@@ 120,6 120,96 @@
#:use-module (srfi srfi-1)
#:use-module (ice-9 match))
+(define-public jags
+ (package
+ (name "jags")
+ (version "4.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
+ (version-major version) ".x/Source/"
+ "JAGS-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list #:configure-flags
+ #~(list "--with-lapack=-lopenblas"
+ "--with-blas=-lopenblas")))
+ (home-page "https://mcmc-jags.sourceforge.net/")
+ (native-inputs
+ (list gfortran openblas))
+ (synopsis "Gibbs sampler")
+ (description "JAGS is Just Another Gibbs Sampler. It is a program for
+analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
+simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
+
+@enumerate
+@item To have a cross-platform engine for the BUGS language;
+@item To be extensible, allowing users to write their own functions,
+ distributions and samplers;
+@item To be a platform for experimentation with ideas in Bayesian modelling.
+@end enumerate\n")
+ (license license:gpl2)))
+
+(define-public java-jdistlib
+ (package
+ (name "java-jdistlib")
+ (version "0.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
+ version "-src.jar"))
+ (sha256
+ (base32
+ "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:jar-name "jdistlib.jar"
+ #:jdk ,icedtea-8
+ #:tests? #f ; no dedicated test directory
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-broken-encoding
+ (lambda _
+ (with-fluids ((%default-port-encoding "ISO-8859-1"))
+ (substitute* "src/jdistlib/Beta.java"
+ (("Scheff.+-Tukey") "Scheffe-Tukey")))
+ #t)))))
+ (propagated-inputs
+ (list java-jtransforms))
+ (native-inputs
+ (list java-junit))
+ (home-page "https://jdistlib.sourceforge.net/")
+ (synopsis "Java library of statistical distributions")
+ (description "JDistlib is the Java Statistical Distribution Library, a
+Java package that provides routines for various statistical distributions.")
+ ;; The files that were translated from R code are under GPLv2+; some files
+ ;; are under the GPLv3, which is a mistake. The author confirmed in an
+ ;; email that this whole project should be under GPLv2+.
+ (license license:gpl2+)))
+
+(define-public libxls
+ (package
+ (name "libxls")
+ (version "1.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/libxls/libxls/releases/download/"
+ "v" version "/libxls-" version ".tar.gz"))
+ (sha256
+ (base32 "0b327zafbwnfxj75n722z6a6zw195rs5bjmm5wskl9dml1p87yxj"))))
+ (build-system gnu-build-system)
+ (home-page "https://github.com/libxls/libxls")
+ (synopsis "Read binary (.xls) Excel spreadsheet files")
+ (description
+ "libxls is a C library to read .xls spreadsheet files in the binary OLE
+BIFF8 format as created by Excel 97 and later versions. It cannot write them.
+
+This package also provides @command{xls2csv} to export Excel files to CSV.")
+ (license license:bsd-2)))
(define-public pspp
(package
@@ 175,60 265,6 @@ can be imported from spreadsheets, text files and database sources and it can
be output in text, PostScript, PDF or HTML.")
(license license:gpl3+)))
-(define-public jags
- (package
- (name "jags")
- (version "4.3.1")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
- (version-major version) ".x/Source/"
- "JAGS-" version ".tar.gz"))
- (sha256
- (base32
- "0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr"))))
- (build-system gnu-build-system)
- (arguments
- (list #:configure-flags
- #~(list "--with-lapack=-lopenblas"
- "--with-blas=-lopenblas")))
- (home-page "https://mcmc-jags.sourceforge.net/")
- (native-inputs
- (list gfortran openblas))
- (synopsis "Gibbs sampler")
- (description "JAGS is Just Another Gibbs Sampler. It is a program for
-analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
-simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
-
-@enumerate
-@item To have a cross-platform engine for the BUGS language;
-@item To be extensible, allowing users to write their own functions,
- distributions and samplers;
-@item To be a platform for experimentation with ideas in Bayesian modelling.
-@end enumerate\n")
- (license license:gpl2)))
-
-(define-public libxls
- (package
- (name "libxls")
- (version "1.6.3")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://github.com/libxls/libxls/releases/download/"
- "v" version "/libxls-" version ".tar.gz"))
- (sha256
- (base32 "0b327zafbwnfxj75n722z6a6zw195rs5bjmm5wskl9dml1p87yxj"))))
- (build-system gnu-build-system)
- (home-page "https://github.com/libxls/libxls")
- (synopsis "Read binary (.xls) Excel spreadsheet files")
- (description
- "libxls is a C library to read .xls spreadsheet files in the binary OLE
-BIFF8 format as created by Excel 97 and later versions. It cannot write them.
-
-This package also provides @command{xls2csv} to export Excel files to CSV.")
- (license license:bsd-2)))
-
;; Update this package together with the set of recommended packages: r-boot,
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
@@ 469,6 505,42 @@ publication-quality data plots. A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
(license license:gpl3+)))
+(define-public python-chaospy
+ (package
+ (name "python-chaospy")
+ (version "4.3.13")
+ (source (origin ;; PyPI misses Pytest fixtures.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jonathf/chaospy")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The deprecation warnings break the tests.
+ (add-after 'unpack 'dont-treat-deprecation-warnings-as-error
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("\"error::DeprecationWarning\",") "")))))))
+ (propagated-inputs (list python-importlib-metadata python-numpoly
+ python-numpy python-scipy))
+ (native-inputs (list python-pytest python-scikit-learn python-setuptools
+ python-wheel))
+ (home-page "https://chaospy.readthedocs.io/en/master/")
+ (synopsis "Numerical tool for performing uncertainty quantification")
+ (description "Chaospy is a numerical toolbox for performing uncertainty
+quantification using polynomial chaos expansions, advanced Monte Carlo
+methods implemented in Python. It also include a full suite of tools for
+doing low-discrepancy sampling, quadrature creation, polynomial manipulations,
+and a lot more.")
+ (license license:expat)))
+
(define-public python-dcor
(package
(name "python-dcor")
@@ 887,6 959,31 @@ and Vega-Lite examples.")
"Vega-Altair is a declarative statistical visualization library for Python.")
(license license:expat)))
+(define-public python-emcee
+ (package
+ (name "python-emcee")
+ (version "3.1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "emcee" version))
+ (sha256
+ (base32 "0zb3ihja3hyj6zjbhkpxhyyppnv58q2jjg0yd1lwmydqdaplvbqi"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-numpy))
+ (native-inputs (list python-coverage
+ python-pytest
+ python-pytest-cov
+ python-setuptools
+ python-setuptools-scm
+ python-wheel))
+ (home-page "https://emcee.readthedocs.io/en/stable/")
+ (synopsis "Ensemble sampling toolkit for MCMC")
+ (description
+ "@code{emcee} is a Python implementation of the affine-invariant ensemble
+sampler for Markov chain Monte Carlo (MCMC).")
+ (license license:expat)))
+
(define-public python-george
(package
(name "python-george")
@@ 1142,42 1239,6 @@ modeling focusing on advanced Markov chain Monte Carlo (MCMC) and variational
inference (VI) algorithms.")
(license license:asl2.0)))
-(define-public python-chaospy
- (package
- (name "python-chaospy")
- (version "4.3.13")
- (source (origin ;; PyPI misses Pytest fixtures.
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/jonathf/chaospy")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- ;; The deprecation warnings break the tests.
- (add-after 'unpack 'dont-treat-deprecation-warnings-as-error
- (lambda _
- (substitute* "pyproject.toml"
- (("\"error::DeprecationWarning\",") "")))))))
- (propagated-inputs (list python-importlib-metadata python-numpoly
- python-numpy python-scipy))
- (native-inputs (list python-pytest python-scikit-learn python-setuptools
- python-wheel))
- (home-page "https://chaospy.readthedocs.io/en/master/")
- (synopsis "Numerical tool for performing uncertainty quantification")
- (description "Chaospy is a numerical toolbox for performing uncertainty
-quantification using polynomial chaos expansions, advanced Monte Carlo
-methods implemented in Python. It also include a full suite of tools for
-doing low-discrepancy sampling, quadrature creation, polynomial manipulations,
-and a lot more.")
- (license license:expat)))
-
(define-public python-patsy
(package
(name "python-patsy")
@@ 1302,31 1363,6 @@ uncertainties and are backed by strong theoretical guarantees thanks to
conformal prediction methods intervals.")
(license license:bsd-3)))
-(define-public python-emcee
- (package
- (name "python-emcee")
- (version "3.1.6")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "emcee" version))
- (sha256
- (base32 "0zb3ihja3hyj6zjbhkpxhyyppnv58q2jjg0yd1lwmydqdaplvbqi"))))
- (build-system pyproject-build-system)
- (propagated-inputs (list python-numpy))
- (native-inputs (list python-coverage
- python-pytest
- python-pytest-cov
- python-setuptools
- python-setuptools-scm
- python-wheel))
- (home-page "https://emcee.readthedocs.io/en/stable/")
- (synopsis "Ensemble sampling toolkit for MCMC")
- (description
- "@code{emcee} is a Python implementation of the affine-invariant ensemble
-sampler for Markov chain Monte Carlo (MCMC).")
- (license license:expat)))
-
(define-public python-statsmodels
(package
(name "python-statsmodels")
@@ 3096,43 3132,6 @@ editing and rich syntax highlight. One would consider Radian as a IPython
clone for R, though its design is more aligned to Julia.")
(license license:expat)))
-(define-public java-jdistlib
- (package
- (name "java-jdistlib")
- (version "0.4.5")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
- version "-src.jar"))
- (sha256
- (base32
- "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
- (build-system ant-build-system)
- (arguments
- `(#:jar-name "jdistlib.jar"
- #:jdk ,icedtea-8
- #:tests? #f ; no dedicated test directory
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-broken-encoding
- (lambda _
- (with-fluids ((%default-port-encoding "ISO-8859-1"))
- (substitute* "src/jdistlib/Beta.java"
- (("Scheff.+-Tukey") "Scheffe-Tukey")))
- #t)))))
- (propagated-inputs
- (list java-jtransforms))
- (native-inputs
- (list java-junit))
- (home-page "https://jdistlib.sourceforge.net/")
- (synopsis "Java library of statistical distributions")
- (description "JDistlib is the Java Statistical Distribution Library, a
-Java package that provides routines for various statistical distributions.")
- ;; The files that were translated from R code are under GPLv2+; some files
- ;; are under the GPLv3, which is a mistake. The author confirmed in an
- ;; email that this whole project should be under GPLv2+.
- (license license:gpl2+)))
-
(define-public emacs-ess
(package
(name "emacs-ess")
@@ 3277,32 3276,6 @@ statistical analysis programs such as R, Julia, and JAGS.")
files, including Rmarkdown files.")
(license license:gpl3+)))
-(define-public readstat
- (let ((commit "718d49155e327471ed9bf4a8c157f849f285b46c")
- (revision "0"))
- (package
- (name "readstat")
- (version (git-version "1.1.9" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/WizardMac/ReadStat")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "121axcx4shd0fqlcr1mk7y841sd59r9mx473c4av8gs81xfhcg0h"))))
- (build-system gnu-build-system)
- (native-inputs
- (list autoconf automake gettext-minimal libtool))
- (inputs
- (list zlib))
- (home-page "https://github.com/WizardMac/ReadStat")
- (synopsis "Convert SAS, Stata, and SPSS files")
- (description "Command-line tool and C library for reading files from
-popular stats packages like SAS, Stata and SPSS.")
- (license license:expat))))
-
(define-public python-pyreadstat
(package
(name "python-pyreadstat")
@@ 3347,59 3320,6 @@ files into/from Pandas DataFrames. It is a wrapper around the C library
@code{readstat}.")
(license license:asl2.0)))
-(define-public xlispstat
- (let ((commit "f1bea6053df658ee48612bf1f63c35de99e2c649")
- (revision "0"))
- (package
- (name "xlispstat")
- (version (git-version "3.52.23" revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/jhbadger/xlispstat.git")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1p0cmgy19kbkxia139cb5w9dnkp2cdqp5n3baag6cq3prn3n71mf"))))
- (build-system gnu-build-system)
- (arguments
- `(#:parallel-build? #f ; Parallel builds are not supported
- #:configure-flags (list "--with-gcc")
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (with-output-to-file "exit.lsp"
- (lambda () (display "(exit)")))
- (invoke "./xlisp" "tests/test" "exit")))))))
- (inputs (list tcsh
- libx11
- libxmu
- libxext
- libxpm
- libxaw
- ncurses
- gnuplot))
- (native-inputs (list pkg-config))
- (synopsis "Statistical analysis environment with interactive graphics")
- (description "XLISP-STAT is a statistical environment based on a Lisp
-dialect called XLISP. To facilitate statistical computations, standard
-functions for addition, logarithms, etc., have been modified to operate on
-lists and arrays of numbers, and a number of basic statistical functions have
-been added. Many of these functions have been written in Lisp, and additional
-functions can be added easily by a user. Several basic forms of plots,
-including histograms, scatterplots, rotatable plots and scatterplot matrices
-are provided. These plots support various forms of interactive highlighting
-operations and can be linked so points highlighted in one plot will be
-highlighted in all linked plots. Interactions with the plots are controlled
-by the mouse, menus and dialog boxes. An object-oriented programming system
-is used to allow menus, dialogs, and the response to mouse actions to be
- customized.")
- (home-page "https://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/")
- (license license:expat))))
-
(define-public r-rlrsim
(package
(name "r-rlrsim")
@@ 3573,6 3493,32 @@ package can generate VPCs for continuous, categorical, censored, and
(repeated) time-to-event data.")
(license license:expat)))
+(define-public readstat
+ (let ((commit "718d49155e327471ed9bf4a8c157f849f285b46c")
+ (revision "0"))
+ (package
+ (name "readstat")
+ (version (git-version "1.1.9" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/WizardMac/ReadStat")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "121axcx4shd0fqlcr1mk7y841sd59r9mx473c4av8gs81xfhcg0h"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ (list autoconf automake gettext-minimal libtool))
+ (inputs
+ (list zlib))
+ (home-page "https://github.com/WizardMac/ReadStat")
+ (synopsis "Convert SAS, Stata, and SPSS files")
+ (description "Command-line tool and C library for reading files from
+popular stats packages like SAS, Stata and SPSS.")
+ (license license:expat))))
+
(define-public ruby-enumerable-statistics
(package
(name "ruby-enumerable-statistics")
@@ 3670,3 3616,56 @@ statistical summary in arrays and enumerables.")
can be used for learning (Structure and Parameter), inference (Probabilistic
and Causal), and simulations in Bayesian Networks.")
(license license:expat)))
+
+(define-public xlispstat
+ (let ((commit "f1bea6053df658ee48612bf1f63c35de99e2c649")
+ (revision "0"))
+ (package
+ (name "xlispstat")
+ (version (git-version "3.52.23" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jhbadger/xlispstat.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1p0cmgy19kbkxia139cb5w9dnkp2cdqp5n3baag6cq3prn3n71mf"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:parallel-build? #f ; Parallel builds are not supported
+ #:configure-flags (list "--with-gcc")
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-output-to-file "exit.lsp"
+ (lambda () (display "(exit)")))
+ (invoke "./xlisp" "tests/test" "exit")))))))
+ (inputs (list tcsh
+ libx11
+ libxmu
+ libxext
+ libxpm
+ libxaw
+ ncurses
+ gnuplot))
+ (native-inputs (list pkg-config))
+ (synopsis "Statistical analysis environment with interactive graphics")
+ (description "XLISP-STAT is a statistical environment based on a Lisp
+dialect called XLISP. To facilitate statistical computations, standard
+functions for addition, logarithms, etc., have been modified to operate on
+lists and arrays of numbers, and a number of basic statistical functions have
+been added. Many of these functions have been written in Lisp, and additional
+functions can be added easily by a user. Several basic forms of plots,
+including histograms, scatterplots, rotatable plots and scatterplot matrices
+are provided. These plots support various forms of interactive highlighting
+operations and can be linked so points highlighted in one plot will be
+highlighted in all linked plots. Interactions with the plots are controlled
+by the mouse, menus and dialog boxes. An object-oriented programming system
+is used to allow menus, dialogs, and the response to mouse actions to be
+ customized.")
+ (home-page "https://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/")
+ (license license:expat))))