diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 361 |
1 files changed, 361 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 58e9ad09c7..efcc2dccb5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5895,3 +5895,364 @@ hemoglobin to reticulocytes (OFF-score), as well as example data.") based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks.") (license license:agpl3+))) + +(define-public r-pscl + (package + (name "r-pscl") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pscl" version)) + (sha256 + (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://github.com/atahk/pscl/") + (synopsis "Political science computational laboratory") + (description + "The @code{pscl} is an R package providing classes and methods for: +@enumerate +@item Bayesian analysis of roll call data (item-response models); +@item elementary Bayesian statistics; +@item maximum likelihood estimation of zero-inflated and hurdle models for count +data; +@item utility functions. +@end enumerate") + (license license:gpl2))) + +(define-public r-accelmissing + (package + (name "r-accelmissing") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "accelmissing" version)) + (sha256 + (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mice" ,r-mice) + ("r-pscl" ,r-pscl))) + (home-page "https://cran.r-project.org/web/packages/accelmissing/") + (synopsis "Missing value imputation for accelerometer data") + (description + "This package provides a statistical method to impute the missing values in +accelerometer data. The methodology includes both parametric and +semi-parametric multiple imputations under the zero-inflated Poisson lognormal +model. It also provides multiple functions to preprocess the accelerometer data +previous to the missing data imputation. These include detecting the wearing +and the non-wearing time, selecting valid days and subjects, and creating plots.") + (license license:gpl2+))) + +(define-public r-mhsmm + (package + (name "r-mhsmm") + (version "0.4.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "mhsmm" version)) + (sha256 + (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) + (build-system r-build-system) + (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) + (home-page "https://github.com/jaredo/mhsmm/") + (synopsis "Inference for hidden Markov and semi-Markov models") + (description + "The @code{r-mhsmm} package implements estimation and prediction methods for +hidden Markov and semi-Markov models for multiple observation sequences. Such +techniques are of interest when observed data is thought to be dependent on some +unobserved (or hidden) state. Also, this package is suitable for equidistant +time series data, with multivariate and/or missing data. Allows user defined +emission distributions.") + (license license:gpl2+))) + +(define-public r-nleqslv + (package + (name "r-nleqslv") + (version "3.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "nleqslv" version)) + (sha256 + (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/nleqslv/") + (synopsis "Solve systems of nonlinear equations") + (description + "The @code{r-nleqslv} package solves a system of nonlinear equations using a +Broyden or a Newton method with a choice of global strategies such as line +search and trust region. There are options for using a numerical or user +supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a +singular or ill-conditioned Jacobian.") + (license license:gpl2+))) + +(define-public r-physicalactivity + (package + (name "r-physicalactivity") + (version "0.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "PhysicalActivity" version)) + (sha256 + (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln")))) + (properties + `((upstream-name . "PhysicalActivity"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/") + (synopsis "Procesing accelerometer data for physical activity measurement") + (description + "This @code{r-physicalactivity} package provides a function @code{wearingMarking} +for classification of monitor wear and nonwear time intervals in accelerometer +data collected to assess physical activity. The package also contains functions +for making plots of accelerometer data and obtaining the summary of various +information including daily monitor wear time and the mean monitor wear time +during valid days. The revised package version 0.2-1 improved the functions +regarding speed, robustness and add better support for time zones and daylight +saving. In addition, several functions were added: +@enumerate +@item the @code{markDelivery} can classify days for ActiGraph delivery by mail; +@item the @code{markPAI} can categorize physical activity intensity level based +on user-defined cut-points of accelerometer counts. +@end enumerate + It also supports importing ActiGraph (AGD) files with @code{readActigraph} and +@code{queryActigraph} functions.") + (license license:gpl3+))) + +(define-public r-acc + (package + (name "r-acc") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acc" version)) + (sha256 + (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-dbi" ,r-dbi) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-mhsmm" ,r-mhsmm) + ("r-nleqslv" ,r-nleqslv) + ("r-physicalactivity" ,r-physicalactivity) + ("r-plyr" ,r-plyr) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsqlite" ,r-rsqlite) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/acc/") + (synopsis "Exploring accelerometer data") + (description + "This package processes accelerometer data from uni-axial and tri-axial devices +and generates data summaries. Also, includes functions to plot, analyze, and +simulate accelerometer data.") + (license license:gpl2+))) + +(define-public r-rbenchmark + (package + (name "r-rbenchmark") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbenchmark" version)) + (sha256 + (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rbenchmark/") + (synopsis "Benchmarking routine for R") + (description + "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark, +and is intended to facilitate benchmarking of arbitrary R code. The library +consists of just one function, benchmark, which is a simple wrapper around +system.time. Given a specification of the benchmarking process (counts of +replications, evaluation environment) and an arbitrary number of expressions, +benchmark evaluates each of the expressions in the specified environment, +replicating the evaluation as many times as specified, and returning the results +conveniently wrapped into a data frame.") + (license license:gpl2+))) + +(define-public r-dvmisc + (package + (name "r-dvmisc") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "dvmisc" version)) + (sha256 + (base32 "1dy0yykskwhkql19bhzmbwsgv028afc8jh9yqwbczj6f3vpv31zh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rbenchmark" ,r-rbenchmark) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/dvmisc/") + (synopsis "Faster computation of common statistics and miscellaneous functions") + (description + "This package implements faster versions of base R functions (e.g. mean, standard +deviation, covariance, weighted mean), mostly written in C++, along with +miscellaneous functions for various purposes (e.g. create the histogram with +fitted probability density function or probability mass function curve, create +the body mass index groups, assess the linearity assumption in logistic +regression).") + (license license:gpl2))) + +(define-public r-accelerometry + (package + (name "r-accelerometry") + (version "3.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "accelerometry" version)) + (sha256 + (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dvmisc" ,r-dvmisc) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/accelerometry/") + (synopsis "Functions for processing accelerometer data") + (description + "This package provides a collection of functions that perform operations on +time-series accelerometer data, such as identify the non-wear time, flag minutes +that are part of an activity bout, and find the maximum 10-minute average count +value. The functions are generally very flexible, allowing for a variety of +algorithms to be implemented.") + (license license:gpl3))) + +(define-public r-absim + (package + (name "r-absim") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbSim" version)) + (sha256 + (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m")))) + (properties `((upstream-name . "AbSim"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-powerlaw" ,r-powerlaw))) + (home-page "https://cran.r-project.org/web/packages/AbSim/") + (synopsis "Time resolved simulations of antibody repertoires") + (description + "This package provides simulation methods for the evolution of antibody repertoires. + The heavy and light chain variable region of both human and C57BL/6 mice can +be simulated in a time-dependent fashion. Both single lineages using one set of +V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins +with an initial V-D-J recombination event, starting the first phylogenetic tree. + Upon completion, the main loop of the algorithm begins, with each iteration +representing one simulated time step. Various mutation events are possible at +each time step, contributing to a diverse final repertoire.") + (license license:gpl2))) + +(define-public r-ac3net + (package + (name "r-ac3net") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Ac3net" version)) + (sha256 + (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz")))) + (properties `((upstream-name . "Ac3net"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://cran.r-project.org/web/packages/Ac3net/") + (synopsis "Inferring directional conservative causal core gene networks") + (description "This package infers directional Conservative causal core +(gene) networks (C3NET). This is a version of the algorithm C3NET with +directional network.") + (license license:gpl3+))) + +(define-public r-aca + (package + (name "r-aca") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACA" version)) + (sha256 + (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq")))) + (properties `((upstream-name . "ACA"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACA/") + (synopsis "Abrupt change-point or aberration detection in point series") + (description + "This package offers an interactive function for the detection of breakpoints in +series.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-acceptancesampling + (package + (name "r-acceptancesampling") + (version "1.0-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcceptanceSampling" version)) + (sha256 + (base32 "18krmmyn8pn11aqd81kbvka68lnd36mnpdh7p3pz9r4m4vjj007x")))) + (properties + `((upstream-name . "AcceptanceSampling"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/") + (synopsis "Creation and evaluation of acceptance sampling plans") + (description + "This @code{r-acceptancesampling} provides functionality for creating and evaluating +acceptance sampling plans. Acceptance sampling is a methodology commonly used +in quality control and improvement. International standards of acceptance +sampling provide sampling plans for specific circumstances. The aim of this +package is to provide an easy-to-use interface to visualize single, double or +multiple sampling plans. In addition, methods have been provided to enable the +user to assess sampling plans against pre-specified levels of performance, as +measured by the probability of acceptance for a given level of quality in the +lot.") + (license license:gpl3+))) + +(define-public r-acclma + (package + (name "r-acclma") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACCLMA" version)) + (sha256 + (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v")))) + (properties `((upstream-name . "ACCLMA"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACCLMA/") + (synopsis "ACC & LMA graph plotting") + (description + "This package contains a function that imports data from a @acronym{CSV, +Comma-Separated Values} file, or uses manually entered data from the format (x, +y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration +Curve} vs @acronym{LOI, Line of Independence} graph and +@acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main +function is @code{plotLMA} (source file, header) that takes a data set and plots the +appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a +string) was passed, a manual data entry window is opened. The header parameter +indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has +a header row or not. The dataset should contain only one independent variable +(x) and one dependent variable (y) and can contain a weight for each +observation.") + (license license:gpl2))) |