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Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 413 |
1 files changed, 413 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0750c7d507..f288f76e95 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9390,6 +9390,144 @@ and make comparisons between different methodologies straightforward.") several entropy estimators.") (license license:gpl3+))) +(define-public r-nsprcomp + (package + (name "r-nsprcomp") + (version "0.5.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "nsprcomp" version)) + (sha256 + (base32 + "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) + (properties `((upstream-name . "nsprcomp"))) + (build-system r-build-system) + (home-page "https://sigg-iten.ch/research/") + (synopsis "Non-negative and sparse PCA") + (description + "This package implements two methods for performing a constrained +principal component analysis (PCA), where non-negativity and/or sparsity +constraints are enforced on the principal axes (PAs). The function +@code{nsprcomp} computes one principal component (PC) after the other. Each +PA is optimized such that the corresponding PC has maximum additional variance +not explained by the previous components. In contrast, the function +@code{nscumcomp} jointly computes all PCs such that the cumulative variance is +maximal. Both functions have the same interface as the @code{prcomp} function +from the @code{stats} package (plus some extra parameters).") + (license license:gpl2+))) + +(define-public r-cmplot + (package + (name "r-cmplot") + (version "3.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "CMplot" version)) + (sha256 + (base32 + "13y05j5gsdc712fn7yvcz5nx2pbcdvl201hfb6jzpvl86qx2l0j1")))) + (properties `((upstream-name . "CMplot"))) + (build-system r-build-system) + (home-page "https://github.com/YinLiLin/CMplot") + (synopsis "Circle Manhattan plot") + (description + "Circle Manhattan Plot is an R package that can lay out genome-wide +association study P-value results in both traditional rectangular patterns, +QQ-plot and novel circular ones. United in only one bull's eye style plot, +association results from multiple traits can be compared interactively, +thereby to reveal both similarities and differences between signals. +Additional functions include: highlight signals, a group of SNPs, chromosome +visualization and candidate genes around SNPs.") + (license license:gpl2+))) + +(define-public r-precrec + (package + (name "r-precrec") + (version "0.12.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "precrec" version)) + (sha256 + (base32 + "0vwzaqnh9ymrm52dd79bihwqprnygz0d71ay8fv51hdw0zg6saya")))) + (properties `((upstream-name . "precrec"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-rcpp" ,r-rcpp) + ("r-withr" ,r-withr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://evalclass.github.io/precrec/") + (synopsis "Calculate accurate precision-recall and ROC curves") + (description + "This package provides tools for accurate calculations and visualization +of precision-recall and ROC (Receiver Operator Characteristics) curves.") + (license license:gpl3))) + +(define-public r-netrep + (package + (name "r-netrep") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "NetRep" version)) + (sha256 + (base32 + "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd")))) + (properties `((upstream-name . "NetRep"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-bh" ,r-bh) + ("r-foreach" ,r-foreach) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhpcblasctl" ,r-rhpcblasctl) + ("r-statmod" ,r-statmod))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/package=NetRep") + (synopsis "Permutation testing network module preservation across datasets") + (description + "This package provides functions for assessing the +replication/preservation of a network module's topology across datasets +through permutation testing.") + (license license:gpl2))) + +(define-public r-intergraph + (package + (name "r-intergraph") + (version "2.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "intergraph" version)) + (sha256 + (base32 + "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc")))) + (properties `((upstream-name . "intergraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-network" ,r-network))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://mbojan.github.io/intergraph") + (synopsis "Coercion routines for network data objects") + (description + "Functions implemented in this package allow to coerce (i.e. convert) +network data between classes provided by other R packages. Currently +supported classes are those defined in packages @code{network} and +@code{igraph}.") + (license license:gpl3))) + (define-public r-abcoptim (package (name "r-abcoptim") @@ -9517,6 +9655,233 @@ and coverage methods to tune the choice of threshold.") @end enumerate") (license license:gpl3))) +(define-public r-ggnetwork + (package + (name "r-ggnetwork") + (version "0.5.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggnetwork" version)) + (sha256 + (base32 + "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v")))) + (properties `((upstream-name . "ggnetwork"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-igraph" ,r-igraph) + ("r-network" ,r-network) + ("r-sna" ,r-sna))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/briatte/ggnetwork") + (synopsis "Geometries to plot networks with ggplot2") + (description + "This package provides geometries to plot network objects with the +ggplot2 package.") + (license license:gpl3))) + +(define-public r-cvauc + (package + (name "r-cvauc") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "cvAUC" version)) + (sha256 + (base32 + "13bk97l5nn97h85iz93zxazhr63n21nwyrpnl856as9qp59yvn64")))) + (properties `((upstream-name . "cvAUC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-rocr" ,r-rocr))) + (home-page "https://github.com/ledell/cvAUC") + (synopsis "Cross-validated area under the ROC curve confidence intervals") + (description + "This package contains various tools for working with and evaluating +cross-validated area under the ROC curve (AUC) estimators. The primary +functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which +report cross-validated AUC and compute confidence intervals for +cross-validated AUC estimates based on influence curves for i.i.d. and pooled +repeated measures data, respectively.") + (license license:asl2.0))) + +(define-public r-gam + (package + (name "r-gam") + (version "1.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "gam" version)) + (sha256 + (base32 + "1zhy2fp7pxac8xp3z3hndhprj4s5gx3305b627vc78bal1ml3swi")))) + (properties `((upstream-name . "gam"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/package=gam") + (synopsis "Generalized additive models") + (description + "This package provides functions for fitting and working with generalized +additive models, as described in chapter 7 of \"Statistical Models in +S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive +Models\" (Hastie and Tibshirani, 1990).") + (license license:gpl2))) + +(define-public r-superlearner + (package + (name "r-superlearner") + (version "2.0-28") + (source + (origin + (method url-fetch) + (uri (cran-uri "SuperLearner" version)) + (sha256 + (base32 + "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz")))) + (properties `((upstream-name . "SuperLearner"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cvauc" ,r-cvauc) + ("r-gam" ,r-gam) + ("r-nnls" ,r-nnls))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ecpolley/SuperLearner") + (synopsis "Super learner prediction") + (description + "This package implements the super learner prediction method and contains +a library of prediction algorithms to be used in the super learner.") + (license license:gpl3))) + +(define-public r-drtmle + (package + (name "r-drtmle") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "drtmle" version)) + (sha256 + (base32 + "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa")))) + (properties `((upstream-name . "drtmle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-future-apply" ,r-future-apply) + ("r-np" ,r-np) + ("r-superlearner" ,r-superlearner))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/benkeser/drtmle") + (synopsis "Doubly-robust nonparametric estimation and inference") + (description + "This package implements targeted minimum loss-based estimators of +counterfactual means and causal effects that are doubly-robust with respect +both to consistency and asymptotic normality.") + (license license:expat))) + +(define-public r-dofuture + (package + (name "r-dofuture") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "doFuture" version)) + (sha256 + (base32 + "1hqzdlgcrc5l6xjwdylsc9iiysi2wx8k1j1vmw3wryj26057c9y4")))) + (properties `((upstream-name . "doFuture"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-future" ,r-future) + ("r-globals" ,r-globals) + ("r-iterators" ,r-iterators))) + (native-inputs + `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (home-page "https://github.com/HenrikBengtsson/doFuture") + (synopsis "Foreach parallel adapter using the future API") + (description + "This package provides a @code{%dopar%} adapter such that any type of +futures can be used as backends for the @code{foreach} framework.") + (license license:lgpl2.1+))) + +(define-public r-superheat + (package + (name "r-superheat") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "superheat" version)) + (sha256 + (base32 + "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83")))) + (properties `((upstream-name . "superheat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-scales" ,r-scales))) + (home-page "https://cran.r-project.org/package=superheat") + (synopsis "Graphical tool for exploring complex datasets using heatmaps") + (description + "This package provides a system for generating extendable and +customizable heatmaps for exploring complex datasets, including big data and +data with multiple data types.") + (license license:cc0))) + +(define-public r-qualv + (package + (name "r-qualv") + (version "0.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "qualV" version)) + (sha256 + (base32 + "1yyqk223ydcc0125gsn33a4mcdp8bd76fpn8kj9bfz9g78b8dqmx")))) + (properties `((upstream-name . "qualV"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth))) + (home-page "http://qualV.R-Forge.R-Project.org/") + (synopsis "Qualitative Validation Methods") + (description + "This package provides qualitative methods for the validation of dynamic +models. It contains + +@enumerate +@item an orthogonal set of deviance measures for absolute, relative and + ordinal scale and +@item approaches accounting for time shifts. +@end enumerate + +The first approach transforms time to take time delays and speed differences +into account. The second divides the time series into interval units +according to their main features and finds the @dfn{longest common +subsequence} (LCS) using a dynamic programming algorithm.") + (license license:gpl2+))) + (define-public r-mosaiccore (package (name "r-mosaiccore") @@ -11745,6 +12110,54 @@ builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non-R software.") (license license:expat))) +(define-public r-rslurm + (package + (name "r-rslurm") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rslurm" version)) + (sha256 + (base32 + "0fn2na8prsaxa03x5wi3105gpsxc35qvgmik7wy3nylvx4wdfv9g")))) + (properties `((upstream-name . "rslurm"))) + (build-system r-build-system) + (propagated-inputs `(("r-whisker" ,r-whisker))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "http://cyberhelp.sesync.org/rslurm/") + (synopsis "Submit R calculations to a Slurm cluster") + (description + "This package provides functions that simplify submitting R scripts to a +Slurm workload manager, in part by automating the division of embarrassingly +parallel calculations across cluster nodes.") + (license license:gpl3))) + +(define-public r-chk + (package + (name "r-chk") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "chk" version)) + (sha256 + (base32 + "1fxsxgvd08lkb6amjgs4x48dhqr046mmjngjfgy2ya9cl2shd7ls")))) + (properties `((upstream-name . "chk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lifecycle" ,r-lifecycle) + ("r-rlang" ,r-rlang))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/poissonconsulting/chk") + (synopsis "Check user-supplied function arguments") + (description + "This is a package for developers to check user-supplied function +arguments. It is designed to be simple, fast and customizable. Error +messages follow the tidyverse style guide.") + (license license:expat))) + (define-public r-weights (package (name "r-weights") |