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")
@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")
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")
HCoop / jackhill / guix / guix.git / blobdiff