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Automated CRAN import 2024-03-28
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(list (channel
        (name 'guix)
        (url "https://git.savannah.gnu.org/git/guix.git")
        (branch "master")
        (commit "0e8f7ee3a95011dd9ebdc99e0f3b754160524b5d")
        (introduction
         (make-channel-introduction "9edb3f66fd807b096b48283debdcddccfea34bad"
          (openpgp-fingerprint
           "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA")))))
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User for Guix CRAN updates committed Mar 28, 2024
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137 changes: 28 additions & 109 deletions guix-cran/packages/a.scm
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Expand Up @@ -7424,79 +7424,6 @@ vignettes. The data sets were formerly distributed with @code{ArchaeoPhases}',
however they exceed current CRAN policy for package size.")
(license license:gpl3)))

(define-public r-archaeophases
(package
(name "r-archaeophases")
(version "1.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "ArchaeoPhases" version))
(sha256
(base32 "00d8lpasz96l55v3982mqg85b237lxvsjl65p288yzj87860v2kj"))))
(properties `((upstream-name . "ArchaeoPhases")))
(build-system r-build-system)
(propagated-inputs (list r-toordinal
r-shiny
r-reshape2
r-readr
r-magrittr
r-hdrcde
r-gtools
r-gplots
r-ggraph
r-ggplot2
r-ggalt
r-dplyr
r-digest
r-coda))
(native-inputs (list r-knitr))
(home-page "https://cran.r-project.org/package=ArchaeoPhases")
(synopsis
"Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'")
(description
"This package provides a list of functions for the statistical analysis of
archaeological dates and groups of dates. It is based on the post-processing of
the Markov Chains whose stationary distribution is the posterior distribution of
a series of dates. Such output can be simulated by different applications as
for instance @code{ChronoModel} (see <https://chronomodel.com/>), Oxcal (see
<https://c14.arch.ox.ac.uk/oxcal.html>) or BCal (see
<https://bcal.shef.ac.uk/>). The only requirement is to have a csv file
containing a sample from the posterior distribution. Note that this package
interacts with data available through the @code{ArchaeoPhases.dataset} package
which is available in a separate repository. The size of the
@code{ArchaeoPhases.dataset} package is approximately 4 MB.")
(license license:gpl3)))

(define-public r-archaeochron
(package
(name "r-archaeochron")
(version "0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ArchaeoChron" version))
(sha256
(base32 "1qma2432mm73h72g9ah1k02wlcb6yrhc6mpai9nj7v58s126ffxn"))))
(properties `((upstream-name . "ArchaeoChron")))
(build-system r-build-system)
(propagated-inputs (list r-rjags r-coda r-bchron r-archaeophases))
(native-inputs (list r-knitr))
(home-page "https://cran.r-project.org/package=ArchaeoChron")
(synopsis "Bayesian Modeling of Archaeological Chronologies")
(description
"This package provides a list of functions for the Bayesian modeling of
archaeological chronologies. The Bayesian models are implemented in JAGS ('JAGS
stands for Just Another Gibbs Sampler. It is a program for the analysis of
Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
See <http://mcmc-jags.sourceforge.net/> and \"JAGS Version 4.3.0 user manual\",
Martin Plummer (2017)
<https://sourceforge.net/projects/mcmc-jags/files/Manuals/>.). The inputs are
measurements with their associated standard deviations and the study period.
The output is the MCMC sample of the posterior distribution of the event date
with or without radiocarbon calibration.")
(license license:gpl3)))

(define-public r-arcgisutils
(package
(name "r-arcgisutils")
Expand Down Expand Up @@ -9291,42 +9218,6 @@ all possible comparisons (APC) methodology developed by Miller (2005)
<doi:10.1198/004017004000000608>.")
(license license:gpl3)))

(define-public r-apcalign
(package
(name "r-apcalign")
(version "0.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "APCalign" version))
(sha256
(base32 "1kbkwpf7lzg7lznl0ysnwwilmklqyqd02qc1vl0pfbd407pqlyyv"))))
(properties `((upstream-name . "APCalign")))
(build-system r-build-system)
(propagated-inputs (list r-tibble
r-stringr
r-stringi
r-rlang
r-readr
r-purrr
r-jsonlite
r-httr
r-forcats
r-dplyr
r-curl
r-crayon
r-arrow))
(native-inputs (list r-knitr))
(home-page "https://traitecoevo.github.io/APCalign/")
(synopsis "Resolving Plant Taxon Names Using the Australian Plant Census")
(description
"The process of resolving taxon names is necessary when working with biodiversity
data. APCalign uses the Australian Plant Census (APC) and the Australian Plant
Name Index (APNI) to align and update plant taxon names to current, accepted
standards. APCalign also supplies information about the established status of
plant taxa across different states/territories.")
(license license:expat)))

(define-public r-apc
(package
(name "r-apc")
Expand Down Expand Up @@ -21022,6 +20913,34 @@ frequently used inequality and poverty metrics (such as the Palma ratio, the
concentration and Theil indices and the FGT family of measures).")
(license license:expat)))

(define-public r-accelstab
(package
(name "r-accelstab")
(version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "AccelStab" version))
(sha256
(base32 "072wm4421bir8ij1g5zj0rn26h28vz7np6glmvapv18q4kfz1x88"))))
(properties `((upstream-name . "AccelStab")))
(build-system r-build-system)
(propagated-inputs (list r-scales r-mvtnorm r-minpack-lm r-ggplot2 r-dplyr))
(home-page "https://github.com/AccelStab/AccelStab")
(synopsis "Accelerated Stability Kinetic Modelling")
(description
"Estimate the Š@code{esták–Berggren} kinetic model (degradation model) from
experimental data. A A closed-form (analytic) solution to the degradation model
is implemented as a non-linear fit, allowing for the extrapolation of the
degradation of a drug product - both in time and temperature. Parametric
bootstrap, with kinetic parameters drawn from the multivariate t-distribution,
and analytical formulae (the delta method) are available options to calculate
the confidence and prediction intervals. The results (modelling, extrapolations
and statistical intervals) can be visualised with multiple plots. The examples
illustrate the accelerated stability modelling in drugs and vaccines
development.")
(license license:agpl3+)))

(define-public r-acca
(package
(name "r-acca")
Expand Down
92 changes: 2 additions & 90 deletions guix-cran/packages/b.scm
View file
Expand Up @@ -5865,37 +5865,6 @@ unitary matrices, evaluation of matrix permanents (both real and complex) and
evaluation of complex permanent minors.")
(license license:gpl2)))

(define-public r-boso
(package
(name "r-boso")
(version "1.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "BOSO" version))
(sha256
(base32 "0zax40x2d62vcn8zznmzmykk33mv4vbjfl88i3r1djbvalcdf5cf"))))
(properties `((upstream-name . "BOSO")))
(build-system r-build-system)
(propagated-inputs (list r-matrix r-mass))
(native-inputs (list r-knitr))
(home-page "https://cran.r-project.org/package=BOSO")
(synopsis "Bilevel Optimization Selector Operator")
(description
"This package provides a novel feature selection algorithm for linear regression
called BOSO (Bilevel Optimization Selector Operator). The main contribution is
the use a bilevel optimization problem to select the variables in the training
problem that minimize the error in the validation set. Preprint available:
[Valcarcel, L. V., San Jose-Eneriz, E., Cendoya, X., Rubio, A., Agirre, X.,
Prosper, F., & Planes, F. J. (2020). \"BOSO: a novel feature selection algorithm
for linear regression with high-dimensional data.\" @code{bioRxiv}.
<doi:10.1101/2020.11.18.388579>]. In order to run the vignette, it is
recommended to install the bestsubset package, using the following command:
devtools::install_github(repo=\"ryantibs/best-subset\", subdir=\"bestsubset\"). If
you do not have gurobi, run
devtools::install_github(repo=\"lvalcarcel/best-subset\", subdir=\"bestsubset\").")
(license license:gpl3)))

(define-public r-borrowr
(package
(name "r-borrowr")
Expand Down Expand Up @@ -12348,32 +12317,6 @@ available at <https://status.biobricks.ai>. Documentation for Biobricks.ai is
available at <https://docs.biobricks.ai>.")
(license license:expat)))

(define-public r-bioassays
(package
(name "r-bioassays")
(version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bioassays" version))
(sha256
(base32 "1y32wxkv14l7r0f35y4hxxxh3zpw2gd4hsjmkajhmzmnvg5jdw78"))))
(properties `((upstream-name . "bioassays")))
(build-system r-build-system)
(propagated-inputs (list r-rlang
r-reshape2
r-nplr
r-magrittr
r-ggplot2
r-dplyr))
(native-inputs (list r-knitr))
(home-page "https://cran.r-project.org/package=bioassays")
(synopsis "Summarising Multi Well Plate Cellular Assay")
(description
"The goal is to help users to analyse data from multi wells with minimum effort.
Using these functions several plates can be analyzed automatically.")
(license license:gpl3)))

(define-public r-bioacoustics
(package
(name "r-bioacoustics")
Expand Down Expand Up @@ -14518,13 +14461,13 @@ of functions of R API to communicate with UCI-protocol based chess engines.")
(define-public r-bigbits
(package
(name "r-bigbits")
(version "1.1")
(version "1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bigBits" version))
(sha256
(base32 "0vakcy5ymd4b5mhz5vjbkhp82bikdajh6wag4cgzbl3vdvx85xhf"))))
(base32 "0qrbm4d3rihy7dvc3lvailmarq1n2hs7qv6wqrgjd0pxnz62j7p7"))))
(properties `((upstream-name . "bigBits")))
(build-system r-build-system)
(propagated-inputs (list r-rmpfr r-gmp))
Expand Down Expand Up @@ -20218,37 +20161,6 @@ implementations of the methods of Oh and Raftery (2001)
<doi:10.1198/016214501753208690>.")
(license license:gpl2+)))

(define-public r-baylum
(package
(name "r-baylum")
(version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "BayLum" version))
(sha256
(base32 "1n40zz0156kw6fwqvlhx3svmvwa2049z4ly9lxcid84dwyxxyn0r"))))
(properties `((upstream-name . "BayLum")))
(build-system r-build-system)
(propagated-inputs (list r-runjags
r-rjags
r-luminescence
r-kernsmooth
r-hexbin
r-coda
r-archaeophases))
(native-inputs (list r-r-rsp))
(home-page "https://CRAN.r-project.org/package=BayLum")
(synopsis
"Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating")
(description
"Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models
are based on the following publications: Combes, B. & Philippe, A. (2017)
<doi:10.1016/j.quageo.2017.02.003> and Combes et al (2015)
<doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import,
export, application of age models and palaeodose model.")
(license license:gpl3)))

(define-public r-baygel
(package
(name "r-baygel")
Expand Down
68 changes: 50 additions & 18 deletions guix-cran/packages/c.scm
View file
Expand Up @@ -955,6 +955,37 @@ classification (binary and multiclass). Described in chp. 5 of Jeyaraman, B.
P., Olsen, L. R., & Wambugu M. (2019, ISBN: 9781838550134).")
(license license:expat)))

(define-public r-cvmortalitymult
(package
(name "r-cvmortalitymult")
(version "0.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "CvmortalityMult" version))
(sha256
(base32 "19j24g0x3f6k91r95z8sl4c2l0y2nbjm8068r21pr4fnfsz5gdj1"))))
(properties `((upstream-name . "CvmortalityMult")))
(build-system r-build-system)
(propagated-inputs (list r-tmap r-stmomo r-sf r-gnm r-forecast))
(home-page "https://github.com/davidAtance/CvmortalityMult")
(synopsis "Cross-Validation for Multi-Population Mortality Models")
(description
"Implementation of cross-validation method for testing the forecasting accuracy
of several multi-population mortality models. The family of multi-population
includes several multi-population mortality models proposed through the
actuarial and demography literature. The package includes functions for fitting
and forecast the mortality rates of several populations. Additionally, we
include functions for testing the forecasting accuracy of different
multi-population models. References. Atance, D., Debon, A., and Navarro, E.
(2020) <doi:10.3390/math8091550>. Bergmeir, C. & Benitez, J.M. (2012)
<doi:10.1016/j.ins.2011.12.028>. Debon, A., Montes, F., & Martinez-Ruiz, F.
(2011) <doi:10.1007/s13385-011-0043-z>. Lee, R.D. & Carter, L.R. (1992)
<doi:10.1080/01621459.1992.10475265>. Russolillo, M., Giordano, G., & Haberman,
S. (2011) <doi:10.1080/03461231003611933>. Santolino, M. (2023)
<doi:10.3390/risks11100170>.")
(license license:expat)))

(define-public r-cvmgof
(package
(name "r-cvmgof")
Expand Down Expand Up @@ -29687,22 +29718,23 @@ headless Chrome web browser.")
(define-public r-chromer
(package
(name "r-chromer")
(version "0.6")
(version "0.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "chromer" version))
(sha256
(base32 "1jn5dwl8i1di8hns3kjww6sqyba768j1302w3f43v9965vfr1xnp"))))
(base32 "0x9xhih0a19mqwiqs7bljcdgki874ii653v91frkwsr2y2yd9j7c"))))
(properties `((upstream-name . "chromer")))
(build-system r-build-system)
(propagated-inputs (list r-tibble r-httr r-dplyr))
(home-page "https://docs.ropensci.org/chromer/")
(synopsis "Interface to Chromosome Counts Database API")
(description
"This package provides a programmatic interface to the Chromosome Counts Database
(<https://ccdb.tau.ac.il/>), Rice et al. (2014) <doi:10.1111/nph.13191>. This
package is part of the R@code{OpenSci} suite (<https://ropensci.org>).")
(<https://taux.evolseq.net/CCDB_web/>), Rice et al. (2014)
<doi:10.1111/nph.13191>. This package is part of the R@code{OpenSci} suite
(<https://ropensci.org>).")
(license license:expat)))

(define-public r-chromconverter
Expand Down Expand Up @@ -34364,32 +34396,32 @@ command \"example(@code{fitVolDist})\".")
(define-public r-celltrackr
(package
(name "r-celltrackr")
(version "1.1.0")
(version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "celltrackR" version))
(sha256
(base32 "08hbgpwcpf7v8l7qmszhjh0w4f4zjcizrdsxksihxpwdi9r4al3w"))))
(base32 "1y0bdn75malabyrnrqrw5vh2sr6j09hpy8gbk1vnmkbvg9dy2xh3"))))
(properties `((upstream-name . "celltrackR")))
(build-system r-build-system)
(propagated-inputs (list r-pracma r-ellipse))
(native-inputs (list r-knitr))
(home-page "http://www.motilitylab.net")
(synopsis "Motion Trajectory Analysis")
(description
"This package provides methodology to analyze cells that move in a two- or
three-dimensional space. Available measures include displacement, confinement
ratio, autocorrelation, straightness, turning angle, and fractal dimension.
Measures can be applied to entire tracks, steps, or subtracks with varying
length. While the methodology has been developed for cell trajectory analysis,
it is applicable to anything that moves including animals, people, or vehicles.
Some of the methodology implemented in this packages was described by:
Beauchemin, Dixit, and Perelson (2007) <doi:10.4049/jimmunol.178.9.5505>,
Beltman, Maree, and de Boer (2009) <doi:10.1038/nri2638>, Gneiting and Schlather
(2004) <doi:10.1137/S0036144501394387>, Mokhtari, Mech, Zitzmann, Hasenberg,
Gunzer, and Figge (2013) <doi:10.1371/journal.pone.0080808>, Moreau, Lemaitre,
Terriac, Azar, Piel, Lennon-Dumenil, and Bousso (2012)
"This package provides methods for analyzing (cell) motion in two or three
dimensions. Available measures include displacement, confinement ratio,
autocorrelation, straightness, turning angle, and fractal dimension. Measures
can be applied to entire tracks, steps, or subtracks with varying length. While
the methodology has been developed for cell trajectory analysis, it is
applicable to anything that moves including animals, people, or vehicles. Some
of the methodology implemented in this packages was described by: Beauchemin,
Dixit, and Perelson (2007) <doi:10.4049/jimmunol.178.9.5505>, Beltman, Maree,
and de Boer (2009) <doi:10.1038/nri2638>, Gneiting and Schlather (2004)
<doi:10.1137/S0036144501394387>, Mokhtari, Mech, Zitzmann, Hasenberg, Gunzer,
and Figge (2013) <doi:10.1371/journal.pone.0080808>, Moreau, Lemaitre, Terriac,
Azar, Piel, Lennon-Dumenil, and Bousso (2012)
<doi:10.1016/j.immuni.2012.05.014>, Textor, Peixoto, Henrickson, Sinn, von
Andrian, and Westermann (2011) <doi:10.1073/pnas.1102288108>, Textor, Sinn, and
de Boer (2013) <doi:10.1186/1471-2105-14-S6-S10>, Textor, Henrickson, Mandl, von
Expand Down

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