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 0507b7c..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")
@@ -24856,14 +24927,14 @@ least squares.")
 (define-public r-semtools
   (package
     (name "r-semtools")
-    (version "0.5-5")
+    (version "0.5-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "semTools" version))
        (sha256
         (base32
-         "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x"))))
+         "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
     (properties `((upstream-name . "semTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25030,14 +25101,14 @@ importation and recoding.")
 (define-public r-rockchalk
   (package
     (name "r-rockchalk")
-    (version "1.8.151")
+    (version "1.8.152")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rockchalk" version))
        (sha256
         (base32
-         "17mfaxn3gj0vac5wdmsjj2z2668cszbpvan7hnxp7ic9bvsm1w2y"))))
+         "1d15jlgcy35pvaicaddd4zrhwm5ajb9yc3jk6dyxm99gc5wcn6h3"))))
     (properties `((upstream-name . "rockchalk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25057,14 +25128,14 @@ fairly comprehensive overview.")
 (define-public r-lisreltor
   (package
     (name "r-lisreltor")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lisrelToR" version))
        (sha256
         (base32
-         "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
+         "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
     (properties `((upstream-name . "lisrelToR")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/package=lisrelToR")
@@ -25077,18 +25148,20 @@ output in R.")
 (define-public r-bdgraph
   (package
     (name "r-bdgraph")
-    (version "2.65")
+    (version "2.67")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BDgraph" version))
        (sha256
         (base32
-         "0rg3wi9xwsbj90gb60p3vzkfrf76hwh47nc6fwv6c21yzd3s7vm4"))))
+         "0s2j4462zlgyjnqvvvxg4lynhmwwnjaw1cr1chzmagfvaj94qhhz"))))
     (properties `((upstream-name . "BDgraph")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-igraph))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://www.uva.nl/profile/a.mohammadi")
     (synopsis "Bayesian structure learning in graphical models")
     (description
@@ -25203,14 +25276,14 @@ translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
 (define-public r-cdm
   (package
     (name "r-cdm")
-    (version "7.6-11")
+    (version "8.1-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CDM" version))
        (sha256
         (base32
-         "0k3arkzz7nzswjcsr7fdmpfs94ilg8l265dyn49555fw3673cgqj"))))
+         "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i"))))
     (properties `((upstream-name . "CDM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25234,14 +25307,14 @@ well as Ravand and Robitzsch (2015).")
 (define-public r-tam
   (package
     (name "r-tam")
-    (version "3.7-16")
+    (version "4.0-16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TAM" version))
        (sha256
         (base32
-         "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd"))))
+         "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw"))))
     (properties `((upstream-name . "TAM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25291,18 +25364,20 @@ elimination, and a simulation module for various binary data matrices.")
 (define-public r-irtoys
   (package
     (name "r-irtoys")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "irtoys" version))
        (sha256
         (base32
-         "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
+         "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
     (properties `((upstream-name . "irtoys")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ltm r-sm))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://cran.r-project.org/package=irtoys")
     (synopsis "Collection of functions related to Item Response Theory (IRT)")
     (description
@@ -25358,14 +25433,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.")
 (define-public r-packrat
   (package
     (name "r-packrat")
-    (version "0.7.0")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "packrat" version))
        (sha256
         (base32
-         "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78"))))
+         "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h"))))
     (properties `((upstream-name . "packrat")))
     (build-system r-build-system)
     (home-page "https://github.com/rstudio/packrat/")
@@ -26516,14 +26591,14 @@ estimation.")
 (define-public r-optimx
   (package
     (name "r-optimx")
-    (version "2021-10.12")
+    (version "2022-4.30")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "optimx" version))
        (sha256
         (base32
-         "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r"))))
+         "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
     (properties `((upstream-name . "optimx")))
     (build-system r-build-system)
     (propagated-inputs (list r-numderiv))
@@ -26544,14 +26619,14 @@ here.")
 (define-public r-projpred
   (package
     (name "r-projpred")
-    (version "2.1.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "projpred" version))
        (sha256
         (base32
-         "170pskvcsyk22xl4q8mklx8nw29miqzb42wajcab7bki8ap1ix46"))))
+         "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8"))))
     (properties `((upstream-name . "projpred")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26665,14 +26740,14 @@ inference diagnostics.
 (define-public r-brms
   (package
     (name "r-brms")
-    (version "2.16.3")
+    (version "2.17.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "brms" version))
        (sha256
         (base32
-         "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38"))))
+         "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94"))))
     (properties `((upstream-name . "brms")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26774,14 +26849,14 @@ pies on a map.")
 (define-public r-scrypt
   (package
     (name "r-scrypt")
-    (version "0.1.3")
+    (version "0.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scrypt" version))
        (sha256
         (base32
-         "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
+         "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
     (properties `((upstream-name . "scrypt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27257,14 +27332,14 @@ simple interface for all functions.")
 (define-public r-iml
   (package
     (name "r-iml")
-    (version "0.10.1")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iml" version))
        (sha256
         (base32
-         "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r"))))
+         "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5"))))
     (properties `((upstream-name . "iml")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27274,7 +27349,6 @@ simple interface for all functions.")
            r-future
            r-future-apply
            r-ggplot2
-           r-keras
            r-metrics
            r-prediction
            r-r6))
@@ -27345,14 +27419,14 @@ diagonals.  This package allows you to compute the tensor product of arrays.")
 (define-public r-spatstat-utils
   (package
     (name "r-spatstat-utils")
-    (version "2.3-0")
+    (version "2.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.utils" version))
        (sha256
         (base32
-         "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az"))))
+         "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av"))))
     (properties
      `((upstream-name . "spatstat.utils")))
     (build-system r-build-system)
@@ -27366,14 +27440,14 @@ which may also be useful for other purposes.")
 (define-public r-spatstat-sparse
   (package
     (name "r-spatstat-sparse")
-    (version "2.1-0")
+    (version "2.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.sparse" version))
        (sha256
         (base32
-         "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680"))))
+         "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs"))))
     (properties
      `((upstream-name . "spatstat.sparse")))
     (build-system r-build-system)
@@ -27390,14 +27464,14 @@ matrix calculations that are common in statistics, such as quadratic forms.")
 (define-public r-spatstat-data
   (package
     (name "r-spatstat-data")
-    (version "2.1-4")
+    (version "2.2-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.data" version))
        (sha256
         (base32
-         "0bq9randa3lgkh2q932iss5cxazq743q6p8asiqqf0yi32b003jq"))))
+         "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k"))))
     (properties `((upstream-name . "spatstat.data")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27435,14 +27509,14 @@ for the geometry of linear networks.")
 (define-public r-spatstat-core
   (package
     (name "r-spatstat-core")
-    (version "2.4-2")
+    (version "2.4-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.core" version))
        (sha256
         (base32
-         "0bhdxyw212yf9y9nsvbz4yy08ka3wr3hkjqpag0ys2s1p22c51b9"))))
+         "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
     (properties `((upstream-name . "spatstat.core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28022,14 +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)
@@ -28232,14 +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))
@@ -28690,14 +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
@@ -28811,14 +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
@@ -29011,14 +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
@@ -29100,14 +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
@@ -29279,18 +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
@@ -29304,13 +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
@@ -29629,14 +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
@@ -29793,13 +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
@@ -29856,13 +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))
@@ -29914,13 +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
@@ -29941,14 +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
@@ -29971,13 +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
@@ -30324,14 +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))
@@ -30433,14 +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))
@@ -30779,14 +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))
@@ -31480,16 +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
@@ -31553,13 +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
@@ -31596,14 +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))
@@ -31622,14 +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
@@ -31776,14 +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))
@@ -31807,14 +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
@@ -31993,24 +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
@@ -32500,14 +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
@@ -32554,14 +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