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r-normexpression
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It provides a framework and a fast and simple way for researchers to evaluate methods (particularly some data-driven methods or their own methods) and then select a best one for data normalization in the gene expression analysis, based on the consistency of metrics and the consistency of datasets. Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Deshui Yu, Hua Wang, Gustavo Glusman, Max Robinson, Lin Liu, Jishou Ruan and Shan Gao (2018) <doi:10.1101/251140>.
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2023-06-16 |
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r-nomnoml
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A tool for drawing sassy 'UML' diagrams based on a simple syntax, see <http://www.nomnoml.com>. Supports styling, R Markdown and exporting diagrams in the PNG format.
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2023-06-16 |
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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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2023-06-16 |
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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. 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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-peacock.test
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The original definition of the two and three dimensional Kolmogorov-Smirnov two-sample test statistics given by Peacock (1983) is implemented. Two R-functions: peacock2 and peacock3, are provided to compute the test statistics in two and three dimensional spaces, respectively. Note the Peacock test is different from the Fasano and Franceschini test (1987). The latter is a variant of the Peacock test.
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2023-06-16 |
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r-pch
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Using piecewise constant hazards models is a very flexible approach for the analysis of survival data. The time line is divided into sub-intervals; for each interval, a different hazard is estimated using Poisson regression.
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2023-06-16 |
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r-pbrackets
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Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets.
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2023-06-16 |
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r-password
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Create random passwords of letters, numbers and punctuation.
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2023-06-16 |
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r-partialor
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Computes Odds Ratio adjusted for a vector of possibly continuous covariates
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2023-06-16 |
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r-panelaggregation
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Aggregate Business Tendency Survey Data (and other qualitative surveys) to time series at various aggregation levels. Run aggregation of survey data in a speedy, re-traceable and a easily deployable way. Aggregation is substantially accelerated by use of data.table. This package intends to provide an interface that is less general and abstract than data.table but rather geared towards survey researchers.
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2023-06-16 |
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r-paf
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Calculate unadjusted/adjusted attributable fraction function of a set of covariates for a censored survival outcome from a Cox model using the method proposed by Chen, Lin and Zeng (Biometrika 97, 713-726., 2010).
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2023-06-16 |
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r-optparse
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A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
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2023-06-16 |
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r-optionstrat
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Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and perform graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.
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2023-06-16 |
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r-optimparallel
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Provides a parallel version of the L-BFGS-B method of optim(). The main function of the package is optimParallel(), which has the same usage and output as optim(). Using optimParallel() can significantly reduce the optimization time.
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2023-06-16 |
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r-operator.tools
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Provides a collection of utilities that allow programming with R's operators. Routines allow classifying operators, translating to and from an operator and its underlying function, and inverting some operators (e.g. comparison operators), etc. All methods can be extended to custom infix operators.
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2023-06-16 |
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r-oor
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Implementation of optimistic optimization methods for global optimization of deterministic or stochastic functions. The algorithms feature guarantees of the convergence to a global optimum. They require minimal assumptions on the (only local) smoothness, where the smoothness parameter does not need to be known. They are expected to be useful for the most difficult functions when we have no information on smoothness and the gradients are unknown or do not exist. Due to the weak assumptions, however, they can be mostly effective only in small dimensions, for example, for hyperparameter tuning.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-pdm
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Measures real distances in pictures. With PDM() function, you can choose one '*.jpg' file, select the measure in mm of scale, starting and and finishing point in the graphical scale, the name of the measure, and starting and and finishing point of the measures. After, ask the user for a new measure.
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2023-06-16 |
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r-pdftables
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Allows the user to convert PDF tables to formats more amenable to analysis ('.csv', '.xml', or '.xlsx') by wrapping the PDFTables API. In order to use the package, the user needs to sign up for an API account on the PDFTables website (<https://pdftables.com/pdf-to-excel-api>). The package works by taking a PDF file as input, uploading it to PDFTables, and returning a file with the extracted data.
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2023-06-16 |
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r-pcg
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The package solves linear system of equations Ax=b by using Preconditioned Conjugate Gradient Algorithm where A is real symmetric positive definite matrix. A suitable preconditioner matrix may be provided by user. This can also be used to minimize quadratic function (x'Ax)/2-bx for unknown x.
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2023-06-16 |
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r-pagwas
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Bayesian hierarchical methods for pathway analysis of genomewide association data: Normal/Bayes factors and Sparse Normal/Adaptive lasso. The Frequentist Fisher's product method is included as well.
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2023-06-16 |
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r-oxybs
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Provides utilities for processing of Oxy-Bisulfite microarray data (e.g. via the Illumina Infinium platform, <http://www.illumina.com>) with tandem arrays, one using conventional bisulfite conversion, the other using oxy-bisulfite conversion.
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2023-06-16 |
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r-orgmassspecr
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Organic/biological mass spectrometry data analysis.
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2023-06-16 |
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r-ordinalcont
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A regression framework for response variables which are continuous self-rating scales such as the Visual Analog Scale (VAS) used in pain assessment, or the Linear Analog Self-Assessment (LASA) scales in quality of life studies. These scales measure subjects' perception of an intangible quantity, and cannot be handled as ratio variables because of their inherent non-linearity. We treat them as ordinal variables, measured on a continuous scale. A function (the g function) connects the scale with an underlying continuous latent variable. The link function is the inverse of the CDF of the assumed underlying distribution of the latent variable. A variety of link functions are currently implemented.
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2023-06-16 |
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r-opera
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Misc methods to form online predictions, for regression-oriented time-series, by combining a finite set of forecasts provided by the user.
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2023-06-16 |
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r-oncomodel
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Computing probabilistic tree models for oncogenesis based on genetic data using maximum likelihood.
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2023-06-16 |
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r-pameasures
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We propose a pair of summary measures for the predictive power of a prediction function based on a regression model. The regression model can be linear or nonlinear, parametric, semi-parametric, or nonparametric, and correctly specified or mis-specified. The first measure, R-squared, is an extension of the classical R-squared statistic for a linear model, quantifying the prediction function's ability to capture the variability of the response. The second measure, L-squared, quantifies the prediction function's bias for predicting the mean regression function. When used together, they give a complete summary of the predictive power of a prediction function. Please refer to Gang Li and Xiaoyan Wang (2016) <arXiv:1611.03063> for more details.
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2023-06-16 |
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r-oxcaar
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A set of tools that enables using 'OxCal' from within R. 'OxCal' (<https://c14.arch.ox.ac.uk/oxcal.html>) is a standard archaeological tool intended to provide 14C calibration and analysis of archaeological and environmental chronological information. 'OxcAAR' allows simple calibration with 'Oxcal' and plotting of the results as well as the execution of sophisticated ('OxCal') code and the import of the results of bulk analysis and complex Bayesian sequential calibration.
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2023-06-16 |
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r-optauc
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Searches for optimal linear combination of multiple diagnostic tests (markers) that maximizes the area under the receiver operating characteristic curve (AUC); performs an approximated cross-validation for estimating the AUC associated with the estimated coefficients.
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2023-06-16 |
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r-oompabase
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Provides the class unions that must be preloaded in order for the basic tools in the OOMPA (Object-Oriented Microarray and Proteomics Analysis) project to be defined and loaded. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new color schemes. Details on the packages in the OOMPA project can be found at <http://oompa.r-forge.r-project.org/>.
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2023-06-16 |
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r-ocomposition
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Regression model where the response variable is a rank-indexed compositional vector (non-negative values that sum up to one and are ordered from the largest to the smallest). Parameters are estimated in the Bayesian framework using MCMC methods.
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2023-06-16 |
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r-nutshell.bbdb
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This package contains the baseball databank data set used as an example in the book "R in a Nutshell" from O'Reilly Media. For more information about this book, see http://shop.oreilly.com/product/0636920022008.do
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2023-06-16 |
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r-nutshell.audioscrobbler
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This package contains the Audio Scrobbler data set used as an example in the book "R in a Nutshell" from O'Reilly Media. For more information about this book, see http://shop.oreilly.com/product/0636920022008.do
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2023-06-16 |
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r-numform
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Format numbers and plots for publication; includes the removal of leading zeros, standardization of number of digits, addition of affixes, and a p-value formatter. These tools combine the functionality of several 'base' functions such as 'paste()', 'format()', and 'sprintf()' into specific use case functions that are named in a way that is consistent with usage, making their names easy to remember and easy to deploy.
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2023-06-16 |
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r-npmv
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Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
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2023-06-16 |
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r-normalp
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Collection of utilities referred to Exponential Power distribution, also known as General Error Distribution (see Mineo, A.M. and Ruggieri, M. (2005), A software Tool for the Exponential Power Distribution: The normalp package. In Journal of Statistical Software, Vol. 12, Issue 4).
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2023-06-16 |
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r-nonpar
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Contains the following 5 nonparametric hypothesis tests: The Sign Test, The 2 Sample Median Test, Miller's Jackknife Procedure, Cochran's Q Test, & The Stuart-Maxwell Test.
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2023-06-16 |
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r-nomclust
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Package for hierarchical clustering of objects characterized by nominal variables.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-pbm
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Binding models which are useful when analysing protein-ligand interactions by techniques such as Biolayer Interferometry (BLI) or Surface Plasmon Resonance (SPR). Naman B. Shah, Thomas M. Duncan (2014) <doi:10.3791/51383>. Hoang H. Nguyen et al. (2015) <doi:10.3390/s150510481>. After initial binding parameters are known, binding curves can be simulated and parameters can be varied. The models within this package may also be used to fit a curve to measured binding data using non-linear regression.
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2023-06-16 |
