|
r-blendedlink
|
public |
A new link function that equals one specified link function up to a cutover then a linear rescaling of another specified link function. For use in glm() or glm2(). The intended use is in binary regression, in which case the first link should be set to "log" and the second to "logit". This ensures that fitted probabilities are between 0 and 1 and that exponentiated coefficients can be interpreted as relative risks for probabilities up to the cutoff.
|
2025-04-22 |
|
r-blandaltmanleh
|
public |
Bland-Altman Plots using either base graphics or ggplot2, augmented with confidence intervals, with detailed return values and a sunflowerplot option for data with ties.
|
2025-04-22 |
|
r-blakerci
|
public |
Fast and accurate calculation of Blaker's binomial and Poisson confidence limits (and some related stuff).
|
2025-04-22 |
|
r-bizdays
|
public |
Business days calculations based on a list of holidays and nonworking weekdays. Quite useful for fixed income and derivatives pricing.
|
2025-04-22 |
|
r-bivgeom
|
public |
Implements Roy's bivariate geometric model (Roy (1993) <doi:10.1006/jmva.1993.1065>): joint probability mass function, distribution function, survival function, random generation, parameter estimation, and more.
|
2025-04-22 |
|
r-bivgeo
|
public |
Computes the joint probability mass function (pmf), the joint cumulative function (cdf), the joint survival function (sf), the correlation coefficient, the covariance, the cross-factorial moment and generate random deviates for the Basu-Dhar bivariate geometric distribution as well the joint probability mass, cumulative and survival function assuming the presence of a cure fraction given by the standard bivariate mixture cure fraction model. The package also computes the estimators based on the method of moments.
|
2025-04-22 |
|
r-bivarripower
|
public |
Implements sample size calculations for bivariate random intercept regression model that are described in Comulada and Weiss (2010)
|
2025-04-22 |
|
r-bisrna
|
public |
Bisulfite-treated RNA non-conversion in a set of samples is analysed as follows : each sample's non-conversion distribution is identified to a Poisson distribution. P-values adjusted for multiple testing are calculated in each sample. Combined non-conversion P-values and standard errors are calculated on the intersection of the set of samples. For further details, see C Legrand, F Tuorto, M Hartmann, R Liebers, D Jakob, M Helm and F Lyko (2017) <doi:10.1101/gr.210666.116>.
|
2025-04-22 |
|
r-bisectr
|
public |
Tools to find bad commits with git bisect. See https://github.com/wch/bisectr for examples and test script templates.
|
2025-04-22 |
|
r-bisect
|
public |
An implementation of Bisect, a method for inferring cell type composition of samples based on methylation sequencing data (Whole Genome Bisulfite Sequencing and Reduced Representation Sequencing). The method is specifically tailored for sequencing data, and therefore works better than methods developed for methylation arrays. It contains a supervised mode that requires a reference (the methylation probabilities in the pure cell types), and a semi-supervised mode, that requires cell counts for a subset of the samples, but does not require a reference.
|
2025-04-22 |
|
r-birtr
|
public |
R functions for "The Basics of Item Response Theory Using R" by Frank B. Baker and Seock-Ho Kim (Springer, 2017, ISBN-13: 978-3-319-54204-1) including iccplot(), icccal(), icc(), iccfit(), groupinv(), tcc(), ability(), tif(), and rasch(). For example, iccplot() plots an item characteristic curve under the two-parameter logistic model.
|
2025-04-22 |
|
r-birk
|
public |
Collection of tools to make R more convenient. Includes tools to summarize data using statistics not available with base R and manipulate objects for analyses.
|
2025-04-22 |
|
r-biotic
|
public |
Calculates a range of UK freshwater invertebrate biotic indices including BMWP, Whalley, WHPT, Habitat-specific BMWP, AWIC, LIFE and PSI.
|
2025-04-22 |
|
r-bionetdata
|
public |
Data Package that includes several examples of chemical and biological data networks, i.e. data graph structured.
|
2025-04-22 |
|
r-biom.utils
|
public |
Provides utilities to facilitate import, export and computation with the BIOM (Biological Observation Matrix) format (http://biom-format.org).
|
2025-04-22 |
|
r-bio.infer
|
public |
Imports benthic count data, reformats this data, and computes environmental inferences from this data.
|
2025-04-22 |
|
r-biogas
|
public |
High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Biogas quantity and composition can be predicted from substrate composition and additional, optional data. Lastly, inoculum and substrate mass can be determined for planning BMP experiments.
|
2025-04-22 |
|
r-bioftf
|
public |
The main drawback of the most common biodiversity indices is that different measures may lead to different rankings among communities. This instrument overcomes this limit using some functional tools with the diversity profiles. In particular, the derivatives, the curvature, the radius of curvature, the arc length, and the surface area are proposed. The goal of this method is to interpret in detail the diversity profiles and obtain an ordering between different ecological communities on the basis of diversity. In contrast to the typical indices of diversity, the proposed method is able to capture the multidimensional aspect of biodiversity, because it takes into account both the evenness and the richness of the species present in an ecological community.
|
2025-04-22 |
|
r-biodem
|
public |
The Biodem package provides a number of functions for Biodemographic analysis.
|
2025-04-22 |
|
r-biocmanager
|
public |
A convenient tool to install and update Bioconductor packages.
|
2025-04-22 |
|
r-biocircos
|
public |
Implement in 'R' interactive Circos-like visualizations of genomic data, to map information such as genetic variants, genomic fusions and aberrations to a circular genome, as proposed by the 'JavaScript' library 'BioCircos.js', based on the 'JQuery' and 'D3' technologies. The output is by default displayed in stand-alone HTML documents or in the 'RStudio' viewer pane. Moreover it can be integrated in 'R Markdown' documents and 'Shiny' applications.
|
2025-04-22 |
|
r-binst
|
public |
Various supervised and unsupervised binning tools including using entropy, recursive partition methods and clustering.
|
2025-04-22 |
|
r-binr
|
public |
Implementation of algorithms for cutting numerical values exhibiting a potentially highly skewed distribution into evenly distributed groups (bins). This functionality can be applied for binning discrete values, such as counts, as well as for discretization of continuous values, for example, during generation of features used in machine learning algorithms.
|
2025-04-22 |
|
r-binomlogit
|
public |
The R package contains different MCMC schemes to estimate the regression coefficients of a binomial (or binary) logit model within a Bayesian framework: a data-augmented independence MH-sampler, an auxiliary mixture sampler and a hybrid auxiliary mixture (HAM) sampler. All sampling procedures are based on algorithms using data augmentation, where the regression coefficients are estimated by rewriting the logit model as a latent variable model called difference random utility model (dRUM).
|
2025-04-22 |
|
r-binomialcftp
|
public |
Binomial random numbers are generated via the perfect sampling algorithm. At each iteration dual markov chains are generated and coalescence is checked. In case coalescence occurs, the resulting number is outputted. In case not, then the algorithm is restarted from T(t)=2*T(t) until coalescence occurs.
|
2025-04-22 |
