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r-planets
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public |
The goal of 'planets' is to provide of very simple and accessible data containing basic information from all known planets.
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2025-03-25 |
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r-planesmuestra
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public |
Calculates an acceptance sampling plan, (sample size and acceptance number) based in MIL STD 105E, Dodge Romig and MIL STD 414 tables and procedures. The arguments for each function are related to lot size, inspection level and quality level. The specific plan operating curve (OC), is calculated by the binomial distribution.
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2025-03-25 |
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r-plan
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Supports the creation of 'burndown' charts and 'gantt' diagrams.
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2025-03-25 |
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r-pla
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Parallel Line Assays: Completely randomized design, Randomized Block design, and Latin squares design. Balanced data are fitted as described in the Ph.Eur. In the presence of missing values complete data analysis can be performed (with computation of Fieller's confidence intervals for the estimated potency), or imputation of values can be applied. The package contains a script such that a pdf-document with a report of an analysis of an assay can be produced from an input file with data of the assay. Here no knowledge of R is needed by the user.
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2025-03-25 |
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r-pksea
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A tool for inferring kinase activity changes from phosphoproteomics data. 'pKSEA' uses kinase-substrate prediction scores to weight observed changes in phosphopeptide abundance to calculate a phosphopeptide-level contribution score, then sums up these contribution scores by kinase to obtain a phosphoproteome-level kinase activity change score (KAC score). 'pKSEA' then assesses the significance of changes in predicted substrate abundances for each kinase using permutation testing. This results in a permutation score (pKSEA significance score) reflecting the likelihood of a similarly high or low KAC from random chance, which can then be interpreted in an analogous manner to an empirically calculated p-value. 'pKSEA' contains default databases of kinase-substrate predictions from 'NetworKIN' (NetworKINPred_db) <http://networkin.info> Horn, et. al (2014) <doi:10.1038/nmeth.2968> and of known kinase-substrate links from 'PhosphoSitePlus' (KSEAdb) <https://www.phosphosite.org/> Hornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>.
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2025-03-25 |
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r-pkpdmodels
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Provides functions to evaluate common pharmacokinetic/pharmacodynamic models and their gradients.
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2025-03-25 |
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r-pkmon
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We implement two least-squares estimators under k-monotony constraint using a method based on the Support Reduction Algorithm from Groeneboom et al (2008) <DOI:10.1111/j.1467-9469.2007.00588.x>. The first one is a projection estimator on the set of k-monotone discrete functions. The second one is a projection on the set of k-monotone discrete probabilities. This package provides functions to generate samples from the spline basis from Lefevre and Loisel (2013) <DOI:10.1239/jap/1378401239>, and from mixtures of splines.
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2025-03-25 |
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r-pkgkitten
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Provides a function kitten() which creates cute little packages which pass R package checks. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative. Unit test support can be added via the 'tinytest' package (if present), and documentation-creation support can be added via 'roxygen2' (if present).
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2025-03-25 |
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r-pkgcond
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This provides utilities for creating classed error and warning conditions based on where the error originated.
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2025-03-25 |
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r-pkconverter
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Pharmacokinetics is the study of drug absorption, distribution, metabolism, and excretion. The pharmacokinetics model explains that how the drug concentration change as the drug moves through the different compartments of the body. For pharmacokinetic modeling and analysis, it is essential to understand the basic pharmacokinetic parameters. All parameters are considered, but only some of parameters are used in the model. Therefore, we need to convert the estimated parameters to the other parameters after fitting the specific pharmacokinetic model. This package is developed to help this converting work. For more detailed explanation of pharmacokinetic parameters, see "Gabrielsson and Weiner" (2007), "ISBN-10: 9197651001"; "Benet and Zia-Amirhosseini" (1995) <DOI: 10.1177/019262339502300203>; "Mould and Upton" (2012) <DOI: 10.1038/psp.2012.4>; "Mould and Upton" (2013) <DOI: 10.1038/psp.2013.14>.
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2025-03-25 |
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r-pk
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public |
Estimation of pharmacokinetic parameters using non-compartmental theory.
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2025-03-25 |
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r-pixmap
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public |
Functions for import, export, plotting and other manipulations of bitmapped images.
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2025-03-25 |
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r-pixels
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public |
Provides tools to show and draw image pixels using 'HTML' widgets and 'Shiny' applications. It can be used to visualize the 'MNIST' dataset for handwritten digit recognition or to create new image recognition datasets.
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2025-03-25 |
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r-pivotaltrackr
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'Pivotal Tracker' <https://www.pivotaltracker.com> is a project management software-as-a-service that provides a REST API. This package provides an R interface to that API, allowing you to query it and work with its responses.
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2025-03-25 |
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r-pips
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public |
Generate Predicted Interval Plots. Simulate and plot confidence intervals of an effect estimate given observed data and a hypothesis about the distribution of future data.
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2025-03-25 |
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r-piper
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public |
Provides various styles of function chaining methods: Pipe operator, Pipe object, and pipeline function, each representing a distinct pipeline model yet sharing almost a common set of features: A value can be piped to the first unnamed argument of a function and to dot symbol in an enclosed expression. The syntax is designed to make the pipeline more readable and friendly to a wide range of operations.
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2025-03-25 |
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r-pipeliner
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A framework for defining 'pipelines' of functions for applying data transformations, model estimation and inverse-transformations, resulting in predicted value generation (or model-scoring) functions that automatically apply the entire pipeline of functions required to go from input to predicted output.
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2025-03-25 |
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r-pipegs
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Code for various permutation p-values estimation methods for gene set test. The description of corresponding methods can be found in the dissertation of Yu He(2016) "Efficient permutation P-value estimation for gene set tests" <https://searchworks.stanford.edu/view/11849351>. One of the methods also corresponds to the paper "Permutation p-value approximation via generalized Stolarsky invariance" <arXiv:1603.02757>.
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2025-03-25 |
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r-pipefittr
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To take nested function calls and convert them to a more readable form using pipes from package 'magrittr'.
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2025-03-25 |
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r-pins
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public |
Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'RStudio' connect, Amazon S3, and more.
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2025-03-25 |
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r-pinp
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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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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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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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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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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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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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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. "deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail; "deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete days and removing low activity days; "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.
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2025-03-25 |
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r-physactbedrest
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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. Version 1.1 adds preschool thresholds and corrects for possible errors in algorithm implementation.
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2025-03-25 |
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r-phyreg
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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, Thoresen and Finos (2021) <doi:10.1080/00949655.2020.1836183>.
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2025-03-25 |
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r-ph2mult
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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 |
