(define-module (gn packages statistics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system python)
  #:use-module (guix build-system r)
  #:use-module (gnu packages)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages cran)
  #:use-module (past packages python27)

  ;; for python-rpy2 and dependencies
  #:use-module (gnu packages python-build)
  #:use-module (guix build-system pyproject); python-rpy2-rinterface
  #:use-module (gnu packages libffi); python-rpy2-rinterface
  #:use-module (gnu packages check); python-rpy2-rinterface
  #:use-module (gnu packages compression); python-rpy2-rinterface
  #:use-module (gnu packages icu4c); python-rpy2-rinterface
  #:use-module (gnu packages time); python-rpy2-robjects
  )

(define-public r-hmisc-3
  (package
    (name "r-hmisc")
    (version "3.17-2")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Hmisc" version))
        (sha256
         (base32
          "110w5hbrl10isslqs0iq6w2ll0dafqyqznb50cdcallnlnvbvxrg"))))
    (properties `((upstream-name . "Hmisc")))
    (build-system r-build-system)
    (inputs
     `(("gfortran" ,gfortran)))
    (arguments
     `(#:tests? #f))   ; no 'setup.py test'
    (propagated-inputs
     `(("r-acepack" ,r-acepack)
       ("r-cluster" ,r-cluster)
       ("r-foreign" ,r-foreign)
       ("r-formula" ,r-formula)
       ("r-ggplot2" ,r-ggplot2)
       ; ("r-grid" ,r-grid)
       ("r-gridextra" ,r-gridextra)
       ("r-gtable" ,r-gtable)
       ("r-lattice" ,r-lattice)
       ("r-latticeextra" ,r-latticeextra)
       ; ("r-methods" ,r-methods)
       ("r-nnet" ,r-nnet)
       ("r-rpart" ,r-rpart)
       ("r-survival" ,r-survival)
       ))
    (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
    (synopsis "Harrell Miscellaneous")
    (description
     "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.")
    (license license:gpl2+)))

(define-public r-graphics
  (package
    (name "r-graphics")
    (version "2.0-13")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RGraphics" version))
        (sha256
         (base32
          "10c6wiqh074bmbg2gwdscwp5kj8afs152ipv0byyqw5n2r8fw0w1"))))
    (properties `((upstream-name . "RGraphics")))
    (build-system r-build-system)
    (propagated-inputs
     `(;; ("r-datasets" ,r-datasets)
       ("r-ggplot2" ,r-ggplot2)
       ;; ("r-graphics" ,r-graphics)
       ;; ("r-grdevices" ,r-grdevices)
       ;; ("r-grid" ,r-grid)
       ("r-lattice" ,r-lattice)
       ;; ("r-methods" ,r-methods)
       ;; ("r-stats" ,r-stats)
       ))
    (home-page "http://www.stat.auckland.ac.nz/~paul/RG2e/index.html")
    (synopsis
     "Data and Functions from the Book R Graphics, Second Edition")
    (description
     "Data and Functions from the book R Graphics, Second Edition.  There is a function to produce each figure in the book, plus several functions, classes, and methods defined in Chapter 8.")
    (license license:gpl2+)))

(define-public pylmm-gn2
  (let ((commit "3c6d1cac8"))
    (package
      (name "pylmm-gn2")
      (version (string-append "1.0-" commit ))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                       (url "https://github.com/genenetwork/pylmm.git")
                       (commit commit)))
                (file-name (string-append name "-" commit))
                (sha256
                 (base32
                  "0wryaadb36i275p9d2i1kzflahvbl9kj5wlk8jlbvjij8gpqg964"))))
      (build-system python-build-system)
      (inputs `(
                ("python2-setuptools" ,python2-setuptools)
                ("python2-scipy" ,python2-scipy)
                ("python2-numpy" ,python2-numpy)
                ))
      (arguments
       `(#:python ,python-2
         #:tests? #f        ; no 'setup.py test'
         #:phases
         (modify-phases %standard-phases
           (add-before
             'build 'change-paths
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((out (assoc-ref outputs "out")))
                 (substitute* "scripts/pylmm_redis"
                   (("/usr/bin/python") (which "python"))
                   (("\\$PACKAGEDIR") (string-append out "/lib/python2.7/site-packages")))
                 ))))))

      (home-page "http://genenetwork.org/")
      (synopsis "LMM resolver")
      (description "Fast and lightweight linear mixed-model (LMM) solver
for use in genome-wide association studies (GWAS).")
      (license license:agpl3+))))

(define-public r-ctl ; guix: ready
  (package
    (name "r-ctl")
    (version "1.0.0-7")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ctl" version))
        (sha256
         (base32
          "1a01rha6sgv8zmcfjb1c438s9d9bjzdjf2pmyml1m5jmz93q70ds"))))
    (build-system r-build-system)
    (inputs `(
              ("r-qtl" ,r-qtl)
              ("r-mass" ,r-mass)
              ))
    (home-page "https://github.com/DannyArends/CTLmapping")
    (synopsis "R package for analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL)")
    (description "Analysis of experimental crosses to identify genetic
markers associated with correlation changes in quantitative
traits (CTL).  The additional correlation information obtained can be
combined with QTL information to perform de novo reconstruction of
interaction networks.")
    (license license:gpl3)))


(define-public python-rpy2-rinterface
  (package
    (name "python-rpy2-rinterface")
    (version "3.6.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "rpy2_rinterface" version))
       (sha256
        (base32 "1hjnc4143dvcrp9m4vnxm4fs2ahiagp5lklsqp1nki341kh0samn"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-cffi
                             python-packaging
                             ;;python-backports-zoneinfo ; needed for python_version<3.9
                             r-minimal))
    (native-inputs (list zlib
                         icu4c
                         libdeflate
                         python-cffi
                         python-coverage
                         python-packaging
                         python-pytest
                         python-pytest-cov
                         python-setuptools
                         python-wheel
                         r-survival))
    (home-page "https://rpy2.github.io/")
    (synopsis "Low-level interface from Python to the R")
    (description "Low-level interface for rpy2. rpy2 is an interface to R
 running embedded in a Python process.")
    (license license:gpl2)))


(define-public python-rpy2-robjects
  (package
    (name "python-rpy2-robjects")
    (version "3.6.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "rpy2_robjects" version))
       (sha256
        (base32 "0yn4nq26na9hzlm08vsxr050ls5nmngpyma49fpfwc9mhxc7njlk"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-jinja2
                             python-packaging
                             python-rpy2-rinterface
                             ;;python-backports-zoneinfo; needed for python_version<3.9
                             python-tzlocal))
    (native-inputs (list python-coverage
                         python-ipython
                         python-numpy
                         python-packaging
                         python-pandas
                         python-pytest
                         python-pytest-cov
                         python-setuptools
                         python-wheel))
    (home-page #f)
    (synopsis "Python interface to the R language (embedded R)")
    (description "Python interface to the R language (embedded R).")
    (license #f)))