gnu: r-enrichr: Update to 2.0.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3f0d819..14419ba 100644 (file)
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -78,14 +78,14 @@
 (define-public r-clipr
   (package
     (name "r-clipr")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "clipr" version))
        (sha256
         (base32
-         "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m"))))
+         "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
     (build-system r-build-system)
     (home-page "https://github.com/mdlincoln/clipr")
     (synopsis "Read and write from the system clipboard")
@@ -97,14 +97,14 @@ the system clipboards.")
 (define-public r-ellipsis
   (package
     (name "r-ellipsis")
-    (version "0.2.0")
+    (version "0.2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ellipsis" version))
        (sha256
         (base32
-         "0hdk79q4wn5nq52p8qd65kqz81l0b8gfzsbzyvmfais0p24qclib"))))
+         "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)))
@@ -118,6 +118,51 @@ experiment that allows a generic to warn if any arguments passed in @code{...}
 are not used.")
     (license license:gpl3)))
 
+(define-public r-grr
+  (package
+    (name "r-grr")
+    (version "0.9.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "grr" version))
+       (sha256
+        (base32
+         "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/grr")
+    (synopsis "Alternative implementations of base R functions")
+    (description
+     "This package provides alternative implementations of some base R
+functions, including @code{sort}, @code{order}, and @code{match}.  The
+functions are simplified but can be faster or have other advantages.")
+    (license license:gpl3)))
+
+(define-public r-matrix-utils
+  (package
+    (name "r-matrix-utils")
+    (version "0.9.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Matrix.utils" version))
+       (sha256
+        (base32
+         "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
+    (properties `((upstream-name . "Matrix.utils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-grr" ,r-grr)
+       ("r-matrix" ,r-matrix)))
+    (home-page "https://github.com/cvarrichio/Matrix.utils")
+    (synopsis
+     "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
+    (description
+     "This package implements data manipulation methods such as @code{cast},
+@code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
+objects.")
+    (license license:gpl3)))
+
 (define-public r-sys
   (package
     (name "r-sys")
@@ -325,14 +370,14 @@ such as copy/paste from an R session.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "3.2.0")
+    (version "3.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b"))))
+         "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-r6" ,r-r6)
@@ -569,13 +614,13 @@ LaTeX.")
 (define-public r-curl
   (package
     (name "r-curl")
-    (version "3.3")
+    (version "4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "curl" version))
               (sha256
                (base32
-                "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c"))))
+                "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -822,6 +867,121 @@ this gives the user direct access to the file system without the need to
 well as file saving is available.")
     (license license:gpl2+)))
 
+;; The package sources include minified variants of d3.js and non-minified
+;; source code of d3-jetpack.
+(define-public r-d3r
+  (package
+    (name "r-d3r")
+    (version "0.8.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "d3r" version))
+       (sha256
+        (base32
+         "0vcmiyhd000xyl28k6rm7ba50x5sz5b2cpllxnq36q13qhdnqw6k"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (srfi srfi-1)
+                  (ice-9 popen))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'process-javascript
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion "inst/www/d3/"
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `((,(assoc-ref inputs "d3.v3.js")
+                         "v3/dist/d3.min.js")
+                        (,(assoc-ref inputs "d3.v4.js")
+                         "v4/dist/d3.min.js")
+                        (,(assoc-ref inputs "d3.v5.js")
+                         "v5/dist/d3.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (delete-file target)
+                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+                                 (call-with-output-file target
+                                   (lambda (port)
+                                     (dump-port minified port)))))
+                             sources targets))))
+             #t)))))
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-htmltools" ,r-htmltools)
+       ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)
+       ("d3.v3.js"
+        ,(origin
+           (method url-fetch)
+           (uri "https://d3js.org/d3.v3.js")
+           (sha256
+            (base32
+             "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
+       ("d3.v4.js"
+        ,(origin
+           (method url-fetch)
+           (uri "https://d3js.org/d3.v4.js")
+           (sha256
+            (base32
+             "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
+       ("d3.v5.js"
+        ,(origin
+           (method url-fetch)
+           (uri "https://d3js.org/d3.v5.js")
+           (sha256
+            (base32
+             "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
+    (home-page "https://github.com/timelyportfolio/d3r")
+    (synopsis "d3.js utilities for R")
+    (description
+     "This package provides a suite of functions to help ease the use of the
+d3.js visualization library in R.  These helpers include
+@code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
+tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
+R objects into the JSON format that the d3.js library expects.")
+    (license license:bsd-3)))
+
+;; We use the latest commit here because the last release was in 2016 while
+;; the latest commit was in 2018.
+(define-public r-sankeyd3
+  (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
+        (revision "1"))
+    (package
+      (name "r-sankeyd3")
+      (version (git-version "0.3.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/fbreitwieser/sankeyD3.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-d3r" ,r-d3r)
+         ("r-htmlwidgets" ,r-htmlwidgets)
+         ("r-shiny" ,r-shiny)
+         ("r-magrittr" ,r-magrittr)))
+      (home-page "https://github.com/fbreitwieser/sankeyD3")
+      (synopsis "Sankey network graphs from R")
+      (description
+       "This package provides an R library to generate Sankey network graphs
+in R and Shiny via the D3 visualization library.")
+      ;; The R code is licensed under GPLv3+.  It includes the non-minified
+      ;; JavaScript source code of d3-sankey, which is released under the
+      ;; 3-clause BSD license.
+      (license (list license:gpl3+ license:bsd-3)))))
+
 (define-public r-crosstalk
   (package
     (name "r-crosstalk")
@@ -1045,14 +1205,14 @@ including functions for geolocation and routing.")
 (define-public r-haven
   (package
     (name "r-haven")
-    (version "2.1.0")
+    (version "2.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "haven" version))
        (sha256
         (base32
-         "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
+         "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -1281,14 +1441,14 @@ processes.  Most of its code is based on the @code{psutil} Python package.")
 (define-public r-pkgbuild
   (package
     (name "r-pkgbuild")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgbuild" version))
        (sha256
         (base32
-         "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
+         "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -1337,13 +1497,13 @@ you to rapidly iterate while developing a package.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
+        (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
@@ -2070,14 +2230,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
 (define-public r-lpsolve
   (package
     (name "r-lpsolve")
-    (version "5.6.13.1")
+    (version "5.6.13.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lpSolve" version))
        (sha256
         (base32
-         "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
+         "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m"))))
     (properties `((upstream-name . "lpSolve")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -2155,14 +2315,14 @@ data).  Weighted versions of MLE, MME and QME are available.")
 (define-public r-energy
   (package
     (name "r-energy")
-    (version "1.7-5")
+    (version "1.7-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "energy" version))
        (sha256
         (base32
-         "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
+         "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-boot" ,r-boot)
@@ -2290,14 +2450,14 @@ available in a vignette.")
 (define-public r-lava
   (package
     (name "r-lava")
-    (version "1.6.5")
+    (version "1.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lava" version))
        (sha256
         (base32
-         "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f"))))
+         "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-numderiv" ,r-numderiv)
@@ -2480,20 +2640,41 @@ to access PostgreSQL database systems.")
     ;; under the PostgreSQL license.
     (license license:gpl2)))
 
+(define-public r-linprog
+  (package
+    (name "r-linprog")
+    (version "0.9-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "linprog" version))
+       (sha256
+        (base32
+         "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
+    (home-page "http://linprog.r-forge.r-project.org/")
+    (synopsis "Linear programming and optimization")
+    (description
+     "This package can be used to solve Linear Programming / Linear
+Optimization problems by using the simplex algorithm.")
+    (license license:gpl2+)))
+
 (define-public r-geometry
   (package
     (name "r-geometry")
-    (version "0.4.1")
+    (version "0.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "geometry" version))
        (sha256
         (base32
-         "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm"))))
+         "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magic" ,r-magic)
+       ("r-linprog" ,r-linprog)
        ("r-lpsolve" ,r-lpsolve)
        ("r-rcpp" ,r-rcpp)
        ("r-rcppprogress" ,r-rcppprogress)))
@@ -2711,14 +2892,14 @@ provides a one-row summary of model-level statistics.")
 (define-public r-recipes
   (package
     (name "r-recipes")
-    (version "0.1.5")
+    (version "0.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "recipes" version))
        (sha256
         (base32
-         "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg"))))
+         "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -2730,7 +2911,6 @@ provides a one-row summary of model-level statistics.")
        ("r-magrittr" ,r-magrittr)
        ("r-matrix" ,r-matrix)
        ("r-purrr" ,r-purrr)
-       ("r-rcpproll" ,r-rcpproll)
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
@@ -2896,14 +3076,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.6-8")
+    (version "2.6-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
+         "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
@@ -2969,14 +3149,14 @@ analysis of multiply imputed data sets.")
 (define-public r-mice
   (package
     (name "r-mice")
-    (version "3.5.0")
+    (version "3.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mice" version))
        (sha256
         (base32
-         "0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g"))))
+         "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -3052,14 +3232,14 @@ programming} (SQP) based solver).")
 (define-public r-hardyweinberg
   (package
     (name "r-hardyweinberg")
-    (version "1.6.2")
+    (version "1.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "HardyWeinberg" version))
        (sha256
         (base32
-         "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9"))))
+         "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
     (properties `((upstream-name . "HardyWeinberg")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3129,14 +3309,14 @@ structure.")
 (define-public r-vioplot
   (package
     (name "r-vioplot")
-    (version "0.3.0")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vioplot" version))
        (sha256
         (base32
-         "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn"))))
+         "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-sm" ,r-sm)
@@ -3471,14 +3651,14 @@ constants, and control debugging of packages via environment variables.")
 (define-public r-processx
   (package
     (name "r-processx")
-    (version "3.3.1")
+    (version "3.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "processx" version))
        (sha256
         (base32
-         "1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1"))))
+         "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ps" ,r-ps)
@@ -3679,18 +3859,19 @@ to variables on the left-hand side of the assignment.")
 (define-public r-vctrs
   (package
     (name "r-vctrs")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vctrs" version))
        (sha256
         (base32
-         "13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"))))
+         "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)
        ("r-digest" ,r-digest)
+       ("r-ellipsis" ,r-ellipsis)
        ("r-glue" ,r-glue)
        ("r-rlang" ,r-rlang)
        ("r-zeallot" ,r-zeallot)))
@@ -3717,14 +3898,14 @@ to variables on the left-hand side of the assignment.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
+         "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -4468,14 +4649,14 @@ files.")
 (define-public r-shinyace
   (package
     (name "r-shinyace")
-    (version "0.3.3")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyAce" version))
        (sha256
         (base32
-         "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
+         "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1"))))
     (properties `((upstream-name . "shinyAce")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4518,14 +4699,14 @@ systems.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "0.9.9")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
+         "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -4980,14 +5161,14 @@ misclassification probabilities of different models.")
 (define-public r-zip
   (package
     (name "r-zip")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zip" version))
        (sha256
         (base32
-         "1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix"))))
+         "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
     (build-system r-build-system)
     (home-page "https://github.com/gaborcsardi/zip")
     (synopsis "Cross-platform Zip compression")
@@ -5138,14 +5319,14 @@ promises, but with a syntax that is idiomatic R.")
 (define-public r-dosnow
   (package
     (name "r-dosnow")
-    (version "1.0.16")
+    (version "1.0.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doSNOW" version))
        (sha256
         (base32
-         "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
+         "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
     (properties `((upstream-name . "doSNOW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5271,14 +5452,14 @@ obtain a better initial configuration in non-metric MDS.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.12")
+    (version "1.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
+         "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
     (build-system r-build-system)
     (inputs `(("python" ,python)))
     (propagated-inputs
@@ -5468,14 +5649,14 @@ clustering.")
 (define-public r-factominer
   (package
     (name "r-factominer")
-    (version "1.41")
+    (version "1.42")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FactoMineR" version))
        (sha256
         (base32
-         "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
+         "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
     (properties `((upstream-name . "FactoMineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5758,20 +5939,19 @@ to help insert or delete content at a specific location in the document.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "1.3")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
+         "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
     (build-system r-build-system)
     (inputs
      `(("gsl" ,gsl)))
     (propagated-inputs
-     `(("r-cairo" ,r-cairo)
-       ("r-lme4" ,r-lme4)
+     `(("r-lme4" ,r-lme4)
        ("r-mass" ,r-mass)
        ("r-nnet" ,r-nnet)
        ("r-rcpp" ,r-rcpp)
@@ -5910,14 +6090,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.3.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb"))))
+         "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
     (build-system r-build-system)
     (home-page "https://easystats.github.io/insight/")
     (synopsis "Easy access to model information for various model objects")
@@ -6367,14 +6547,14 @@ containing one or more SNPs that evolved under directional selection.")
 (define-public r-proc
   (package
     (name "r-proc")
-    (version "1.15.0")
+    (version "1.15.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pROC" version))
        (sha256
         (base32
-         "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
+         "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
     (properties `((upstream-name . "pROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6740,14 +6920,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "2.9-5")
+    (version "2.9-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk"))))
+         "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -7308,14 +7488,14 @@ multiple-imputation datasets.")
 (define-public r-magick
   (package
     (name "r-magick")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magick" version))
        (sha256
         (base32
-         "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
+         "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
     (build-system r-build-system)
     (inputs
      `(("imagemagick" ,imagemagick)
@@ -7697,14 +7877,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.3.5.1")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "0rgzjvmp3yqhwgfg96v17wi8gbafzbrmz134shj2jsf5bsmw6vbj"))))
+         "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -7954,14 +8134,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
+         "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -7981,14 +8161,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k"))))
+         "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -8015,14 +8195,14 @@ results using @code{ggplot2}.")
 (define-public r-sjplot
   (package
     (name "r-sjplot")
-    (version "2.6.3")
+    (version "2.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjPlot" version))
        (sha256
         (base32
-         "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
+         "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
     (properties `((upstream-name . "sjPlot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8032,6 +8212,7 @@ results using @code{ggplot2}.")
        ("r-forcats" ,r-forcats)
        ("r-ggeffects" ,r-ggeffects)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
        ("r-glmmtmb" ,r-glmmtmb)
        ("r-insight" ,r-insight)
        ("r-knitr" ,r-knitr)
@@ -8151,14 +8332,14 @@ terminals that do not support Unicode.")
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "1.5.0")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
+         "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-clipr" ,r-clipr)
@@ -8514,14 +8695,14 @@ analysing multivariate abundance data in community ecology.")
 (define-public r-afex
   (package
     (name "r-afex")
-    (version "0.23-0")
+    (version "0.24-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "afex" version))
        (sha256
         (base32
-         "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
+         "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-car" ,r-car)
@@ -8675,6 +8856,29 @@ package provides a minimal R interface by relying on the Rcpp package.")
     ;; hnswlib is released under Version 2.0 of the Apache License.
     (license (list license:gpl3 license:asl2.0))))
 
+(define-public r-rcppparallel
+  (package
+    (name "r-rcppparallel")
+    (version "4.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppParallel" version))
+       (sha256
+        (base32
+         "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s"))))
+    (properties `((upstream-name . "RcppParallel")))
+    (build-system r-build-system)
+    (home-page "http://rcppcore.github.io/RcppParallel")
+    (synopsis "Parallel programming tools for Rcpp")
+    (description
+     "This package provides high level functions for parallel programming with
+Rcpp.  For example, the @code{parallelFor()} function can be used to convert
+the work of a standard serial @code{for} loop into a parallel one and the
+@code{parallelReduce()} function can be used for accumulating aggregates or
+other values.")
+    (license license:gpl2)))
+
 (define-public r-ncdf4
   (package
     (name "r-ncdf4")
@@ -8725,14 +8929,14 @@ Bioconductor packages.")
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.100.24")
+    (version "0.100.26")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "0nm3iyvhhmh0zlywkfmrq3vyh8z1l296xxfmcky0ifd2qnysfcqj"))))
+         "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
     (build-system r-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -9191,14 +9395,14 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.2.4")
+    (version "0.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
         (base32
-         "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
+         "0vfjv33352dmk9cr2qn0knzg761068rdk6jg32csd9vpmcma8awp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
@@ -9259,14 +9463,14 @@ giving it a description in the specific format.")
 (define-public r-sparsesvd
   (package
     (name "r-sparsesvd")
-    (version "0.1-4")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sparsesvd" version))
        (sha256
         (base32
-         "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
+         "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-matrix" ,r-matrix)))
     (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
@@ -9279,6 +9483,29 @@ only sparse real matrices in Matrix package format are supported.")
     ;; BSD-3.
     (license (list license:bsd-3 license:bsd-2))))
 
+(define-public r-speedglm
+  (package
+    (name "r-speedglm")
+    (version "0.3-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "speedglm" version))
+       (sha256
+        (base32
+         "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)))
+    (home-page "https://cran.r-project.org/web/packages/speedglm")
+    (synopsis "Fit linear and generalized linear models to large data sets")
+    (description
+     "This package provides tools for fitting linear models and generalized
+linear models to large data sets by updating algorithms.")
+    ;; Any version of the GPL
+    (license license:gpl2+)))
+
 (define-public r-densityclust
   (package
     (name "r-densityclust")
@@ -9458,14 +9685,14 @@ diagnostics for controlling type-1 errors are also provided.")
 (define-public r-flare
   (package
     (name "r-flare")
-    (version "1.6.0")
+    (version "1.6.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flare" version))
        (sha256
         (base32
-         "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
+         "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-igraph" ,r-igraph)
@@ -9558,14 +9785,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "0.11.0")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "0zs8ffa6gpi9cygxk7xjin6k3vpvfgb540a506zlk50bf6kc5nlf"))))
+         "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -9581,14 +9808,14 @@ used by other packages.")
 (define-public r-shades
   (package
     (name "r-shades")
-    (version "1.3.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shades" version))
        (sha256
         (base32
-         "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
+         "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
     (build-system r-build-system)
     (home-page "https://github.com/jonclayden/shades")
     (synopsis "Simple color manipulation")
@@ -9937,23 +10164,51 @@ library.")
 and manipulating sets of ontological terms.")
     (license license:gpl2+)))
 
+(define-public r-gargle
+  (package
+    (name "r-gargle")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gargle" version))
+       (sha256
+        (base32
+         "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fs" ,r-fs)
+       ("r-glue" ,r-glue)
+       ("r-httr" ,r-httr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-rlang" ,r-rlang)
+       ("r-withr" ,r-withr)))
+    (home-page "https://gargle.r-lib.org")
+    (synopsis "Utilities for working with Google APIs")
+    (description
+     "This package provides utilities for working with Google APIs.  This
+includes functions and classes for handling common credential types and for
+preparing, executing, and processing HTTP requests.")
+    (license license:expat)))
+
 (define-public r-bigrquery
   (package
     (name "r-bigrquery")
-    (version "1.1.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bigrquery" version))
        (sha256
         (base32
-         "1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is"))))
+         "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-bit64" ,r-bit64)
        ("r-curl" ,r-curl)
        ("r-dbi" ,r-dbi)
+       ("r-gargle" ,r-gargle)
        ("r-glue" ,r-glue)
        ("r-httr" ,r-httr)
        ("r-jsonlite" ,r-jsonlite)
@@ -9961,6 +10216,7 @@ and manipulating sets of ontological terms.")
        ("r-progress" ,r-progress)
        ("r-rapidjsonr" ,r-rapidjsonr)
        ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)))
     (home-page "https://github.com/rstats-db/bigrquery")
     (synopsis "R interface to Google's BigQuery API")
@@ -10518,14 +10774,14 @@ covariance functions for large data sets.")
 (define-public r-spatialextremes
   (package
     (name "r-spatialextremes")
-    (version "2.0-7")
+    (version "2.0-7.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SpatialExtremes" version))
        (sha256
         (base32
-         "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
+         "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
     (properties
      `((upstream-name . "SpatialExtremes")))
     (build-system r-build-system)
@@ -10971,14 +11227,14 @@ them in distributed compute environments.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.13.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz"))))
+         "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -11031,14 +11287,14 @@ machine or distributed on a compute cluster.")
 (define-public r-rsvd
   (package
     (name "r-rsvd")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rsvd" version))
        (sha256
         (base32
-         "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
+         "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -11239,14 +11495,14 @@ identifying outliers.")
 (define-public r-bayesm
   (package
     (name "r-bayesm")
-    (version "3.1-1")
+    (version "3.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayesm" version))
        (sha256
         (base32
-         "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
+         "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -11643,14 +11899,14 @@ probabilities from a standard bivariate normal CDF.")
 (define-public r-lavaan
   (package
     (name "r-lavaan")
-    (version "0.6-3")
+    (version "0.6-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lavaan" version))
        (sha256
         (base32
-         "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
+         "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -11867,14 +12123,14 @@ running IRkernel session.")
 (define-public r-irkernel
   (package
     (name "r-irkernel")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "IRkernel" version))
        (sha256
         (base32
-         "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
+         "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
     (properties `((upstream-name . "IRkernel")))
     (build-system r-build-system)
     (arguments
@@ -11986,14 +12242,14 @@ R, enabling interactive analysis and visualization of genome-scale data.")
 (define-public r-rematch2
   (package
     (name "r-rematch2")
-    (version "2.0.1")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rematch2" version))
        (sha256
         (base32
-         "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
+         "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-tibble" ,r-tibble)))
@@ -12335,14 +12591,14 @@ classes.")
 (define-public r-classint
   (package
     (name "r-classint")
-    (version "0.3-3")
+    (version "0.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "classInt" version))
        (sha256
         (base32
-         "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
+         "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir"))))
     (properties `((upstream-name . "classInt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12410,14 +12666,14 @@ sampling.")
 (define-public r-deldir
   (package
     (name "r-deldir")
-    (version "0.1-21")
+    (version "0.1-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "deldir" version))
        (sha256
         (base32
-         "03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr"))))
+         "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/deldir")
@@ -12434,14 +12690,14 @@ tessellation.")
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.7-4")
+    (version "0.7-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
+         "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)
@@ -12816,18 +13072,19 @@ inbred lines, F2 intercrosses, and association mapping populations.")
 (define-public r-ldheatmap
   (package
     (name "r-ldheatmap")
-    (version "0.99-5")
+    (version "0.99-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "LDheatmap" version))
        (sha256
         (base32
-         "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
+         "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
     (properties `((upstream-name . "LDheatmap")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-genetics" ,r-genetics)
+       ("r-rcpp" ,r-rcpp)
        ("r-snpstats" ,r-snpstats)))
     (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
     (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
@@ -12906,13 +13163,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.11")
+    (version "0.12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
+                "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
@@ -14199,6 +14456,25 @@ Molecular Epidemiology\" (SCRIME).  The main focus is on SNP data, but most of
 the functions can also be applied to other types of categorical data.")
     (license license:gpl2)))
 
+(define-public r-pbmcapply
+  (package
+    (name "r-pbmcapply")
+    (version "1.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbmcapply" version))
+       (sha256
+        (base32
+         "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/kvnkuang/pbmcapply")
+    (synopsis "Track the progress of apply procedures with a progress bar")
+    (description
+     "This light-weight package helps you track and visualize the progress of
+parallel versions of vectorized R functions of the @code{mc*apply} family.")
+    (license license:expat)))
+
 (define-public r-blme
   (package
     (name "r-blme")
@@ -14337,14 +14613,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "0.4")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a"))))
+         "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
@@ -14363,14 +14639,14 @@ and model output.")
 (define-public r-enrichr
   (package
     (name "r-enrichr")
-    (version "1.0")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "enrichR" version))
        (sha256
         (base32
-         "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
+         "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
     (properties `((upstream-name . "enrichR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14530,3 +14806,140 @@ including regression, classification and ranking.  The package is made to be
 extensible, so that users are also allowed to define their own objectives
 easily.")
     (license license:asl2.0)))
+
+(define-public r-umap
+  (package
+    (name "r-umap")
+    (version "0.2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "umap" version))
+       (sha256
+        (base32
+         "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-reticulate" ,r-reticulate)
+       ("r-rspectra" ,r-rspectra)))
+    (home-page "https://github.com/tkonopka/umap")
+    (synopsis "Uniform manifold approximation and projection")
+    (description
+     "Uniform manifold approximation and projection is a technique for
+dimension reduction.  This package provides an interface to the UMAP algorithm
+in R, including a translation of the original algorithm into R.")
+    (license license:expat)))
+
+(define-public r-uwot
+  (package
+    (name "r-uwot")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "uwot" version))
+       (sha256
+        (base32
+         "1mq6qi8q9xslh1b99srj480s2a08pfv4bs9m2ykyijj44j9fcdj9"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dqrng" ,r-dqrng)
+       ("r-fnn" ,r-fnn)
+       ("r-irlba" ,r-irlba)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppannoy" ,r-rcppannoy)
+       ("r-rcppparallel" ,r-rcppparallel)
+       ("r-rcppprogress" ,r-rcppprogress)
+       ("r-rspectra" ,r-rspectra)))
+    (home-page "https://github.com/jlmelville/uwot")
+    (synopsis "Uniform manifold approximation and projection")
+    (description
+     "This package provides an implementation of the Uniform Manifold
+Approximation and Projection dimensionality reduction by McInnes et
+al. (2018).  It also provides means to transform new data and to carry out
+supervised dimensionality reduction.  An implementation of the related
+LargeVis method of Tang et al. (2016) is also provided.")
+    (license license:gpl3)))
+
+(define-public r-kableextra
+  (package
+    (name "r-kableextra")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "kableExtra" version))
+       (sha256
+        (base32
+         "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
+    (properties `((upstream-name . "kableExtra")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-digest" ,r-digest)
+       ("r-glue" ,r-glue)
+       ("r-htmltools" ,r-htmltools)
+       ("r-knitr" ,r-knitr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-readr" ,r-readr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-rstudioapi" ,r-rstudioapi)
+       ("r-rvest" ,r-rvest)
+       ("r-scales" ,r-scales)
+       ("r-stringr" ,r-stringr)
+       ("r-viridislite" ,r-viridislite)
+       ("r-webshot" ,r-webshot)
+       ("r-xml2" ,r-xml2)))
+    (home-page "https://haozhu233.github.io/kableExtra/")
+    (synopsis "Construct complex tables with pipe syntax")
+    (description
+     "Build complex HTML or LaTeX tables using @code{kable()} from
+@code{knitr} and the piping syntax from @code{magrittr}.  The function
+@code{kable()} is a light weight table generator coming from @code{knitr}.
+This package simplifies the way to manipulate the HTML or LaTeX codes
+generated by @code{kable()} and allows users to construct complex tables and
+customize styles using a readable syntax.")
+    (license license:expat)))
+
+(define-public r-glasso
+  (package
+    (name "r-glasso")
+    (version "1.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "glasso" version))
+       (sha256
+        (base32
+         "0nshpx14v2yny7lr8ll6nnz71n0f02sddh2c2dglfprbk89p9yp6"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://www-stat.stanford.edu/~tibs/glasso")
+    (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
+    (description
+     "This is a package for estimation of a sparse inverse covariance matrix
+using a lasso (L1) penalty.  Facilities are provided for estimates along a
+path of values for the regularization parameter.")
+    (license license:gpl2)))
+
+(define-public r-rhpcblasctl
+  (package
+    (name "r-rhpcblasctl")
+    (version "0.18-205")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RhpcBLASctl" version))
+       (sha256
+        (base32
+         "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
+    (properties `((upstream-name . "RhpcBLASctl")))
+    (build-system r-build-system)
+    (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
+    (synopsis "Control the number of threads on BLAS")
+    (description
+     "This package allows you to control the number of threads the BLAS
+library uses.  It is also possible to control the number of threads in
+OpenMP.")
+    (license license:agpl3+)))