diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 249 |
1 files changed, 85 insertions, 164 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index be66533b0b..0939c4d5a6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -253,17 +253,18 @@ series of numeric vectors/matrices and factors.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin")))) + "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) + ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-lubridate" ,r-lubridate) @@ -783,14 +784,14 @@ same time tries to group instances from the same class together.") (define-public r-callr (package (name "r-callr") - (version "3.4.3") + (version "3.4.4") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1")))) + "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -917,13 +918,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq")))) + "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -2260,14 +2261,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.") (define-public r-shape (package (name "r-shape") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 - "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) + "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") @@ -2788,14 +2789,14 @@ or excesses over a high threshold.") (define-public r-lmtest (package (name "r-lmtest") - (version "0.9-37") + (version "0.9-38") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 - "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx")))) + "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) @@ -2833,13 +2834,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.15") + (version "0.3.16") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z")))) + "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -3400,7 +3401,7 @@ Optimization problems by using the simplex algorithm.") ("r-rcpp" ,r-rcpp) ("r-rcppprogress" ,r-rcppprogress))) (home-page "http://geometry.r-forge.r-project.org/") - (synopsis "Mesh generation and surface tesselation") + (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace @@ -3524,14 +3525,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.0.7") + (version "2.0.8") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc")))) + "0ymds7ql2dv994m73h68dnhbsws8bl09p2rqvl6xsq6c6xr0yryg")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -3742,7 +3743,7 @@ color labels, layout, etc.") (description "This package implements an approximate string matching version of R's native @code{match} function. It can calculate various string distances based -on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), +on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding @@ -4111,14 +4112,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.12-0") + (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz")))) + "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/xts") @@ -4408,13 +4409,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.3") + (version "3.4.4") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj")))) + (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -4555,13 +4556,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.16") + (version "0.17") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg")))) + (base32 "1zd5qi1rrz3b1lpisapa2yscanz39ghaamf28g7aq3z9ai2a2ymj")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -5077,20 +5078,21 @@ University Press, 2000.") (define-public r-tsa (package (name "r-tsa") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "TSA" version)) (sha256 (base32 - "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q")))) + "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb")))) (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs `(("r-leaps" ,r-leaps) ("r-locfit" ,r-locfit) - ("r-mgcv" ,r-mgcv))) + ("r-mgcv" ,r-mgcv) + ("r-tseries" ,r-tseries))) (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description @@ -5102,14 +5104,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.11") + (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3")))) + "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs @@ -6857,14 +6859,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.13") + (version "0.3.14") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr")))) + "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) @@ -7124,14 +7126,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.9.1") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6")))) + "0853kq4j8kic8z2gh5mxfqkwxjs4bdphlajzyvxka7af4r04bfmi")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7258,14 +7260,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.5.10") + (version "0.5.11") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8")))) + "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -7913,18 +7915,17 @@ and coverage methods to tune the choice of threshold.") (define-public r-mosaiccore (package (name "r-mosaiccore") - (version "0.6.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 - (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z")))) + (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) ("r-mass" ,r-mass) ("r-rlang" ,r-rlang) ("r-tidyr" ,r-tidyr))) @@ -7966,13 +7967,13 @@ while providing the intuitive capabilities of @code{r-ggplot2}.") (define-public r-mosaicdata (package (name "r-mosaicdata") - (version "0.18.0") + (version "0.20.1") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 - (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz")))) + (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji")))) (properties `((upstream-name . "mosaicData"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mosaicData/") @@ -9251,14 +9252,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.4.8") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l")))) + "01csmn52d6rhlmcj7gi6ckc6v6a8pymnrpx9l729h13igxsnaf28")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -9278,14 +9279,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.15.1") + (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47")))) + "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -9970,14 +9971,14 @@ This package provides an R interface.") (define-public r-rcpphnsw (package (name "r-rcpphnsw") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppHNSW" version)) (sha256 (base32 - "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv")))) + "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -10124,14 +10125,14 @@ to colexicographical order.") (define-public r-misc3d (package (name "r-misc3d") - (version "0.8-4") + (version "0.9-0") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 - "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) + "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") @@ -10967,14 +10968,14 @@ Touzet and Varre (2007).") (define-public r-rnifti (package (name "r-rnifti") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10")))) + "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -11934,13 +11935,13 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "10.3") + (version "11.4") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 - (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9")))) + (base32 "0x8hbl0rn7gnhn7w45wd757g9in27884qr6vy30xrk150qaq941y")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps) @@ -12199,14 +12200,14 @@ JASA, 94:496-509.") (define-public r-etm (package (name "r-etm") - (version "1.1") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "etm" version)) (sha256 (base32 - "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd")))) + "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -12854,20 +12855,22 @@ transformation, respectively.") (define-public r-shinyjs (package (name "r-shinyjs") - (version "1.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 - "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9")))) + "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description @@ -13888,14 +13891,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-28") + (version "0.1-29") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5")))) + "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -13912,14 +13915,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-5") + (version "0.9-6") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf")))) + "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -14474,44 +14477,6 @@ authoring books and technical documents with R Markdown.") that accept short and long options.") (license license:gpl2+))) -(define-public r-wgcna - (package - (name "r-wgcna") - (version "1.69") - (source - (origin - (method url-fetch) - (uri (cran-uri "WGCNA" version)) - (sha256 - (base32 - "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) - (properties `((upstream-name . "WGCNA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore))) - (home-page - "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") - (synopsis "Weighted correlation network analysis") - (description - "This package provides functions necessary to perform Weighted -Correlation Network Analysis on high-dimensional data. It includes functions -for rudimentary data cleaning, construction and summarization of correlation -networks, module identification and functions for relating both variables and -modules to sample traits. It also includes a number of utility functions for -data manipulation and visualization.") - (license license:gpl2+))) - (define-public r-kernlab (package (name "r-kernlab") @@ -16097,14 +16062,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "1.3.1.1") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs")))) + "1yn61cbqvyycn617pzhd7kgd34xsnmqvj3s10inn2ywycybk7byi")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -16532,7 +16497,7 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") "The @code{ggplot2} package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API to allow for arbitrarily -complex composition of plots by providing mathmatical operators for combining +complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) @@ -16689,14 +16654,14 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax")))) + "0ldxgcayyisp2gcbv4xw9zpb48bp4czi8016kq5nqdqhv1qb3sz0")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs @@ -16837,14 +16802,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.8.2") + (version "0.8.5") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh")))) + "1vax5p1znq2ddbks2i614hbrnn2x6x71942xx49p813qk8dh284l")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -18155,14 +18120,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.1-7") + (version "5.2-0") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8")))) + "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -19651,7 +19616,7 @@ on distances rather than on unit x variables.") "This package provides tools for depth functions methodology applied to multivariate analysis. Besides allowing calculation of depth values and depth-based location estimators, the package includes functions or drawing -contour plots and perspective plots of depth functions. Euclidian and +contour plots and perspective plots of depth functions. Euclidean and spherical depths are supported.") (license license:gpl2))) @@ -20304,14 +20269,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.12") + (version "8.13") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b")))) + "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -21934,7 +21899,7 @@ appropriate dog and cat images for many status codes.") (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) - ("r-magrittr", r-magrittr))) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to @@ -22138,7 +22103,7 @@ general, via different versions of bridge sampling.") (description "This package provides different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the -AMSE-criterion or atleast by reducing the bias of the assumed GPD-model. +AMSE-criterion or at least by reducing the bias of the assumed GPD-model. Others are heuristically motivated by searching for stable sample paths, i.e. a nearly constant region of the tail index estimator with respect to k, which is the number of data in the tail. The third class is motivated by graphical @@ -22478,14 +22443,14 @@ multi-state models.") (define-public r-scatterpie (package (name "r-scatterpie") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "scatterpie" version)) (sha256 (base32 - "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb")))) + "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1")))) (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs @@ -22572,50 +22537,6 @@ Try a demo of the LSD by running @code{demotour()}.") ;; Either version (license (list license:gpl2 license:gpl3)))) -(define-public r-fourcseq - (package - (name "r-fourcseq") - (version "1.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "FourCSeq" version)) - (sha256 - (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b")))) - (properties `((upstream-name . "FourCSeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page - "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") - (synopsis "Analysis of multiplexed 4C sequencing data") - (description - "This package is an R package dedicated to the analysis of (multiplexed) -4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific -interactions between DNA elements and identify differential interactions -between conditions. The statistical analysis in R starts with individual bam -files for each sample as inputs. To obtain these files, the package contains -a Python script to demultiplex libraries and trim off primer sequences. With -a standard alignment software the required bam files can be then be -generated.") - (license license:gpl3+))) - (define-public r-phylogram (package (name "r-phylogram") @@ -23215,14 +23136,14 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy")))) + "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs @@ -24434,18 +24355,17 @@ as allowing spectra with different resolutions.") (define-public r-seurat (package (name "r-seurat") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2")))) + "0jipc4xpmx56jzc31w6nsl77ah8x8wq7jclg2mxhjql4ixkwmz54")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-cluster" ,r-cluster) + `(("r-cluster" ,r-cluster) ("r-cowplot" ,r-cowplot) ("r-fitdistrplus" ,r-fitdistrplus) ("r-future" ,r-future) @@ -24463,6 +24383,7 @@ as allowing spectra with different resolutions.") ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) ("r-miniui" ,r-miniui) ("r-patchwork" ,r-patchwork) ("r-pbapply" ,r-pbapply) @@ -24527,14 +24448,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-13") + (version "0.9-14") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix")))) + "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) |