Merge branch 'wip-r'

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2a4ccd3..5a8285b 100644 (file)
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -347,6 +347,29 @@ visualization of their differences.")
     (description "This package implements Dirichlet regression models.")
     (license license:gpl2+)))
 
+(define-public r-dixontest
+  (package
+    (name "r-dixontest")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dixonTest" version))
+       (sha256
+        (base32 "1a3yc30g5rbb0jhm2b0iir5i1dy4jyl67spkhx4yysg4snz131wv"))))
+    (properties `((upstream-name . "dixonTest")))
+    (build-system r-build-system)
+    (native-inputs (list gfortran))
+    (home-page "https://cran.r-project.org/package=dixonTest")
+    (synopsis "Dixon's ratio test for outlier detection")
+    (description
+     "For outlier detection in small and normally distributed samples the ratio
+test of Dixon (Q-test) can be used.  Density, distribution function, quantile
+function and random generation for Dixon's ratio statistics are provided as
+wrapper functions.  The core applies McBane's Fortran functions that use
+Gaussian quadrature for a numerical solution.")
+    (license license:gpl3)))
+
 (define-public r-emdist
   (package
     (name "r-emdist")
@@ -402,6 +425,33 @@ Distance (EMD).")
     (description "This package lets you manage Google Drive files from R.")
     (license license:expat)))
 
+(define-public r-googlevis
+  (package
+    (name "r-googlevis")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "googleVis" version))
+       (sha256
+        (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz"))))
+    (properties `((upstream-name . "googleVis")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-jsonlite))
+    (native-inputs (list r-knitr))
+    (home-page "https://mages.github.io/googleVis/")
+    (synopsis "R interface to Google Charts")
+    (description
+     "The @code{googleVis} package provides an interface between R and the Google
+Charts API.  Google Charts offer interactive charts which can be embedded into
+web pages.  The functions of the @code{googleVis} package allow the user to
+visualise data stored in R data frames with Google Charts without uploading
+the data to Google.  The output of a @code{googleVis} function is HTML code
+that contains the data and references to JavaScript functions hosted by
+Google.  @code{googleVis} makes use of the internal R HTTP server to display
+the output locally.")
+    (license license:gpl2+)))
+
 (define-public r-guix-install
   (package
     (name "r-guix-install")
@@ -3831,6 +3881,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
 @code{citation(\"Rcpp\")} for details on these last two.")
     (license license:gpl2+)))
 
+(define-public r-rcppml
+  (package
+    (name "r-rcppml")
+    (version "0.3.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppML" version))
+       (sha256
+        (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
+    (properties `((upstream-name . "RcppML")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/zdebruine/RcppML")
+    (synopsis "Rcpp machine learning library")
+    (description
+     "This package provides fast machine learning algorithms including matrix
+factorization and divisive clustering for large sparse and dense matrices.")
+    (license license:gpl2+)))
+
 (define-public r-rcppthread
   (package
     (name "r-rcppthread")
@@ -28025,14 +28096,14 @@ the @code{survival} package.")
 (define-public r-exactranktests
   (package
     (name "r-exactranktests")
-    (version "0.8-34")
+    (version "0.8-35")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "exactRankTests" version))
        (sha256
         (base32
-         "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9"))))
+         "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
     (properties
      `((upstream-name . "exactRankTests")))
     (build-system r-build-system)
@@ -28235,14 +28306,14 @@ model.")
 (define-public r-igraph
   (package
     (name "r-igraph")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "igraph" version))
        (sha256
         (base32
-         "09dzc8lslljvhj2q46075vxcmlgkvq2qs500zdqyy9g8scq6iqbi"))))
+         "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran))
@@ -28693,14 +28764,14 @@ models without involving a test set.")
 (define-public r-tidypredict
   (package
     (name "r-tidypredict")
-    (version "0.4.8")
+    (version "0.4.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidypredict" version))
        (sha256
         (base32
-         "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
+         "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
     (properties `((upstream-name . "tidypredict")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28814,14 +28885,14 @@ vignettes in all common formats.")
 (define-public r-tidytext
   (package
     (name "r-tidytext")
-    (version "0.3.2")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytext" version))
        (sha256
         (base32
-         "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g"))))
+         "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm"))))
     (properties `((upstream-name . "tidytext")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29014,14 +29085,14 @@ data structures of the tidyverse.")
 (define-public r-lsa
   (package
     (name "r-lsa")
-    (version "0.73.2")
+    (version "0.73.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lsa" version))
        (sha256
         (base32
-         "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
+         "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
     (properties `((upstream-name . "lsa")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29103,14 +29174,14 @@ phylogenetic relatedness) can also be conducted.")
 (define-public r-altmeta
   (package
     (name "r-altmeta")
-    (version "3.3")
+    (version "4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "altmeta" version))
        (sha256
         (base32
-         "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm"))))
+         "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5"))))
     (properties `((upstream-name . "altmeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29282,18 +29353,26 @@ data to rasters.  It speeds up plotting of data with millions of points.")
 (define-public r-seuratobject
   (package
     (name "r-seuratobject")
-    (version "4.0.4")
+    (version "4.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SeuratObject" version))
        (sha256
         (base32
-         "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq"))))
+         "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w"))))
     (properties `((upstream-name . "SeuratObject")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-matrix r-rcpp r-rcppeigen r-rlang))
+     (list r-future
+           r-future-apply
+           r-matrix
+           r-progressr
+           r-rcpp
+           r-rcppeigen
+           r-rgeos
+           r-rlang
+           r-sp))
     (home-page "https://satijalab.org/seurat")
     (synopsis "Data structures for single cell data")
     (description
@@ -29307,13 +29386,13 @@ other R users.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "4.1.0")
+    (version "4.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195"))))
+                "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29632,14 +29711,14 @@ kernel estimators.")
 (define-public r-lpme
   (package
     (name "r-lpme")
-    (version "1.1.2")
+    (version "1.1.3")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "lpme" version))
         (sha256
           (base32
-            "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw"))))
+            "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
     (properties `((upstream-name . "lpme")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29796,13 +29875,13 @@ package also supersedes the package @code{BBmisc}.")
 (define-public r-mlr3pipelines
   (package
     (name "r-mlr3pipelines")
-    (version "0.4.0")
+    (version "0.4.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3pipelines" version))
               (sha256
                (base32
-                "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p"))))
+                "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports
@@ -29859,13 +29938,13 @@ performing ordinal regression.")
 (define-public r-paradox
   (package
     (name "r-paradox")
-    (version "0.8.0")
+    (version "0.9.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "paradox" version))
               (sha256
                (base32
-                "1jfzbpqi1rp3r8hnk37dqwggp48ha5bnilmdz7dwzfdaskssycxa"))))
+                "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
@@ -29917,13 +29996,13 @@ computational operations, add-on packages provide additional functionality.")
 (define-public r-mlr3learners
   (package
     (name "r-mlr3learners")
-    (version "0.5.2")
+    (version "0.5.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3learners" version))
               (sha256
                (base32
-                "1d9hcrnj622ynrzg0ii0fkhz2n66ip46yln21jq1pwpwkqwqzv35"))))
+                "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-checkmate
@@ -29944,14 +30023,14 @@ vector machines, and gradient boosting.")
 (define-public r-bbotk
   (package
     (name "r-bbotk")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bbotk" version))
        (sha256
         (base32
-         "0k1vlh14mfbcgdw2yfhab7shkrqm4d2h6af12mybr9gks26xmw82"))))
+         "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734"))))
     (properties `((upstream-name . "bbotk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29974,13 +30053,13 @@ annealing.")
 (define-public r-mlr3tuning
   (package
     (name "r-mlr3tuning")
-    (version "0.13.0")
+    (version "0.13.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3tuning" version))
               (sha256
                (base32
-                "0czlpi8bshn8cjq7pa1cyy7lpv35g4hv2nbyhc59zrcykzfv8afm"))))
+                "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bbotk
@@ -30327,14 +30406,14 @@ in output to the equivalent HTML.")
 (define-public r-pkgdown
   (package
     (name "r-pkgdown")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgdown" version))
        (sha256
         (base32
-         "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h"))))
+         "0wqga9bcl7wmvkwpkkmf5hx1cl7rjq5ddvqmxhl4p1dczys3adnr"))))
     (properties `((upstream-name . "pkgdown")))
     (build-system r-build-system)
     (inputs (list pandoc))
@@ -30436,14 +30515,14 @@ visualized at any level of the experiment's design.")
 (define-public r-qdapregex
   (package
     (name "r-qdapregex")
-    (version "0.7.2")
+    (version "0.7.5")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "qdapRegex" version))
         (sha256
           (base32
-            "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
+            "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
     (properties `((upstream-name . "qdapRegex")))
     (build-system r-build-system)
     (propagated-inputs (list r-stringi))
@@ -30782,14 +30861,14 @@ data you need the @code{pdftools} package.")
 (define-public r-pdftools
   (package
     (name "r-pdftools")
-    (version "3.1.1")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pdftools" version))
        (sha256
         (base32
-         "1lflqf2ypdm4w033vyjykmsy8cl34sp42fzkfgfdhvl2d0xjhl96"))))
+         "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi"))))
     (properties `((upstream-name . "pdftools")))
     (build-system r-build-system)
     (inputs (list zlib poppler))
@@ -31483,16 +31562,16 @@ asynchronously from formatting.")
 (define-public r-rmisc
   (package
     (name "r-rmisc")
-    (version "1.5")
+    (version "1.5.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Rmisc" version))
               (sha256
                (base32
-                "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8"))))
+                "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-plyr r-rcpp r-lattice))
+     (list r-plyr r-lattice))
     (home-page "https://cran.r-project.org/web/packages/Rmisc/")
     (synopsis "Ryan Miscellaneous")
     (description "The Rmisc library contains functions for data analysis and
@@ -31556,13 +31635,13 @@ reading and writing arbitrary protocol-buffer data in R.")
 (define-public r-opencpu
   (package
     (name "r-opencpu")
-    (version "2.2.7")
+    (version "2.2.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "opencpu" version))
        (sha256
-        (base32 "06jpmk95hm39ib5c75xw0mdrdv9x9zz1qil3m8ysb6pp1xx47jz0"))))
+        (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
     (properties `((upstream-name . "opencpu")))
     (build-system r-build-system)
     (inputs
@@ -31599,14 +31678,14 @@ Apache2.")
 (define-public r-exactextractr
   (package
     (name "r-exactextractr")
-    (version "0.8.1")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "exactextractr" version))
        (sha256
         (base32
-         "11s58vc63r9kah815a18ihb0x2nmnjnpngybw3yr2d6715sz89nc"))))
+         "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc"))))
     (properties `((upstream-name . "exactextractr")))
     (build-system r-build-system)
     (inputs (list geos))
@@ -31625,14 +31704,14 @@ the @code{raster} package that is suitable for extracting raster values using
 (define-public r-stringfish
   (package
     (name "r-stringfish")
-    (version "0.15.5")
+    (version "0.15.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringfish" version))
        (sha256
         (base32
-         "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx"))))
+         "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
     (properties `((upstream-name . "stringfish")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31779,14 +31858,14 @@ Tensorflow graphs.")
 (define-public r-tensorflow
   (package
     (name "r-tensorflow")
-    (version "2.8.0")
+    (version "2.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tensorflow" version))
        (sha256
         (base32
-         "19ayjvlxmgjais0kx6fj9an1h1i8mh4c9dhah7dj6390p53pgz93"))))
+         "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
     (properties `((upstream-name . "tensorflow")))
     (build-system r-build-system)
     (inputs (list tensorflow))
@@ -31810,14 +31889,14 @@ between them.")
 (define-public r-keras
   (package
     (name "r-keras")
-    (version "2.8.0")
+    (version "2.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "keras" version))
        (sha256
         (base32
-         "10zvy4lmhb2sbn0gsm12pf95pxj9bmi8241ap1n6170xsld9phcf"))))
+         "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
     (properties `((upstream-name . "keras")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31996,24 +32075,25 @@ with the dynamic plots from @code{dygraphs}.")
 (define-public r-rfigshare
   (package
     (name "r-rfigshare")
-    (version "0.3.7")
+    (version "0.3.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rfigshare" version))
        (sha256
         (base32
-         "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq"))))
+         "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
     (properties `((upstream-name . "rfigshare")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2
            r-httpuv
            r-httr
-           r-plyr
            r-rjsonio
            r-xml
            r-yaml))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://github.com/ropensci/rfigshare")
     (synopsis "R Interface to figshare")
     (description
@@ -32503,14 +32583,14 @@ zoom/navigate any plot when called with any active plot.")
 (define-public r-zoolog
   (package
     (name "r-zoolog")
-    (version "0.4.1")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zoolog" version))
        (sha256
         (base32
-         "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks"))))
+         "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p"))))
     (properties `((upstream-name . "zoolog")))
     (build-system r-build-system)
     (propagated-inputs
@@ -32557,14 +32637,14 @@ large datasets.")
 (define-public r-mlearning
   (package
     (name "r-mlearning")
-    (version "1.0-0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mlearning" version))
        (sha256
         (base32
-         "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r"))))
+         "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
     (properties `((upstream-name . "mlearning")))
     (build-system r-build-system)
     (propagated-inputs