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r-mycolorstb 0.1.1
Propagated dependencies: r-ggtree@3.16.0 r-ggplot2@3.5.2 r-ape@5.8-1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=mycolorsTB
Licenses: GPL 3
Synopsis: Color Palettes for Mycobacterium Tuberculosis Data Visualization
Description:

Colour palettes and helper functions for visualising Mycobacterium tuberculosis genomic and epidemiological data with ggplot2 and ggtree'. The package provides predefined palettes, scale functions, tree/cladogram helpers, and convenient preview tools to ensure consistent branding in pathogen-omics visualisations. The palettes were developed as part of the mycolorsTB project <https://github.com/PathoGenOmics-Lab/mycolorsTB>.

r-multiridge 1.11
Propagated dependencies: r-survival@3.8-3 r-snowfall@1.84-6.3 r-proc@1.18.5 r-mgcv@1.9-3
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=multiridge
Licenses: GPL 3+
Synopsis: Fast Cross-Validation for Multi-Penalty Ridge Regression
Description:

Multi-penalty linear, logistic and cox ridge regression, including estimation of the penalty parameters by efficient (repeated) cross-validation and marginal likelihood maximization. Multiple high-dimensional data types that require penalization are allowed, as well as unpenalized variables. Paired and preferential data types can be specified. See Van de Wiel et al. (2021), <arXiv:2005.09301>.

r-natmanager 0.5.1
Propagated dependencies: r-withr@3.0.2 r-usethis@3.1.0 r-remotes@2.5.0 r-pak@0.9.0 r-gh@1.5.0 r-curl@6.2.3
Channel: guix-cran
Location: guix-cran/packages/n.scm (guix-cran packages n)
Home page: https://github.com/natverse/natmanager
Licenses: GPL 3
Synopsis: Install the 'Natverse' Packages from Scratch
Description:

This package provides streamlined installation for packages from the natverse', a suite of R packages for computational neuroanatomy built on top of the nat NeuroAnatomy Toolbox package. Installation of the complete natverse suite requires a GitHub user account and personal access token GITHUB_PAT'. natmanager will help the end user set this up if necessary.

r-otusummary 0.1.2
Propagated dependencies: r-reshape2@1.4.4
Channel: guix-cran
Location: guix-cran/packages/o.scm (guix-cran packages o)
Home page: https://github.com/cam315/otuSummary
Licenses: GPL 3+
Synopsis: Summarizing OTU Table Regarding the Composition, Abundance and Beta Diversity of Abundant and Rare Biospheres
Description:

Summarizes the taxonomic composition, diversity contribution of the rare and abundant community by using OTU (operational taxonomic unit) table which was generated by analyzing pipeline of QIIME or mothur'. The rare biosphere in this package is subset by the relative abundance threshold (for details about rare biosphere please see Lynch and Neufeld (2015) <doi:10.1038/nrmicro3400>).

r-pgee-mixed 0.1.0
Propagated dependencies: r-rcpparmadillo@14.4.3-1 r-rcpp@1.0.14 r-mvtnorm@1.3-3 r-copula@1.1-6
Channel: guix-cran
Location: guix-cran/packages/p.scm (guix-cran packages p)
Home page: http://github.com/kaos42/pgee.mixed
Licenses: GPL 2
Synopsis: Penalized Generalized Estimating Equations for Bivariate Mixed Outcomes
Description:

Perform simultaneous estimation and variable selection for correlated bivariate mixed outcomes (one continuous outcome and one binary outcome per cluster) using penalized generalized estimating equations. In addition, clustered Gaussian and binary outcomes can also be modeled. The SCAD, MCP, and LASSO penalties are supported. Cross-validation can be performed to find the optimal regularization parameter(s).

r-permchacko 1.0.1
Channel: guix-cran
Location: guix-cran/packages/p.scm (guix-cran packages p)
Home page: https://ocbe-uio.github.io/permChacko/
Licenses: GPL 3+
Synopsis: Chacko Test for Order-Restriction with Permutation
Description:

This package implements an extension of the Chacko chi-square test for ordered vectors (Chacko, 1966, <https://www.jstor.org/stable/25051572>). Our extension brings the Chacko test to the computer age by implementing a permutation test to offer a numeric estimate of the p-value, which is particularly useful when the analytic solution is not available.

r-provdebugr 1.0.1
Propagated dependencies: r-textutils@0.4-2 r-provparser@1.0 r-provgraphr@1.0.1 r-jsonlite@2.0.0 r-httr@1.4.7
Channel: guix-cran
Location: guix-cran/packages/p.scm (guix-cran packages p)
Home page: https://cran.r-project.org/package=provDebugR
Licenses: GPL 3
Synopsis: Time-Travelling Debugger
Description:

Uses provenance post-execution to help the user understand and debug their script by providing functions to look at intermediate steps and data values, their forwards and backwards lineage, and to understand the steps leading up to warning and error messages. provDebugR uses provenance produced by rdtLite (available on CRAN), stored in PROV-JSON format.

r-packagepal 0.1.0
Propagated dependencies: r-usethis@3.1.0 r-cli@3.6.5 r-available@1.1.0
Channel: guix-cran
Location: guix-cran/packages/p.scm (guix-cran packages p)
Home page: https://github.com/lddurbin/packagepal
Licenses: Expat
Synopsis: Guidelines and Checklists for Building CRAN-Worthy Packages
Description:

This package provides essential checklists for R package developers, whether you're creating your first package or beginning a new project. This tool guides you through each step of the development process, including specific considerations for submitting your package to the Comprehensive R Archive Network (CRAN). Simplify your workflow and ensure adherence to best practices with packagepal'.

r-qcauchyreg 1.0
Propagated dependencies: r-quantreg@6.1
Channel: guix-cran
Location: guix-cran/packages/q.scm (guix-cran packages q)
Home page: <https://www.r-project.org>
Licenses: GPL 3
Synopsis: Quantile Regression Quasi-Cauchy
Description:

Quasi-Cauchy quantile regression, proposed by de Oliveira, Ospina, Leiva, Figueroa-Zuniga and Castro (2023) <doi:10.3390/fractalfract7090667>. This regression model is useful for the case where you want to model data of a nature limited to the intervals [0,1], (0,1], [0,1) or (0,1) and you want to use a quantile approach.

r-testdesign 1.7.0
Propagated dependencies: r-rcpparmadillo@14.4.3-1 r-rcpp@1.0.14 r-lpsolve@5.6.23 r-logitnorm@0.8.39 r-foreach@1.5.2 r-crayon@1.5.3
Channel: guix-cran
Location: guix-cran/packages/t.scm (guix-cran packages t)
Home page: https://choi-phd.github.io/TestDesign/
Licenses: GPL 2+
Synopsis: Optimal Test Design Approach to Fixed and Adaptive Test Construction
Description:

Uses the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> to construct fixed, adaptive, and parallel tests. Supports the following mixed-integer programming (MIP) solver packages: Rsymphony', highs', gurobi', lpSolve', and Rglpk'. The gurobi package is not available from CRAN; see <https://www.gurobi.com/downloads/>.

r-tatooheene 0.19.0
Propagated dependencies: r-tidyr@1.3.1 r-dplyr@1.1.4 r-assertthat@0.2.1
Channel: guix-cran
Location: guix-cran/packages/t.scm (guix-cran packages t)
Home page: https://cran.r-project.org/package=tatooheene
Licenses: Expat
Synopsis: Technology Appraisal Toolbox for Health Economic Evaluations in the Netherlands
Description:

This package provides functions to support economic modelling in R based on the methods of the Dutch guideline for economic evaluations in healthcare <https://www.zorginstituutnederland.nl/publicaties/publicatie/2024/01/16/richtlijn-voor-het-uitvoeren-van-economische-evaluaties-in-de-gezondheidszorg>, CBS data <https://www.cbs.nl/>, and OECD data <https://www.oecd.org/en.html>.

r-tidycensus 1.7.3
Propagated dependencies: r-xml2@1.3.8 r-units@0.8-7 r-tigris@2.2.1 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-stringr@1.5.1 r-sf@1.0-21 r-rvest@1.0.4 r-rlang@1.1.6 r-readr@2.1.5 r-rappdirs@0.3.3 r-purrr@1.0.4 r-jsonlite@2.0.0 r-httr@1.4.7 r-dplyr@1.1.4 r-crayon@1.5.3
Channel: guix-cran
Location: guix-cran/packages/t.scm (guix-cran packages t)
Home page: https://walker-data.com/tidycensus/
Licenses: Expat
Synopsis: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Description:

An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.

r-altcdfenvs 2.70.0
Propagated dependencies: r-affy@1.86.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-hypergraph@1.80.0 r-makecdfenv@1.84.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/altcdfenvs
Licenses: GPL 2+
Synopsis: Convenience data structures and functions to handle CDF environments
Description:

The package is usable with Affymetrix GeneChip short oligonucleotide arrays, and it can be adapted or extended to other platforms. It is able to modify or replace the grouping of probes in the probe sets. Also, the package contains simple functions to read R connections in the FASTA format and it can create an alternative mapping from sequences.

r-hdcytodata 1.28.0
Propagated dependencies: r-experimenthub@2.16.0 r-flowcore@2.20.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/lmweber/HDCytoData
Licenses: Expat
Synopsis: Set of high-dimensional flow cytometry and mass cytometry benchmark datasets
Description:

HDCytoData contains a set of high-dimensional cytometry benchmark datasets. These datasets are formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels and labels identifying spiked in cells. Column metadata includes channel names, protein marker names, and protein marker classes.

r-transformr 0.1.5
Propagated dependencies: r-cpp11@0.5.2 r-lpsolve@5.6.23 r-rlang@1.1.6 r-sf@1.0-21 r-tweenr@2.0.3 r-vctrs@0.6.5
Channel: guix
Location: gnu/packages/cran.scm (gnu packages cran)
Home page: https://github.com/thomasp85/transformr
Licenses: Expat
Synopsis: Polygon and path transformations
Description:

In order to smoothly animate the transformation of polygons and paths, many aspects needs to be taken into account, such as differing number of control points, changing center of rotation, etc. The transformr package provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the tweenr package.

r-conflicted 1.2.0
Propagated dependencies: r-cli@3.6.5 r-memoise@2.0.1 r-rlang@1.1.6
Channel: guix
Location: gnu/packages/cran.scm (gnu packages cran)
Home page: https://github.com/r-lib/conflicted
Licenses: GPL 3
Synopsis: Alternative conflict resolution strategy
Description:

R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. The conflicted package takes a different approach, making every conflict an error and forcing you to choose which function to use.

r-multitaper 1.0-17
Channel: guix
Location: gnu/packages/cran.scm (gnu packages cran)
Home page: https://github.com/wesleyburr/multitaper/
Licenses: GPL 2+
Synopsis: Multitaper spectral analysis tools
Description:

This package implements multitaper spectral estimation techniques using prolate spheroidal sequences (Slepians) and sine tapers for time series analysis. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.

randomjungle 2.1.0
Dependencies: boost@1.83.0 gsl@2.8 libxml2@2.9.14 zlib@1.3
Channel: guix
Location: gnu/packages/machine-learning.scm (gnu packages machine-learning)
Home page: https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224
Licenses: GPL 3+
Synopsis: Implementation of the Random Forests machine learning method
Description:

Random Jungle is an implementation of Random Forests. It is supposed to analyse high dimensional data. In genetics, it can be used for analysing big Genome Wide Association (GWA) data. Random Forests is a powerful machine learning method. Most interesting features are variable selection, missing value imputation, classifier creation, generalization error estimation and sample proximities between pairs of cases.

r-mixedpower 2.0-2.b2b8706
Propagated dependencies: r-doparallel@1.0.17 r-foreach@1.5.2 r-ggplot2@3.5.2 r-lme4@1.1-37 r-reshape2@1.4.4
Channel: guix
Location: gnu/packages/statistics.scm (gnu packages statistics)
Home page: https://github.com/DejanDraschkow/mixedpower
Licenses: GPL 3
Synopsis: Pilotdata based simulations for estimating power in linear mixed models
Description:

Mixedpower uses pilotdata and a linear mixed model fitted with lme4 to simulate new data sets. Power is computed separate for every effect in the model output as the relation of significant simulations to all simulations. More conservative simulations as a protection against a bias in the pilotdata are available as well as methods for plotting the results.

r-comparator 0.1.4
Propagated dependencies: r-rcpp@1.0.14 r-proxy@0.4-27 r-clue@0.3-66
Channel: guix-cran
Location: guix-cran/packages/c.scm (guix-cran packages c)
Home page: https://github.com/ngmarchant/comparator
Licenses: GPL 2+
Synopsis: Comparison Functions for Clustering and Record Linkage
Description:

This package implements functions for comparing strings, sequences and numeric vectors for clustering and record linkage applications. Supported comparison functions include: generalized edit distances for comparing sequences/strings, Monge-Elkan similarity for fuzzy comparison of token sets, and L-p distances for comparing numeric vectors. Where possible, comparison functions are implemented in C/C++ to ensure good performance.

r-cmanalysis 1.0.0
Propagated dependencies: r-stringr@1.5.1 r-pheatmap@1.0.12 r-igraph@2.1.4 r-ggplot2@3.5.2 r-factoextra@1.0.7 r-cluster@2.1.8.1 r-clue@0.3-66
Channel: guix-cran
Location: guix-cran/packages/c.scm (guix-cran packages c)
Home page: https://cran.r-project.org/package=cmAnalysis
Licenses: GPL 3
Synopsis: Process and Visualise Concept Mapping Data
Description:

Processing and visualizing concept mapping data. Concept maps are versatile tools used across disciplines to enhance understanding, teaching, brainstorming, and information organization. The analysis of concept mapping data involves the sequential use of cluster analysis (for sorting participants and statements), multidimensional scaling (for positioning statements in a conceptual space), and visualization techniques, including point cluster maps and dendrograms.

r-ensemblepp 1.0-0
Channel: guix-cran
Location: guix-cran/packages/e.scm (guix-cran packages e)
Home page: https://cran.r-project.org/package=ensemblepp
Licenses: GPL 2 GPL 3
Synopsis: Ensemble Postprocessing Data Sets
Description:

Data sets for the chapter "Ensemble Postprocessing with R" of the book Stephane Vannitsem, Daniel S. Wilks, and Jakob W. Messner (2018) "Statistical Postprocessing of Ensemble Forecasts", Elsevier, 362pp. These data sets contain temperature and precipitation ensemble weather forecasts and corresponding observations at Innsbruck/Austria. Additionally, a demo with the full code of the book chapter is provided.

r-geemediate 1.1.4
Propagated dependencies: r-gee@4.13-29
Channel: guix-cran
Location: guix-cran/packages/g.scm (guix-cran packages g)
Home page: https://cran.r-project.org/package=GEEmediate
Licenses: GPL 3+
Synopsis: Mediation Analysis for Generalized Linear Models Using the Difference Method
Description:

Causal mediation analysis for a single exposure/treatment and a single mediator, both allowed to be either continuous or binary. The package implements the difference method and provides point and interval estimates as well as testing for the natural direct and indirect effects and the mediation proportion. Nevo, Xiao and Spiegelman (2017) <doi:10.1515/ijb-2017-0006>.

r-ipwboxplot 0.1.2
Propagated dependencies: r-isotone@1.1-2
Channel: guix-cran
Location: guix-cran/packages/i.scm (guix-cran packages i)
Home page: https://cran.r-project.org/package=IPWboxplot
Licenses: GPL 2+
Synopsis: Adapted Boxplot to Missing Observations
Description:

Boxplots adapted to the happenstance of missing observations where drop-out probabilities can be given by the practitioner or modelled using auxiliary covariates. The paper of "Zhang, Z., Chen, Z., Troendle, J. F. and Zhang, J.(2012) <doi:10.1111/j.1541-0420.2011.01712.x>", proposes estimators of marginal quantiles based on the Inverse Probability Weighting method.

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