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r-pins
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public |
Pin remote resources into a local cache to work offline, improve speed and avoid recomputing; discover and share resources in local folders, 'GitHub', 'Kaggle' or 'RStudio Connect'. Resources can be anything from 'CSV', 'JSON', or image files to arbitrary R objects.
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2025-03-25 |
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r-pinp
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public |
A 'PNAS'-alike style for 'rmarkdown', derived from the 'Proceedings of the National Academy of Sciences of the United States of America' ('PNAS', see <https://www.pnas.org>) 'LaTeX' style, and adapted for use with 'markdown' and 'pandoc'.
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2025-03-25 |
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r-pinochet
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public |
Packages data about the victims of the Pinochet regime as compiled by the Chilean National Commission for Truth and Reconciliation Report (1991, ISBN:9780268016463).
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2025-03-25 |
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r-pinnacle.api
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public |
An interface to the API by Pinnacle that allows Pinnacle customers to interact with the sports market data in R.See <https://www.pinnacle.com/en/api> for more information. The Pinnacle API can be used to place wagers, retrieve line information, retrieve account information.Please be aware that the TOC of Pinnacle apply <https://www.pinnacle.com/en/termsandconditions>. An account with Pinnacle is necessary to use the Pinnacle API.
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2025-03-25 |
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r-pinfsc50
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public |
Genomic data for the plant pathogen "Phytophthora infestans." It includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.
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2025-03-25 |
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r-pigshift
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public |
Fits models of gene expression evolution to expression data from coregulated groups of genes, assuming inverse gamma distributed rate variation.
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2025-03-25 |
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r-piggyback
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public |
Because larger (> 50 MB) data files cannot easily be committed to git, a different approach is required to manage data associated with an analysis in a GitHub repository. This package provides a simple work-around by allowing larger (up to 2 GB) data files to piggyback on a repository as assets attached to individual GitHub releases. These files are not handled by git in any way, but instead are uploaded, downloaded, or edited directly by calls through the GitHub API. These data files can be versioned manually by creating different releases. This approach works equally well with public or private repositories. Data can be uploaded and downloaded programmatically from scripts. No authentication is required to download data from public repositories.
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2025-03-25 |
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r-physicalactivity
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public |
It provides a function "wearingMarking" for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plot for accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. The revised package version 0.2-1 improved the functions in the previous version regarding speed and robustness. In addition, several functions were added: "markDelivery" can classify days for ActiGraph delivery by mail; "markPAI" can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. It also supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions. The package also better supports time zones and daylight saving.
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2025-03-25 |
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r-physactbedrest
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public |
Contains a function to categorize accelerometer readings collected in free-living (e.g., for 24 hours/day for 7 days), preprocessed and compressed as counts (unit-less value) in a specified time period termed epoch (e.g., 1 minute) as either bedrest (sleep) or active. The input is a matrix with a timestamp column and a column with number of counts per epoch. The output is the same dataframe with an additional column termed bedrest. In the bedrest column each line (epoch) contains a function-generated classification 'br' or 'a' denoting bedrest/sleep and activity, respectively. The package is designed to be used after wear/nonwear marking function in the 'PhysicalActivity' package.
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2025-03-25 |
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r-phyreg
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public |
Provides general linear model facilities (single y-variable, multiple x-variables with arbitrary mixture of continuous and categorical and arbitrary interactions) for cross-species data. The method is, however, based on the nowadays rather uncommon situation in which uncertainty about a phylogeny is well represented by adopting a single polytomous tree. The theory is in A. Grafen (1989, Proc. R. Soc. B 326, 119-157) and aims to cope with both recognised phylogeny (closely related species tend to be similar) and unrecognised phylogeny (a polytomy usually indicates ignorance about the true sequence of binary splits).
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2025-03-25 |
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r-phylotools
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public |
A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.
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2025-03-25 |
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r-phylotate
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public |
Functions to read and write APE-compatible phylogenetic trees in NEXUS and Newick formats, while preserving annotations.
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2025-03-25 |
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r-phylometrics
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public |
Provides functions to estimate statistical errors of phylogenetic metrics particularly to detect binary trait influence on diversification, as well as a function to simulate trees with fixed number of sampled taxa and trait prevalence.
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2025-03-25 |
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r-phylogram
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public |
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
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2025-03-25 |
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r-phylogr
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public |
Manipulation and analysis of phylogenetically simulated data sets and phylogenetically based analyses using GLS.
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2025-03-25 |
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r-phyloclim
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public |
Implements some methods in phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.
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2025-03-25 |
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r-phylin
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public |
The spatial interpolation of genetic distances between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.
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2025-03-25 |
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r-phuse
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public |
Make it easy to review, download and execute scripts stored in Github 'phuse-scripts' repository <https://github.com/phuse-org/phuse-scripts>. Some examples included show the web application framework using the script metadata. The 'PhUSE' is Pharmaceutical Users Software Exchange <http://www.phuse.eu>.
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2025-03-25 |
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r-phuassess
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public |
Assessment of habitat selection by means of the permutation-based combination of sign tests (Fattorini et al., 2014 <DOI:10.1007/s10651-013-0250-7>). To exemplify the application of this procedure, habitat selection is assessed for a population of European Brown Hares settled in central Italy.
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2025-03-25 |
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r-phtt
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public |
The package provides estimation procedures for panel data with large dimensions n, T, and general forms of unobservable heterogeneous effects. Particularly, the estimation procedures are those of Bai (2009) and Kneip, Sickles, and Song (2012), which complement one another very well: both models assume the unobservable heterogeneous effects to have a factor structure. The method of Bai (2009) assumes that the factors are stationary, whereas the method of Kneip et al. (2012) allows the factors to be non-stationary. Additionally, the 'phtt' package provides a wide range of dimensionality criteria in order to estimate the number of the unobserved factors simultaneously with the remaining model parameters.
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2025-03-25 |
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r-phontools
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public |
Contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.
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2025-03-25 |
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r-phonenumber
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public |
Convert English letters to numbers or numbers to English letters as on a telephone keypad. When converting letters to numbers, a character vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F" becoming 3, etc. When converting numbers to letters, a character vector is returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and "C").
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2025-03-25 |
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r-phidelta
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public |
Analysis of features by phi delta diagrams. In particular, functions for reading data and calculating phi and delta as well as the functionality to plot it. Moreover it is possible to do further analysis on the data by generating rankings. For more information on phi delta diagrams, see also Giuliano Armano (2015) <doi:10.1016/j.ins.2015.07.028>.
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2025-03-25 |
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r-pheval
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public |
Provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
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2025-03-25 |
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r-phenocamapi
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public |
A bundle to facilitate working with PhenoCam timeseries and data. The user would be able to obtain phenological time-series and site metadata from the PhenoCam network <https://phenocam.sr.unh.edu/webcam/>.
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2025-03-25 |
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r-phenability
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public |
An alternative to carrying out phenotypic adaptability and stability analyses, taking into account nonparametric statistics. Can be used as a robust approach, less sensitive to departures from common genotypic, environmental, and GxE effects data assumptions (e.g., normal distribution of errors).
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2025-03-25 |
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r-pheatmap
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public |
Implementation of heatmaps that offers more control over dimensions and appearance.
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2025-03-25 |
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r-phd
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public |
Provides permutation methods for testing in high-dimensional linear models. The tests are often robust against heteroscedasticity and non-normality and usually perform well under anti-sparsity. See Hemerik and Goeman (2018) <doi:10.1007/s11749-017-0571-1>.
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2025-03-25 |
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r-ph2mult
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public |
Provide multinomial design methods under intersection-union test (IUT) and union-intersection test (UIT) scheme for Phase II trial. The design types include : Minimax (minimize the maximum sample size), Optimal (minimize the expected sample size), Admissible (minimize the Bayesian risk) and Maxpower (maximize the exact power level).
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2025-03-25 |
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r-pgnorm
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Evaluation of the pdf and the cdf of the univariate, noncentral, p-generalized normal distribution. Sampling from the univariate, noncentral, p-generalized normal distribution using either the p-generalized polar method, the p-generalized rejecting polar method, the Monty Python method, the Ziggurat method or the method of Nardon and Pianca. The package also includes routines for the simulation of the bivariate, p-generalized uniform distribution and the simulation of the corresponding angular distribution.
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2025-03-25 |
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r-pgm2
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Construction method of nested resolvable designs from a projective geometry defined on Galois field of order 2. The obtained Resolvable designs are used to build uniform design. The presented results are based on <https://eudml.org/doc/219563> and A. Boudraa et al. (See references).
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2025-03-25 |
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r-pgls
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Based on the Generalized Least Square model for comparative Phylogenetics (ref).
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2025-03-25 |
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r-pgee
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public |
Fits penalized generalized estimating equations to longitudinal data with high-dimensional covariates.
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2025-03-25 |
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r-petitr
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Calculates the relative growth rate (RGR) of a series of individuals by building a life table and solving the Lotka-Birch equation. (See Birch, L. C. 1948. The intrinsic rate of natural increase of an insect population. - Journal of Animal Ecology 17: 15-26) <doi:10.2307/1605>.
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2025-03-25 |
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r-petfinder
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public |
Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.
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2025-03-25 |
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r-pesel
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Automatic estimation of number of principal components in PCA with PEnalized SEmi-integrated Likelihood (PESEL). See Piotr Sobczyk, Malgorzata Bogdan, Julie Josse 'Bayesian dimensionality reduction with PCA using penalized semi-integrated likelihood' (2017) <doi:10.1080/10618600.2017.1340302>.
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2025-03-25 |
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r-perturb
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Use the perturb() function to evaluates collinearity by adding random noise to selected variables (Hendrickx & Pelzer 2004). The colldiag function() calculates condition numbers and variance decomposition proportions to test for collinearity and uncover its sources (Belsley 1980).
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2025-03-25 |
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r-persianstemmer
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public |
Allows users to stem Persian texts for text analysis.
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2025-03-25 |
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r-persiandictionary
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public |
Translate words from English to Persian (Over 67,000 words)
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2025-03-25 |
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r-permute
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A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
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2025-03-25 |
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r-permgs
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Permutational group-sequential tests for time-to-event data based on the log-rank test statistic. Supports exact permutation test when the censoring distributions are equal in the treatment and the control group and approximate imputation-permutation methods when the censoring distributions are different.
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2025-03-25 |
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r-permalgo
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This version of the permutational algorithm generates a dataset in which event and censoring times are conditional on an user-specified list of covariates, some or all of which are time-dependent.
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2025-03-25 |
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r-periodictable
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Provides a dataset containing properties for chemical elements. Helper functions are also provided to access some atomic properties.
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2025-03-25 |
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r-perc
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To find the certainty of dominance interactions with indirect interactions being considered.
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2025-03-25 |
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r-pepsavims
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An implementation of the data processing and data analysis portion of a pipeline named the PepSAVI-MS which is currently under development by the Hicks laboratory at the University of North Carolina. The statistical analysis package presented herein provides a collection of software tools used to facilitate the prioritization of putative bioactive peptides from a complex biological matrix. Tools are provided to deconvolute mass spectrometry features into a single representation for each peptide charge state, filter compounds to include only those possibly contributing to the observed bioactivity, and prioritize these remaining compounds for those most likely contributing to each bioactivity data set.
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2025-03-25 |
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r-pemm
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This package provides functions to perform multivariate Gaussian parameter estimation based on data with abundance-dependent missingness. It implements a penalized Expectation-Maximization (EM) algorithm. The package is tailored for but not limited to proteomics data applications, in which a large proportion of the data are often missing-not-at-random with lower values (or absolute values) more likely to be missing.
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2025-03-25 |
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r-pegrouptesting
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The population proportion using group testing can be estimated by different methods. Four functions including p.mle(), p.gart(), p.burrow() and p.order() are provided to implement four estimating methods including the maximum likelihood estimate, Gart's estimate, Burrow's estimate, and order statistic estimate.
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2025-03-25 |
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r-peerperformance
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Provides functions to perform the peer performance analysis of funds' returns as described in Ardia and Boudt (2018) <doi:10.1016/j.jbankfin.2017.10.014>.
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2025-03-25 |
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r-pearsonica
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The Pearson-ICA algorithm is a mutual information-based method for blind separation of statistically independent source signals. It has been shown that the minimization of mutual information leads to iterative use of score functions, i.e. derivatives of log densities. The Pearson system allows adaptive modeling of score functions. The flexibility of the Pearson system makes it possible to model a wide range of source distributions including asymmetric distributions. The algorithm is designed especially for problems with asymmetric sources but it works for symmetric sources as well.
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2025-03-25 |
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r-pearson7
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Supports maximum likelihood inference for the Pearson VII distribution with shape parameter 3/2 and free location and scale parameters. This distribution is relevant when estimating the velocity of processive motor proteins with random detachment.
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2025-03-25 |
