Even more, there are several utility functions for data handling and management.")
+    (license license:gpl2+)))
+
 (define-public r-fractal
   (package
     (name "r-fractal")
-- 
2.38.1

[bug#59870] [PATCH 07/12] gnu: Add r-modeest.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-modeest): 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 6239a53d85..4e35435e46 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -31049,6 +31049,31 @@ (define-public r-modeldata
 model-related packages.")
     (license license:expat)))
 
+(define-public r-modeest
+  (package
+    (name "r-modeest")
+    (version "2.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "modeest" version))
+              (sha256
+               (base32
+                "087dw0013y4m7fcl06mxylh9lnp6acysl80d80r9srv4pw4r950s"))))
+    (properties `((upstream-name . "modeest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-fbasics
+           r-stable
+           r-stabledist
+           r-statip))
+    (home-page "https://github.com/paulponcet/modeest")
+    (synopsis "Mode estimations for univariate data or distributions")
+    (description
+     "The package provides estimators of the mode of univariate unimodal (and
+sometimes multimodal) data and values of the modes of usual probability
+distributions.")
+    (license license:gpl3)))
+
 (define-public r-conflicted
   (package
     (name "r-conflicted")
-- 
2.38.1

[bug#59870] [PATCH 08/12] gnu: Add r-dirmult.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-dirmult): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4e35435e46..415098aed3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -399,6 +399,25 @@ (define-public r-dirichletreg
     (description "This package implements Dirichlet regression models.")
     (license license:gpl2+)))
 
+(define-public r-dirmult
+  (package
+    (name "r-dirmult")
+    (version "0.1.3-5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "dirmult" version))
+              (sha256
+               (base32
+                "05whzhl81nyag7321hw98xa63r440s9bgj1764346yvm9bvzjqi4"))))
+    (properties `((upstream-name . "dirmult")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=dirmult")
+    (synopsis "Estimation in Dirichlet-Multinomial distribution")
+    (description
+     "This package estimates the parameters in Dirichlet-Multinomial and computes
+log-likelihoods.")
+    (license license:gpl2+)))
+
 (define-public r-dixontest
   (package
     (name "r-dixontest")
-- 
2.38.1

[bug#59870] [PATCH 09/12] gnu: Add r-gunifrac.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-gunifrac): New variable.
---
 gnu/packages/cran.scm | 44 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 415098aed3..646737ea31 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -667,6 +667,50 @@ (define-public r-guix-install
 repositories, replacing the need for installation via @code{devtools}.")
     (license license:gpl3+)))
 
+(define-public r-gunifrac
+  (package
+    (name "r-gunifrac")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "GUniFrac" version))
+              (sha256
+               (base32
+                "13qb5fw9km6p5x8li9x3liqbh833wf2v73npj8jl3msplzfk82vp"))))
+    (properties `((upstream-name . "GUniFrac")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ape
+           r-dirmult
+           r-foreach
+           r-ggplot2
+           r-ggrepel
+           r-mass
+           r-matrix
+           r-matrixstats
+           r-modeest
+           r-rcpp
+           r-rmutil
+           r-statmod
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=GUniFrac")
+    (synopsis
+     "Generalized UniFrac distances and methods for microbiome data analysis")
+    (description
+     "This package provides a suite of methods for powerful and robust microbiome
+data analysis, including data normalization, data simulation, community-level
+association testing and differential abundance analysis.  It implements generalized
+UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization,
+semiparametric data simulator, distance-based statistical methods, and feature-
+based statistical methods.  The distance-based statistical methods include three
+extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme,
+(2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach
+to approximating PERMANOVA p-value.  Feature-based statistical methods include
+linear model-based methods for differential abundance analysis of zero-inflated
+high-dimensional compositional data.")
+    (license license:gpl3)))
+
 (define-public r-ids
   (package
     (name "r-ids")
-- 
2.38.1

[bug#59870] [PATCH 10/12] gnu: Add r-gridsvg.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-gridsvg): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 646737ea31..b61ee1c2dc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16005,6 +16005,30 @@ (define-public r-tractor-base
 handling.")
     (license license:gpl2)))
 
+(define-public r-gridsvg
+  (package
+    (name "r-gridsvg")
+    (version "1.7-4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "gridSVG" version))
+              (sha256
+               (base32
+                "1jspjn56yrkx98hhs98npzm0k0kwpv8x1hg40kphx5ikhvincxmr"))))
+    (properties `((upstream-name . "gridSVG")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-jsonlite
+           r-xml))
+    (home-page "https://cran.r-project.org/package=gridSVG")
+    (synopsis "Export grid gaphics as SVG")
+    (description
+     "This package provides functions to export graphics drawn with package grid
+to SVG format.  Extra functions provide access to SVG features that are not
+available in standard R graphics, such as hyperlinks, animation, filters, masks,
+clipping paths, and gradient and pattern fills.")
+    (license (list license:gpl2 license:gpl3))))  ;;is specified only GPL
+
 (define-public r-grimport
   (package
     (name "r-grimport")
-- 
2.38.1

[bug#59870] [PATCH 11/12] gnu: Add r-plotroc.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-plotroc): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b61ee1c2dc..87c22810d5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21844,6 +21844,36 @@ (define-public r-plot3d
 includes data sets from oceanography.")
     (license license:gpl3+)))
 
+(define-public r-plotroc
+  (package
+    (name "r-plotroc")
+    (version "2.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "plotROC" version))
+              (sha256
+               (base32
+                "0kaz9hrimi9gi7cf7flag9kc9yrg5fdyylqa5hn53x4dy8vhj37g"))))
+    (properties `((upstream-name . "plotROC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-gridsvg
+           r-plyr
+           r-rlang
+           r-shiny))
+    (native-inputs (list r-knitr))
+    (home-page "https://sachsmc.github.io/plotROC/")
+    (synopsis "Generating useful receiver operating characteristic curve charts")
+    (description
+     "This package generates @acronym{ROC, receiver operating characteristic}
+plots.  Most ROC curve plots obscure the cutoff values and inhibit interpretation
+and comparison of multiple curves.  This attempts to address those shortcomings
+by providing plotting and interactive tools.  Functions are provided to generate
+an interactive ROC curve plot for web use, and print versions.  A Shiny application
+implementing the functions is also included.")
+    (license license:expat)))
+
 (define-public r-ggfortify
   (package
     (name "r-ggfortify")
-- 
2.38.1

[bug#59870] [PATCH 12/12] gnu: Add r-animalcules.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-animalcules): New variable.
---
 gnu/packages/bioconductor.scm | 59 +++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c62c5970b8..fa5b38be86 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2337,6 +2337,65 @@ (define-public r-ancombc
 these biases and construct statistically consistent estimators.")
     (license license:artistic2.0)))
 
+(define-public r-animalcules
+  (package
+    (name "r-animalcules")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "animalcules" version))
+              (sha256
+               (base32
+                "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr"))))
+    (properties `((upstream-name . "animalcules")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ape
+           r-assertthat
+           r-biomformat
+           r-caret
+           r-covr
+           r-deseq2
+           r-dplyr
+           r-dt
+           r-forcats
+           r-ggplot2
+           r-glmnet
+           r-gunifrac
+           r-lattice
+           r-limma
+           r-magrittr
+           r-matrix
+           r-multiassayexperiment
+           r-plotly
+           r-plotroc
+           r-rentrez
+           r-reshape2
+           r-s4vectors
+           r-scales
+           r-shiny
+           r-shinyjs
+           r-summarizedexperiment
+           r-tibble
+           r-tsne
+           r-umap
+           r-vegan
+           r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/compbiomed/animalcules")
+    (synopsis "Interactive microbiome analysis toolkit")
+    (description
+     "@code{Animalcules} is an R package for utilizing up-to-date data analytics,
+visualization methods, and machine learning models to provide users an easy-to-use
+interactive microbiome analysis framework.  It can be used as a standalone software
+package or users can explore their data with the accompanying interactive R Shiny
+application.  Traditional microbiome analysis such as alpha/beta diversity and
+differential abundance analysis are enhanced, while new methods like biomarker
+identification are introduced by animalcules.  Powerful interactive and dynamic
+figures generated by animalcules enable users to understand their data better and
+discover new insights.")
+    (license license:artistic2.0)))
+
 (define-public r-aldex2
   (package
     (name "r-aldex2")
-- 
2.38.1

bug#59870: [PATCH 01/12] gnu: Add r-statip.

[Ricardo Wurmus]

I applied this patch series with mostly minor changes, except for
r-plotroc, which required more effort to replace the minified
JavaScript.

-- 
Ricardo