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r-pot
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public |
Some functions useful to perform a Peak Over Threshold analysis in univariate and bivariate cases, see Beirlant et al. (2004) <doi:10.1002/0470012382>. A user's guide is available.
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2025-04-22 |
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r-pop.wolf
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public |
Simulate the dynamic of wolf populations using a specific Individual-Based Model (IBM) compiled in C.
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2025-04-22 |
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r-population
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public |
Run population simulations using an Individual-Based Model (IBM) compiled in C.
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2025-04-22 |
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r-popkin
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public |
Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
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2025-04-22 |
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r-pooh
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public |
Finds equivalence classes corresponding to a symmetric relation or undirected graph. Finds total order consistent with partial order or directed graph (so-called topological sort).
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2025-04-22 |
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r-pomp
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public |
Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
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2025-04-22 |
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r-pomdp
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Provides an interface to pomdp-solve, a solver for Partially Observable Markov Decision Processes (POMDP). The package enables the user to simply define all components of a POMDP model and solve the problem using several methods. The package also contains functions to analyze and visualize the POMDP solutions (e.g., the optimal policy).
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2025-04-22 |
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r-pomaspu
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public |
POM-aSPU test evaluates an association between an ordinal response and multiple phenotypes, for details see Kim and Pan (2017) <DOI:10.1002/gepi.22033>.
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2025-04-22 |
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r-polysat
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public |
A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi', 'POPDIST', 'STRand', and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics and Polymorphic Information Content are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise or global differentiation statistics based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci. polysat is described by Clark and Jasieniuk (2011) <doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2017) <doi:10.1111/1755-0998.12639>.
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2025-04-22 |
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r-polynomf
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public |
Implements univariate polynomial operations in R, including polynomial arithmetic, finding zeros, plotting, and some operations on lists of polynomials.
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2025-04-22 |
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r-polylabelr
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public |
A wrapper around the C++ library 'polylabel' from 'Mapbox', providing an efficient routine for finding the approximate pole of inaccessibility of a polygon, which usually serves as an excellent candidate for labeling of a polygon.
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2025-04-22 |
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r-polyfreqs
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Implements a Gibbs sampling algorithm to perform Bayesian inference on biallelic SNP frequencies, genotypes and heterozygosity (observed and expected) in a population of autopolyploids. See the published paper in Molecular Ecology Resources: Blischak et al. (2016) <doi:10.1111/1755-0998.12493>.
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2025-04-22 |
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r-polycub
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public |
Numerical integration of continuously differentiable functions f(x,y) over simple closed polygonal domains. The following cubature methods are implemented: product Gauss cubature (Sommariva and Vianello, 2007, <doi:10.1007/s10543-007-0131-2>), the simple two-dimensional midpoint rule (wrapping 'spatstat' functions), adaptive cubature for radially symmetric functions via line integrate() along the polygon boundary (Meyer and Held, 2014, <doi:10.1214/14-AOAS743>, Supplement B), and integration of the bivariate Gaussian density based on polygon triangulation. For simple integration along the axes, the 'cubature' package is more appropriate.
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2025-04-22 |
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r-polyclip
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public |
R port of Angus Johnson's open source library Clipper. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.
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2025-04-22 |
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r-poissonpca
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For a multivariate dataset with independent Poisson measurement error, calculates principal components of transformed latent Poisson means. T. Kenney, T. Huang, H. Gu (2019) <arXiv:1904.11745>.
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2025-04-22 |
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r-poisdoublesamp
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public |
Functions to create confidence intervals for ratios of Poisson rates under misclassification using double sampling.
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2025-04-22 |
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r-poisbinom
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Provides the probability, distribution, and quantile functions and random number generator for the Poisson-Binomial distribution. This package relies on FFTW to implement the discrete Fourier transform, so that it is much faster than the existing implementation of the same algorithm in R.
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2025-04-22 |
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r-poilog
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public |
Functions for obtaining the density, random deviates and maximum likelihood estimates of the Poisson lognormal distribution and the bivariate Poisson lognormal distribution.
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2025-04-22 |
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r-poibin
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public |
Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution.
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2025-04-22 |
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r-plugdensity
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Kernel density estimation with global bandwidth selection via "plug-in".
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2025-04-22 |
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r-plordprob
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Multivariate ordered probit model, i.e. the extension of the scalar ordered probit model where the observed variables have dimension greater than one. Estimation of the parameters is done via maximization of the pairwise likelihood, a special case of the composite likelihood obtained as product of bivariate marginal distributions. The package uses the Fortran 77 subroutine SADMVN by Alan Genz, with minor adaptations made by Adelchi Azzalini in his "mvnormt" package for evaluating the two-dimensional Gaussian integrals involved in the pairwise log-likelihood. Optimization of the latter objective function is performed via quasi-Newton box-constrained optimization algorithm, as implemented in nlminb.
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2025-04-22 |
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r-pln
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Performs bivariate composite likelihood and full information maximum likelihood estimation for polytomous logit-normit (graded logistic) item response theory (IRT) models.
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2025-04-22 |
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r-pliable
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Fits a pliable lasso model. For details see Tibshirani and Friedman (2018) <arXiv:1712.00484>.
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2025-04-22 |
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r-plfm
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public |
Functions for estimating probabilistic latent feature models with a disjunctive, conjunctive or additive mapping rule on (aggregated) binary three-way data.
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2025-04-22 |
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r-playerratings
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Implements schemes for estimating player or team skill based on dynamic updating. Implemented methods include Elo, Glicko, Glicko-2 and Stephenson. Contains pdf documentation of a reproducible analysis using approximately two million chess matches.
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2025-04-22 |
