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r-pbapply
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public |
A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options. Supports several parallel processing backends.
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2023-06-16 |
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r-pageviews
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public |
Pageview data from the 'Wikimedia' sites, such as 'Wikipedia' <https://www.wikipedia.org/>, from entire projects to per-article levels of granularity, through the new RESTful API and data source <https:// wikimedia.org/api/rest_v1/?doc>.
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2023-06-16 |
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r-osrmr
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Wrapper around the 'Open Source Routing Machine (OSRM)' API <http://project-osrm.org/>. 'osrmr' works with API versions 4 and 5 and can handle servers that run locally as well as the 'OSRM' webserver.
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2023-06-16 |
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r-oscillatorgenerator
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The supplied code allows for the generation of discrete time series of oscillating species. General shapes can be selected by means of individual functions, which are widely customizable by means of function arguments. All code was developed in the Biological Information Processing Group at the BioQuant Center at Heidelberg University, Germany.
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2023-06-16 |
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r-orderstats
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All the methods in this package generate a vector of uniform order statistics using a beta distribution and use an inverse cumulative distribution function for some distribution to give a vector of random order statistic variables for some distribution. This is much more efficient than using a loop since it is directly sampling from the order statistic distribution.
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2023-06-16 |
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r-optrees
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Finds optimal trees in weighted graphs. In particular, this package provides solving tools for minimum cost spanning tree problems, minimum cost arborescence problems, shortest path tree problems and minimum cut tree problem.
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2023-06-16 |
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r-ocedata
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Several important and Oceanographic data sets are provided. These are particularly useful to the 'oce' package, but can also be helpful in a general context.
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2023-06-16 |
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r-nzilbb.labbcat
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'LaBB-CAT' is a web-based language corpus management system developed by the New Zealand Institute of Language, Brain and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>. This package defines functions for accessing corpus data in a 'LaBB-CAT' instance. You must have at least version 20190425.1121 of 'LaBB-CAT' to use this package. For more information about 'LaBB-CAT', see Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142> or Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
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2023-06-16 |
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r-numgen
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public |
A number series generator that creates number series items based on cognitive models.
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2023-06-16 |
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r-numbersbr
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Validate, format and compare identification numbers used in Brazil. These numbers are used to identify individuals (CPF), vehicles (RENAVAN), companies (CNPJ) and etc. Functions to format, validate and compare these numbers have been implemented in a vectorized way in order to speed up validations and comparisons in big datasets.
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2023-06-16 |
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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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2023-06-16 |
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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.
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2023-06-16 |
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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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2023-06-16 |
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r-peakram
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When working with big data sets, RAM conservation is critically important. However, it is not always enough to just monitor the size of the objects created. So-called "copy-on-modify" behavior, characteristic of R, means that some expressions or functions may require an unexpectedly large amount of RAM overhead. For example, replacing a single value in a matrix duplicates that matrix in the back-end, making this task require twice as much RAM as that used by the matrix itself. This package makes it easy to monitor the total and peak RAM used so that developers can quickly identify and eliminate RAM hungry code.
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2023-06-16 |
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r-pastecs
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Regularisation, decomposition and analysis of space-time series. The pastecs R package is a PNEC-Art4 and IFREMER (Benoit Beliaeff <[email protected]>) initiative to bring PASSTEC 2000 functionalities to R.
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2023-06-16 |
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r-partitionmap
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Low-dimensional embedding, using Random Forests for multiclass classification
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2023-06-16 |
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r-paran
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An implementation of Horn's technique for numerically and graphically evaluating the components or factors retained in a principle components analysis (PCA) or common factor analysis (FA). Horn's method contrasts eigenvalues produced through a PCA or FA on a number of random data sets of uncorrelated variables with the same number of variables and observations as the experimental or observational data set to produce eigenvalues for components or factors that are adjusted for the sample error-induced inflation. Components with adjusted eigenvalues greater than one are retained. paran may also be used to conduct parallel analysis following Glorfeld's (1995) suggestions to reduce the likelihood of over-retention.
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2023-06-16 |
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r-parallelize.dynamic
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Passing a given function name or a call to the parallelize/parallelize_call functions analyses and executes the code, if possible in parallel. Parallel code execution can be performed locally or on remote batch queuing systems.
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2023-06-16 |
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r-parade
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Tool for producing Pen's parade graphs, useful for visualizing inequalities in income, wages or other variables, as proposed by Pen (1971, ISBN: 978-0140212594). Income or another economic variable is captured by the vertical axis, while the population is arranged in ascending order of income along the horizontal axis. Pen's income parades provide an easy-to-interpret visualization of economic inequalities.
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2023-06-16 |
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r-pandocfilters
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The document converter 'pandoc' <http://pandoc.org/> is widely used in the R community. One feature of 'pandoc' is that it can produce and consume JSON-formatted abstract syntax trees (AST). This allows to transform a given source document into JSON-formatted AST, alter it by so called filters and pass the altered JSON-formatted AST back to 'pandoc'. This package provides functions which allow to write such filters in native R code. Although this package is inspired by the Python package 'pandocfilters' <https://github.com/jgm/pandocfilters/>, it provides additional convenience functions which make it simple to use the 'pandocfilters' package as a report generator. Since 'pandocfilters' inherits most of it's functionality from 'pandoc' it can create documents in many formats (for more information see <http://pandoc.org/>) but is also bound to the same limitations as 'pandoc'.
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2023-06-16 |
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r-owea
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An implementation of optimal weight exchange algorithm Yang(2013) <doi:10.1080/01621459.2013.806268> for three models. They are Crossover model with subject dropout, crossover model with proportional first order residual effects and interference model. You can use it to find either A-opt or D-opt approximate designs. Exact designs can be automatically rounded from approximate designs and relative efficiency is provided as well.
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2023-06-16 |
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r-ote
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Functions for creating ensembles of optimal trees for regression, classification and class membership probability estimation are given. A few trees are selected from an initial set of trees grown by random forest for the ensemble on the basis of their individual and collective performance. Trees are assessed on out-of-bag data and on an independent training data set for individual and collective performance respectively. The prediction functions return estimates of the test responses and their class membership probabilities. Unexplained variations, error rates, confusion matrix, Brier scores, etc. are also returned for the test data.
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2023-06-16 |
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r-optionpricing
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Efficient Monte Carlo Algorithms for the price and the sensitivities of Asian and European Options under Geometric Brownian Motion.
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2023-06-16 |
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r-omickriging
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It provides functions to generate a correlation matrix from a genetic dataset and to use this matrix to predict the phenotype of an individual by using the phenotypes of the remaining individuals through kriging. Kriging is a geostatistical method for optimal prediction or best unbiased linear prediction. It consists of predicting the value of a variable at an unobserved location as a weighted sum of the variable at observed locations. Intuitively, it works as a reverse linear regression: instead of computing correlation (univariate regression coefficients are simply scaled correlation) between a dependent variable Y and independent variables X, it uses known correlation between X and Y to predict Y.
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2023-06-16 |
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r-objectsignals
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A mutable Signal object can report changes to its state, clients could register functions so that they are called whenever the signal is emited. The signal could be emited, disconnected, blocked, unblocked, and buffered.
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2023-06-16 |
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r-oak
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Functions and classes to create and manipulate trees and nodes.
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2023-06-16 |
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r-oacolors
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Provides carefully chosen color palettes as used a.o. at OpenAnalytics <http://www.openanalytics.eu>.
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2023-06-16 |
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r-nzpullover
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Datasets of driving offences and fines in New Zealand between 2009 and 2017. Originally published by the New Zealand Police at <http://www.police.govt.nz/about-us/publication/road-policing-driver-offence-data-january-2009-december-2017>.
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2023-06-16 |
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r-noweb
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The noweb system for source code, implemented in R.
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2023-06-16 |
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r-normwhn.test
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Includes Omnibus Univariate and Multivariate Normality Tests (See Doornik and Hansen (1994)). One variation allows for the possibility of weak dependence rather than independence in the variable(s). Also included is an univariate white noise test where the null hypothesis is "white noise" rather than strict "white noise".
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-persianstemmer
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Allows users to stem Persian texts for text analysis.
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2023-06-16 |
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r-peakpick
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Biologically inspired methods for detecting peaks in one-dimensional data, such as time series or genomics data. The algorithms were originally designed by Weber, Ramachandran, and Henikoff, see documentation.
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2023-06-16 |
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r-pcse
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A function to estimate panel-corrected standard errors. Data may contain balanced or unbalanced panels.
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2023-06-16 |
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r-patchplot
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Functions to generate scatterplots with images patches instead of usual glyphs, with associated utilities.
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2023-06-16 |
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r-packs4
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Illustration of the book "Petit Manuel de Programmation Orientee Objet sous R". The english version "A (Not so) Short Introduction to S4" is on CRAN, 'Contributed documentation'.
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2023-06-16 |
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r-overture
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Simplifies MCMC setup by automatically looping through sampling functions and saving the results. Reduces the memory footprint of running MCMC and saves samples to disk as the chain runs. Allows samples from the chain to be analyzed while the MCMC is still running. Provides functions for commonly performed operations such as calculating Metropolis acceptance ratios and creating adaptive Metropolis samplers. References: Roberts and Rosenthal (2009) <doi:10.1198/jcgs.2009.06134>.
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2023-06-16 |
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r-outlierdc
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This package provides three algorithms to detect outlying observations for censored survival data.
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2023-06-16 |
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r-oriclust
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ORIClust is a user-friendly R-based software package for gene clustering. Clusters are given by genes matched to prespecified profiles across various ordered treatment groups. It is particularly useful for analyzing data obtained from short time-course or dose-response microarray experiments.
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2023-06-16 |
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r-orddom
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Computes ordinal, statistics and effect sizes as an alternative to mean comparison: Cliff's delta or success rate difference (SRD), Vargha and Delaney's A or the Area Under a Receiver Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's Common Language Effect Size (CLES) or Grissom & Kim's Probability of Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of Group (Non-)Overlap considerations.
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2023-06-16 |
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r-optismixture
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Code for optimal mixture weights in importance sampling. Workhorse functions penoptpersp() and penoptpersp.alpha.only() minimize estimated variances with and without control variates respectively. It can be used in adaptive mixture importance sampling, for example, function batch.estimation() does two stages, a pilot estimate of mixing alpha and a following importance sampling.
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2023-06-16 |
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r-optiscale
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Tools for performing an optimal scaling transformation on a data vector
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2023-06-16 |
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r-optimalcutpoints
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Computes optimal cutpoints for diagnostic tests or continuous markers. Various approaches for selecting optimal cutoffs have been implemented, including methods based on cost-benefit analysis and diagnostic test accuracy measures (Sensitivity/Specificity, Predictive Values and Diagnostic Likelihood Ratios). Numerical and graphical output for all methods is easily obtained.
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2023-06-16 |
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r-optigrab
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Parse options from the command-line using a simple, clean syntax. It requires little or no specification and supports short and long options, GNU-, Java- or Microsoft- style syntaxes, verb commands and more.
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2023-06-16 |
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r-oaiharvester
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Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0 (for more information, see <http://www.openarchives.org/OAI/openarchivesprotocol.html>).
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2023-06-16 |
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r-nsprcomp
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Two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function 'nsprcomp' computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function 'nscumcomp' jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the 'prcomp' function from the 'stats' package (plus some extra parameters), and both return the result of the analysis as an object of class 'nsprcomp', which inherits from 'prcomp'. See <https://sigg-iten.ch/learningbits/2013/05/27/nsprcomp-is-on-cran/> and Sigg et al. (2008) <doi:10.1145/1390156.1390277> for more details.
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2023-06-16 |
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r-nricens
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Calculating the net reclassification improvement (NRI) for risk prediction models with time to event and binary data.
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2023-06-16 |
