|
r-pkgcache
|
public |
Metadata and package cache for CRAN-like repositories. This is a utility package to be used by package management tools that want to take advantage of caching.
|
2024-01-16 |
|
r-piton
|
public |
A wrapper around the 'Parsing Expression Grammar Template Library', a C++11 library for generating Parsing Expression Grammars, that makes it accessible within Rcpp. With this, developers can implement their own grammars and easily expose them in R packages.
|
2024-01-16 |
|
r-pingr
|
public |
Check if a remote computer is up. It can either just call the system ping command, or check a specified TCP port.
|
2024-01-16 |
|
r-pijavski
|
public |
Global univariate minimization of Lipschitz functions is performed by using Pijavski method, which was published in Pijavski (1972) <DOI:10.1016/0041-5553(72)90115-2>.
|
2024-01-16 |
|
r-picasso
|
public |
Computationally efficient tools for fitting generalized linear model with convex or non-convex penalty. Users can enjoy the superior statistical property of non-convex penalty such as SCAD and MCP which has significantly less estimation error and overfitting compared to convex penalty such as lasso and ridge. Computation is handled by multi-stage convex relaxation and the PathwIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. The computation is memory-optimized using the sparse matrix output.
|
2024-01-16 |
|
r-pieceexpintensity
|
public |
This function fits a reversible jump Bayesian piecewise exponential model that also includes the intensity of each event considered along with the rate of events.
|
2024-01-16 |
|
r-philentropy
|
public |
Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
|
2024-01-16 |
|
r-phyr
|
public |
A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).
|
2024-01-16 |
|
r-physiology
|
public |
A variety of formulae are provided for estimation of physiologic characteristics of infants, children, and adults. Calculations include: body surface area, ideal weight, airway dead-space, the alveolar gas equation, and GFR. Each formula is referenced to the original publication. Future functions will cover more material with a focus on anaesthesia, critical care and peri-operative medicine.
|
2024-01-16 |
|
r-phylobase
|
public |
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
|
2024-01-16 |
|
r-phyclust
|
public |
Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.
|
2024-01-16 |
|
r-phreeqc
|
public |
A geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.
|
2024-01-16 |
|
r-phonics
|
public |
Provides a collection of phonetic algorithms including Soundex, Metaphone, NYSIIS, Caverphone, and others. The package is documented in <doi:10.18637/jss.v095.i08>.
|
2024-01-16 |
|
r-pheno
|
public |
Provides some easy-to-use functions for time series analyses of (plant-) phenological data sets. These functions mainly deal with the estimation of combined phenological time series and are usually wrappers for functions that are already implemented in other R packages adapted to the special structure of phenological data and the needs of phenologists. Some date conversion functions to handle Julian dates are also provided.
|
2024-01-16 |
|
r-phenex
|
public |
Provides some easy-to-use functions for spatial analyses of (plant-) phenological data sets and satellite observations of vegetation.
|
2024-01-16 |
|
r-phangorn
|
public |
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
|
2024-01-16 |
|
r-pgam
|
public |
This work is an extension of the state space model for Poisson count data, Poisson-Gamma model, towards a semiparametric specification. Just like the generalized additive models (GAM), cubic splines are used for covariate smoothing. The semiparametric models are fitted by an iterative process that combines maximization of likelihood and backfitting algorithm.
|
2024-01-16 |
|
r-phase123
|
public |
Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
|
2024-01-16 |
|
r-ph2bayes
|
public |
An implementation of Bayesian single-arm phase II design methods for binary outcome based on posterior probability (Thall and Simon (1994) <doi:10.2307/2533377>) and predictive probability (Lee and Liu (2008) <doi:10.1177/1740774508089279>).
|
2024-01-16 |
|
r-pgsc
|
public |
Computes the generalized synthetic control estimator described in Powell (2017) <doi:10.7249/WR1142>. Provides both point estimates, and hypothesis testing.
|
2024-01-16 |
|
r-pgee.mixed
|
public |
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).
|
2024-01-16 |
|
r-pgmm
|
public |
Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.
|
2024-01-16 |
|
r-pgdraw
|
public |
Generates random samples from the Polya-Gamma distribution using an implementation of the algorithm described in J. Windle's PhD thesis (2013) <https://repositories.lib.utexas.edu/bitstream/handle/2152/21842/WINDLE-DISSERTATION-2013.pdf>. The underlying implementation is in C.
|
2024-01-16 |
|
r-performanceanalytics
|
public |
Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.
|
2024-01-16 |
|
r-pegas
|
public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
|
2024-01-16 |
|
r-pense
|
public |
Robust penalized (adaptive) elastic net S and M estimators for linear regression. The methods are proposed in Cohen Freue, G. V., Kepplinger, D., Salibián-Barrera, M., and Smucler, E. (2019) <https://projecteuclid.org/euclid.aoas/1574910036>. The package implements the extensions and algorithms described in Kepplinger, D. (2020) <doi:10.14288/1.0392915>.
|
2024-01-16 |
|
r-penaltylearning
|
public |
Implementations of algorithms from Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression, by Hocking, Rigaill, Vert, Bach <http://proceedings.mlr.press/v28/hocking13.html> published in proceedings of ICML2013.
|
2024-01-16 |
|
r-peptides
|
public |
Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
|
2024-01-16 |
|
r-pema
|
public |
Conduct penalized meta-analysis, see Van Lissa, Van Erp, & Clapper (2023) <doi:10.31234/osf.io/6phs5>. In meta-analysis, there are often between-study differences. These can be coded as moderator variables, and controlled for using meta-regression. However, if the number of moderators is large relative to the number of studies, such an analysis may be overfit. Penalized meta-regression is useful in these cases, because it shrinks the regression slopes of irrelevant moderators towards zero.
|
2024-01-16 |
|
r-penmsm
|
None |
Structured fusion Lasso penalized estimation of multi-state models with the penalty applied to absolute effects and absolute effect differences (i.e., effects on transition-type specific hazard rates).
|
2024-01-16 |
|
r-pencoxfrail
|
public |
A regularization approach for Cox Frailty Models by penalization methods is provided.
|
2024-01-16 |
|
r-pedigree
|
public |
Pedigree related functions.
|
2024-01-16 |
|
r-penalized
|
public |
Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
|
2024-01-16 |
|
r-pdp
|
public |
A general framework for constructing partial dependence (i.e., marginal effect) plots from various types machine learning models in R.
|
2024-01-16 |
|
r-pedometrics
|
public |
An R implementation of methods employed in the field of pedometrics, soil science discipline dedicated to studying the spatial, temporal, and spatio-temporal variation of soil using statistical and computational methods. The methods found here include the calibration of linear regression models using covariate selection strategies, computation of summary validation statistics for predictions, generation of summary plots, evaluation of the local quality of a geostatistical model of uncertainty, and so on. Other functions simply extend the functionalities of or facilitate the usage of functions from other packages that are commonly used for the analysis of soil data. Formerly available versions of suggested packages no longer available from CRAN can be obtained from the CRAN archive <https://cran.r-project.org/src/contrib/Archive/>.
|
2024-01-16 |
|
r-pedigreetools
|
public |
Tools to sort, edit and prune pedigrees and to extract the inbreeding coefficients and the relationship matrix (includes code for pedigrees from self-pollinated species). The use of pedigree data is central to genetics research within the animal and plant breeding communities to predict breeding values. The relationship matrix between the individuals can be derived from pedigree structure ('Vazquez et al., 2010') <doi:10.2527/jas.2009-1952>.
|
2024-01-16 |
|
r-pedigreemm
|
public |
Fit pedigree-based mixed-effects models.
|
2024-01-16 |
|
r-pec
|
public |
Validation of risk predictions obtained from survival models and competing risk models based on censored data using inverse weighting and cross-validation. Most of the 'pec' functionality has been moved to 'riskRegression'.
|
2024-01-16 |
|
r-pdfcluster
|
public |
Cluster analysis via nonparametric density estimation is performed. Operationally, the kernel method is used throughout to estimate the density. Diagnostics methods for evaluating the quality of the clustering are available. The package includes also a routine to estimate the probability density function obtained by the kernel method, given a set of data with arbitrary dimensions.
|
2024-01-16 |
|
r-peaksegdp
|
public |
A quadratic time dynamic programming algorithm can be used to compute an approximate solution to the problem of finding the most likely changepoints with respect to the Poisson likelihood, subject to a constraint on the number of segments, and the changes which must alternate: up, down, up, down, etc. For more info read <http://proceedings.mlr.press/v37/hocking15.html> "PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data" by TD Hocking et al, proceedings of ICML2015.
|
2024-01-16 |
|
r-pearsonds
|
public |
Implementation of the Pearson distribution system, including full support for the (d,p,q,r)-family of functions for probability distributions and fitting via method of moments and maximum likelihood method.
|
2024-01-16 |
|
r-pcadapt
|
public |
Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <DOI:10.1093/molbev/msaa053>.
|
2024-01-16 |
|
r-peaksegdisk
|
public |
Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints <doi:10.18637/jss.v101.i10> for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).
|
2024-01-16 |
|
r-peakerror
|
public |
Chromatin immunoprecipitation DNA sequencing results in genomic tracks that show enriched regions or peaks where proteins are bound. This package implements fast C code that computes the true and false positives with respect to a database of annotated region labels.
|
2024-01-16 |
|
r-pdsce
|
public |
Compute and tune some positive definite and sparse covariance estimators.
|
2024-01-16 |
|
r-pdist
|
public |
Computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling 'dist', but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.
|
2024-01-16 |
|
r-pdfestimator
|
public |
Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A multivariate nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
|
2024-01-16 |
|
r-pdc
|
public |
Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.
|
2024-01-16 |
|
r-pcirt
|
public |
Estimates the multidimensional polytomous Rasch model (Rasch, 1961) with conditional maximum likelihood estimation.
|
2024-01-16 |
|
r-pcict
|
public |
Provides a work-alike to R's POSIXct class which implements 360- and 365-day calendars in addition to the gregorian calendar.
|
2024-01-16 |
