Merge branch 'master' into core-updates

[jackhill/guix/guix.git] / gnu / packages / statistics.scm

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 73f4a29..ef95a56 100644 (file)
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -183,7 +183,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.6.2")
+    (version "3.6.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -191,7 +191,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0m69pfi0nxyriyb2yz74xfzaxwfkinnf9kpvf1rz727vvmfa8rdx"))))
+                "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -343,7 +343,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("openblas" ,openblas)
        ("gfortran" ,gfortran)
        ("icu4c" ,icu4c)
-       ("libjpeg" ,libjpeg)
+       ("libjpeg" ,libjpeg-turbo)
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
        ("libxt" ,libxt)
@@ -504,14 +504,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-75")
+    (version "0.8-76")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
+         "1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -590,13 +590,13 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-144")
+    (version "3.1-145")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
-        (base32 "1gqyq53fdq23wsi3f4n9vg4mn5i0v18zam5lnzlpg581xifx2779"))))
+        (base32 "1i9a3afdmn2ziks0imz0j09ay9n0zb9mhrymy9mg97vvlz5diwrh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -635,14 +635,14 @@ distributions beyond the exponential family.")
 (define-public r-nnet
   (package
     (name "r-nnet")
-    (version "7.3-12")
+    (version "7.3-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nnet" version))
        (sha256
         (base32
-         "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
+         "1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Feed-forward neural networks and multinomial log-linear models")
@@ -693,14 +693,14 @@ analysis.")
 (define-public r-survival
   (package
     (name "r-survival")
-    (version "3.1-8")
+    (version "3.1-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "survival" version))
        (sha256
         (base32
-         "15fj4y8c107bwq22amx88r5hw7qndlcbr9sapzrpkpr7iqz3kkyf"))))
+         "1fbhbm3bnpg1nmj37h1d76x813ggvwk0cp51ixmmgb3pz47i5xj4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -804,13 +804,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.24")
+    (version "0.6.25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "01xsmcgqva9bza30zh7kj4lzapxgg4yiljfk99g4v6xng50mp604"))))
+        (base32 "1r9dkq0kxkps54gkmgcdngsd068p054va2vhnqhs5jmwp2vsvk0m"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -933,13 +933,13 @@ in which the whole-plots or split-plots or both can be freely exchangeable.")
 (define-public r-plyr
   (package
     (name "r-plyr")
-    (version "1.8.5")
+    (version "1.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "plyr" version))
        (sha256
-        (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a"))))
+        (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "http://had.co.nz/plyr")
@@ -1088,26 +1088,25 @@ using just two functions: melt and dcast (or acast).")
 (define-public r-ggplot2
   (package
     (name "r-ggplot2")
-    (version "3.2.1")
+    (version "3.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggplot2" version))
        (sha256
-        (base32 "0mjswqiqcwm0aqxll16bx2kwa6c9km3aql87bdj4347n1ali94g3"))))
+        (base32 "0j21am605kqqzlwhm45kaj0m2irnmy2vz0j7kzi9f0qdzrv3q3ij"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
+       ("r-glue" ,r-glue)
        ("r-gtable" ,r-gtable)
-       ("r-lazyeval" ,r-lazyeval)
+       ("r-isoband" ,r-isoband)
        ("r-mass" ,r-mass)
        ("r-mgcv" ,r-mgcv)
        ("r-tibble" ,r-tibble)
-       ("r-reshape2" ,r-reshape2)
        ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)
        ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
-       ("r-viridislite" ,r-viridislite)
        ("r-withr" ,r-withr)))
     (home-page "https://ggplot2.tidyverse.org")
     (synopsis "An implementation of the grammar of graphics")
@@ -1415,7 +1414,7 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
        ("r-stringr" ,r-stringr)
        ("r-xfun" ,r-xfun)
        ("r-yaml" ,r-yaml)))
-    (home-page "http://yihui.name/knitr/")
+    (home-page "https://yihui.org/knitr/")
     (synopsis "General-purpose package for dynamic report generation in R")
     (description
      "This package provides a general-purpose tool for dynamic report
@@ -1555,13 +1554,13 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "2.3.1")
+    (version "2.3.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "0m8xchdpgn9iwj6gb2qw46zr85v9zf1gkbr9nnahmy5sp1s9bbky"))))
+                "0v70v2fs0f2ir962z9csbjlj8snrq9mbjfyhhb9dhz3zy26qs9hs"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -1607,13 +1606,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.4.4")
+    (version "0.4.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "1kqmrk00lnkbclnvj1dizjbdav0g1w44yd6ja4yy3bivwan9jf23"))))
+                "1a0h3dr519p3jj6aygbhwi9f2zwlan6d07f1gkh2db56y5vaq7yd"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1651,17 +1650,18 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.8.3")
+    (version "0.8.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
+                "0602b4a9nffxx67q57csqp87nkrv33nn9wlaw1458yys9fzx6l2p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-bh" ,r-bh)
+       ("r-ellipsis" ,r-ellipsis)
        ("r-glue" ,r-glue)
        ("r-magrittr" ,r-magrittr)
        ("r-pkgconfig" ,r-pkgconfig)
@@ -1671,6 +1671,8 @@ and printing capabilities than traditional data frames.")
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
        ("r-tidyselect" ,r-tidyselect)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/dplyr")
     (synopsis "Tools for working with data frames in R")
     (description
@@ -1878,14 +1880,14 @@ building design matrices.")
 (define-public python-statsmodels
   (package
     (name "python-statsmodels")
-    (version "0.9.0")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "statsmodels" version))
        (sha256
         (base32
-         "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
+         "1w6mf8b86vizi2895j11szqryr2v1ckjig3wp9fv94aslfh3zpjv"))))
     (build-system python-build-system)
     (arguments
      `(;; The test suite is very large and rather brittle.  Tests often fail
@@ -1958,17 +1960,19 @@ chain.")
 (define-public r-ade4
   (package
     (name "r-ade4")
-    (version "1.7-13")
+    (version "1.7-15")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "ade4" version))
         (sha256
           (base32
-            "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
+            "1xpxznlqm8wb4d5z2dcrl0wi3jjciq2hr5rcx2b5aaipiiyzm1ij"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-mass" ,r-mass)))
+     `(("r-mass" ,r-mass)
+       ("r-pixmap" ,r-pixmap)
+       ("r-sp" ,r-sp)))
     (home-page "http://pbil.univ-lyon1.fr/ADE-4")
     (synopsis "Multivariate data analysis and graphical display")
     (description
@@ -3147,7 +3151,7 @@ using the multicore functionality of the parallel package.")
        ("r-jsonlite" ,r-jsonlite)
        ("r-magrittr" ,r-magrittr)
        ("r-promises" ,r-promises)))
-    (home-page "http://rstudio.github.io/DT")
+    (home-page "https://rstudio.github.io/DT")
     (synopsis "R wrapper of the DataTables JavaScript library")
     (description
      "This package allows for data objects in R to be rendered as HTML tables
@@ -3550,13 +3554,13 @@ vignettes.")
 (define-public r-mvtnorm
   (package
     (name "r-mvtnorm")
-    (version "1.0-12")
+    (version "1.1-0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mvtnorm" version))
               (sha256
                (base32
-                "03rfmii9j8x8fjv7hp8qd28z0svl4w0x54k2f4jpwv4qa7079i24"))))
+                "0pfb6qk4yb6xaya8i1wvx6dnc3jj4s2g94sq2kzv4p8zn4pf24l1"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -3605,6 +3609,8 @@ memory usage.")
      `(("r-ggplot2" ,r-ggplot2)
        ("r-gridextra" ,r-gridextra)
        ("r-viridislite" ,r-viridislite)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
     (home-page "https://github.com/sjmgarnier/viridis")
     (synopsis "Matplotlib default color map")
     (description
@@ -3646,20 +3652,21 @@ more complete @code{viridis} package.")
 (define-public r-tidyselect
   (package
     (name "r-tidyselect")
-    (version "0.2.5")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyselect" version))
        (sha256
         (base32
-         "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
+         "1bwwsljkg1bxh7xnqxv7n0n1s9y8x407i6lsv826vy1ss1k1fxpy"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-glue" ,r-glue)
+     `(("r-ellipsis" ,r-ellipsis)
+       ("r-glue" ,r-glue)
        ("r-purrr" ,r-purrr)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rlang" ,r-rlang)))
+       ("r-rlang" ,r-rlang)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://cran.r-project.org/web/packages/tidyselect")
     (synopsis "Select from a set of strings")
     (description
@@ -3708,19 +3715,20 @@ and tidyr provides no margins or aggregation.")
 (define-public r-hexbin
   (package
     (name "r-hexbin")
-    (version "1.28.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hexbin" version))
        (sha256
         (base32
-         "0b58jb1kz39wzrnkv077cfzns889xly7psvhxnm3xmnx6yvd986d"))))
+         "1ry6jm3lqz3mj0s5rzbs6mpkz2hxpnvbw8c1vwc4pj7b173r5l22"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
     (native-inputs
-     `(("gfortran" ,gfortran)))
+     `(("gfortran" ,gfortran)
+       ("r-knitr" ,r-knitr))) ; for vignettes
     (home-page "https://github.com/edzer/hexbin")
     (synopsis "Hexagonal binning routines")
     (description
@@ -3914,7 +3922,7 @@ from within R.")
     (propagated-inputs
      `(("r-lattice" ,r-lattice)
        ("r-matrix" ,r-matrix)))
-    (home-page "http://spams-devel.gforge.inria.fr")
+    (home-page "https://spams-devel.gforge.inria.fr")
     (synopsis "Toolbox for solving sparse estimation problems")
     (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
 for solving various sparse estimation problems.  It includes tools for the
@@ -4174,14 +4182,14 @@ including:
 (define-public r-gplots
   (package
     (name "r-gplots")
-    (version "3.0.1.2")
+    (version "3.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gplots" version))
        (sha256
         (base32
-         "0vrm7wqrmqsmfrc070r9chpzb0vv60pay2lyar9qxfry6bsrvx86"))))
+         "0hs6mk48i9yd43rg9wfjc2nxsjjwrnpifxqvxkv8ah18kvpd6xnp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-catools" ,r-catools)
@@ -4520,17 +4528,18 @@ letters, as is often required for scientific publications.")
 (define-public r-mixtools
   (package
     (name "r-mixtools")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mixtools" version))
        (sha256
         (base32
-         "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
+         "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
+       ("r-kernlab" ,r-kernlab)
        ("r-segmented" ,r-segmented)
        ("r-survival" ,r-survival)))
     (home-page "https://cran.r-project.org/web/packages/mixtools")
@@ -4632,14 +4641,14 @@ original public code has been corrected.")
 (define-public r-modeltools
   (package
     (name "r-modeltools")
-    (version "0.2-22")
+    (version "0.2-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "modeltools" version))
        (sha256
         (base32
-         "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
+         "1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/modeltools")
     (synopsis "Tools and classes for statistical models")
@@ -4847,14 +4856,14 @@ generally.")
 (define-public r-robust
   (package
     (name "r-robust")
-    (version "0.4-18.2")
+    (version "0.5-0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "robust" version))
        (sha256
         (base32
-         "02x7d6dgx3skiadvx5m3c44b4bhz37ycpfhc25dhhv50y1db6l3k"))))
+         "1ks5scp8bnicl9j1r8yrmz668fjs6ifdmi540zw6d2ck500bbw42"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fit-models" ,r-fit-models)
@@ -5092,14 +5101,14 @@ expected shortfall risk are also included.")
 (define-public r-nloptr
   (package
     (name "r-nloptr")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nloptr" version))
        (sha256
         (base32
-         "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
+         "19k7nd3a7cg35k5i1cwj1lhgfs02jb7bc2gwlammpq6j41rh4vr7"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr) ; for building vignettes
@@ -5151,17 +5160,18 @@ C++ library for numerical linear algebra and RcppEigen glue.")
 (define-public r-pbkrtest
   (package
     (name "r-pbkrtest")
-    (version "0.4-7")
+    (version "0.4-8.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbkrtest" version))
        (sha256
         (base32
-         "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
+         "0s5xhhrhv5i9680lw6af9lj2x4jc3fygmzzk0jjpxnb8g4b3p1jz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
+       ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)))
     (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
@@ -5245,14 +5255,14 @@ even in multithreaded code, typically using OpenMP.")
 (define-public r-mnormt
   (package
     (name "r-mnormt")
-    (version "1.5-5")
+    (version "1.5-6")
     (source
      (origin
        (method url-fetch)
         (uri (cran-uri "mnormt" version))
         (sha256
           (base32
-           "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
+           "0k8y08gj6z525yvc7y3dl2kzgnafbj3i7lvpamypsmqxf74zql99"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -5288,14 +5298,14 @@ first and second order derivatives.")
 (define-public r-sn
   (package
     (name "r-sn")
-    (version "1.5-4")
+    (version "1.5-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sn" version))
        (sha256
         (base32
-         "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6"))))
+         "0ymyyc0di1g2b11wzljiih05z3rxck48wn74bygg3fiby973z49f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mnormt" ,r-mnormt)
@@ -5473,14 +5483,14 @@ and the corresponding decision threshold.")
 (define-public r-forcats
   (package
     (name "r-forcats")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "forcats" version))
        (sha256
         (base32
-         "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
+         "1i4hblsjgwkrcwgvgsb5yj33pw1hwdj3lr9dvxymkv1kjdw0x5lg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ellipsis" ,r-ellipsis)
@@ -5560,14 +5570,14 @@ parameters.")
 (define-public r-directlabels
   (package
     (name "r-directlabels")
-    (version "2018.05.22")
+    (version "2020.1.31")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "directlabels" version))
        (sha256
         (base32
-         "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
+         "08s1gnwp4bn8xahwjaq0f1qzhwh2dvybzhq3z7xyzn8cnyzmis6c"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)))