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-rw-r--r--gnu/packages/cran.scm361
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)))