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r-proccalibrad
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Package for processing downloaded MODIS Calibrated radiances Product HDF files. Specifically, MOD02 calibrated radiance product files, and the associated MOD03 geolocation files (for MODIS-TERRA). The package will be most effective if the user installs MRTSwath (MODIS Reprojection Tool for swath products; <https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath>, and adds the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.
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2023-06-16 |
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r-primefactr
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Use Prime Factorization for simplifying computations, for instance for ratios of large factorials.
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2023-06-16 |
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r-prettydoc
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Creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the 'html_pretty' output format as an alternative to the 'html_document' and 'html_vignette' engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.
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2023-06-16 |
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r-prettycode
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Replace the standard print method for functions with one that performs syntax highlighting, using ANSI colors, if the terminal supports them.
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2023-06-16 |
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r-prettyb
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Drop-in replacements for standard base graphics functions. The replacements are prettier versions of the originals.
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2023-06-16 |
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r-pragma
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pragma allows for the use of pragma (also sometimes called directives or keywords. These allow assigning arbitrary functionality to a word without requiring the standard function call syntax i.e. with parens.
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2023-06-16 |
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r-pqantimalarials
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This package allows users to calculate the number of under-five child deaths caused by consumption of poor quality antimalarials across 39 sub-Saharan nations. The package supports one function, that starts an interactive web tool created using the shiny R package. The web tool runs locally on the user's machine. The web tool allows users to set input parameters (prevalence of poor quality antimalarials, case fatality rate of children who take poor quality antimalarials, and sample size) which are then used to perform an uncertainty analysis following the Latin hypercube sampling scheme. Users can download the output figures as PDFs, and the output data as CSVs. Users can also download their input parameters for reference. This package was designed to accompany the analysis presented in: J. Patrick Renschler, Kelsey Walters, Paul Newton, Ramanan Laxminarayan "Estimated under-five deaths associated with poor-quality antimalarials in sub-Saharan Africa", 2014. Paper submitted.
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2023-06-16 |
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r-powerlmm
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Calculate power for the 'time x treatment' effect in two- and three-level multilevel longitudinal studies with missing data. Both the third-level factor (e.g. therapists, schools, or physicians), and the second-level factor (e.g. subjects), can be assigned random slopes. Studies with partially nested designs, unequal cluster sizes, unequal allocation to treatment arms, and different dropout patterns per treatment are supported. For all designs power can be calculated both analytically and via simulations. The analytical calculations extends the method described in Galbraith et al. (2002) <doi:10.1016/S0197-2456(02)00205-2>, to three-level models. Additionally, the simulation tools provides flexible ways to investigate bias, Type I errors and the consequences of model misspecification.
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2023-06-16 |
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r-popdemog
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Plot demographic graphs for single/multiple populations from coalescent simulation program input. Currently, this package can support the 'ms', 'msHot', 'MaCS', 'msprime', 'SCRM', and 'Cosi2' simulation programs. It does not check the simulation program input for correctness, but assumes the simulation program input has been validated by the simulation program. More features will be added to this package in the future, please check the 'GitHub' page for the latest updates: <https://github.com/YingZhou001/POPdemog>.
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2023-06-16 |
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r-poissonseq
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This package implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. The description of the method is in Li J, Witten DM, Johnstone I, Tibshirani R (2012). Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3): 523-38. We estimate the sequencing depths of experiments using a new method based on Poisson goodness-of-fit statistic, calculate a score statistic on the basis of a Poisson log-linear model, and then estimate the false discovery rate using a modified version of permutation plug-in method. A more detailed instruction as well as sample data is available at http://www.stanford.edu/~junli07/research.html. In this version, we changed the way of calculating log foldchange for two-class data. The FDR estimation part remains unchanged.
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2023-06-16 |
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r-plotrix
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Lots of plots, various labeling, axis and color scaling functions.
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2023-06-16 |
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r-rts
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This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
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2023-06-16 |
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r-rsfa
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Slow Feature Analysis in R, ported to R based on the matlab versions SFA toolkit 1.0 by Pietro Berkes and SFA toolkit 2.8 by Wolfgang Konen for matlab.
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2023-06-16 |
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r-rsem
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A robust procedure is implemented to estimate means and covariance matrix of multiple variables with missing data using Huber weight and then to estimate a structural equation model.
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2023-06-16 |
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r-rprobsup
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The A() function calculates the A statistic, a nonparametric measure of effect size for two independent groups that’s also known as the probability of superiority (Ruscio, 2008), along with its standard error and a confidence interval constructed using bootstrap methods (Ruscio & Mullen, 2012). Optional arguments can be specified to calculate variants of the A statistic developed for other research designs (e.g., related samples, more than two independent groups or related samples; Ruscio & Gera, 2013). <DOI: 10.1037/1082-989X.13.1.19>. <DOI: 10.1080/00273171.2012.658329>. <DOI: 10.1080/00273171.2012.738184>.
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2023-06-16 |
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r-rpmm
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Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models.
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2023-06-16 |
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r-rpmg
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Really Poor Man's Graphical User Interface, used to create interactive R analysis sessions with simple R commands.
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2023-06-16 |
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r-roundhouse
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An R wrapper to the 'Internet Chuck Norris database' ('ICNDb') API for generating random Chuck Norris facts.
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2023-06-16 |
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r-rotor
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Conditionally rotate or back-up files based on their size or the date of the last backup; inspired by the 'Linux' utility 'logrotate'.
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2023-06-16 |
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r-rnavgraphimagedata
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Image data used as examples in the loon R package.
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2023-06-16 |
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r-rld
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Analyzes data from repeated low-dose challenge experiments and provide vaccine efficacy estimates. In addition, this package can provide guidance to design repeated low-dose challenge studies.
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2023-06-16 |
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r-rkelly
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Calculates the Kelly criterion (Kelly, J.L. (1956) <doi:10.1002/j.1538-7305.1956.tb03809.x>) for bets given quoted prices, model predictions and commissions. Additionally it contains helper functions to calculate the probabilities for wins and draws in multi-leg games.
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2023-06-16 |
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r-ridit
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An extension of the Kruskal-Wallis Test that allow selection of arbitrary reference group. Also provide Mean Ridit for each group. Mean Ridit of a group is an estimate of probability a random observation from that group will be greater than or equal to a random observation from reference group.
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2023-06-16 |
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r-r.huge
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DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)
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2023-06-16 |
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r-rgroovy
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Integrates the Groovy scripting language with the R Project for Statistical Computing.
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2023-06-16 |
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r-rgcca
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Multiblock data analysis concerns the analysis of several sets of variables (blocks) observed on the same group of individuals. The main aims of the RGCCA package are: (i) to study the relationships between blocks and (ii) to identify subsets of variables of each block which are active in their relationships with the other blocks.
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2023-06-16 |
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r-reqs
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This package contains the function run.eqs() which calls an EQS script file, executes the EQS estimation, and, finally, imports the results as R objects. These two steps can be performed separately: call.eqs() calls and executes EQS, whereas read.eqs() imports existing EQS outputs as objects into R. It requires EQS 6.2 (build 98 or higher).
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2023-06-16 |
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r-represtools
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Reproducible research tools automates the creation of an analysis directory structure and work flow. There are R markdown skeletons which encapsulate typical analytic work flow steps. Functions will create appropriate modules which may pass data from one step to another.
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2023-06-16 |
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r-reports
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Assists in writing reports and presentations by providing a frame work that brings together existing R, LaTeX/.docx and Pandoc tools. The package is designed to be used with RStudio, MiKTex/Tex Live/LibreOffice, knitr, knitcitations, Pandoc and pander. The user will want to download these free programs/packages to maximize the effectiveness of the reports package. Functions with two letter names are general text formatting functions for copying text from articles for inclusion as a citation.
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2023-06-16 |
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r-relvalanalysis
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Classes and functions for analyzing the performance of portfolios relative to a benchmark.
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2023-06-16 |
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r-regtest
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Functions for unary and binary regression tests
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2023-06-16 |
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r-recipa
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Pathways in a database could have many redundancies among them. This package allows the user to set a maximum value for the proportion of these redundancies.
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2023-06-16 |
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r-rdnase
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Comprehensive toolkit for generating various numerical representation schemes of DNA sequence. The descriptors and similarity scores included are extensively used in bioinformatics and chemogenomics.
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2023-06-16 |
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r-rd2md
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The native R functionalities only allow PDF exports of reference manuals. This shall be extended by converting the package documentation files into markdown files and combining them into a markdown version of the package reference manual.
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2023-06-16 |
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r-randomglm
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The package implements a bagging predictor based on general linear models
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2023-06-16 |
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r-r2beat
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Multivariate optimal allocation for different domains in one and two stages stratified sample design. R2BEAT extends the Neyman (1934) <doi:10.2307/2342192> – Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethel’s proposal (1989). R2BEAT develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples.
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2023-06-16 |
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r-queryparser
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Translate 'SQL' 'SELECT' statements into lists of 'R' expressions.
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2023-06-16 |
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r-quantumops
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Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>.
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2023-06-16 |
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r-qtlbook
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Datasets for the book, A Guide to QTL Mapping with R/qtl. Broman and Sen (2009) <doi:10.1007/978-0-387-92125-9>.
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2023-06-16 |
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r-qrnn
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Fit quantile regression neural network models with optional left censoring, partial monotonicity constraints, generalized additive model constraints, and the ability to fit multiple non-crossing quantile functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005> and Cannon (2018) <doi:10.1007/s00477-018-1573-6>.
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2023-06-16 |
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r-qrmix
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Implements the robust algorithm for fitting finite mixture models based on quantile regression proposed by Emir et al., 2017 (unpublished).
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2023-06-16 |
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r-qkerntool
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Nonlinear machine learning tool for classification, clustering and dimensionality reduction. It integrates 12 q-kernel functions and 15 conditional negative definite kernel functions and includes the q-kernel and conditional negative definite kernel version of density-based spatial clustering of applications with noise, spectral clustering, generalized discriminant analysis, principal component analysis, multidimensional scaling, locally linear embedding, sammon's mapping and t-Distributed stochastic neighbor embedding.
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2023-06-16 |
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r-ptprocess
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Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
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2023-06-16 |
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r-psyphy
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An assortment of functions that could be useful in analyzing data from psychophysical experiments. It includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice (mafc) data to be used with the binomial family in glm (and possibly other contexts) and self-Start functions for estimating gamma values for CRT screen calibrations.
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2023-06-16 |
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r-properties
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Allows to parse 'Java' properties files in the context of 'R Service Bus' applications.
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2023-06-16 |
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r-priogene
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In gene sequencing methods, the topological features of protein-protein interaction (PPI) networks are often used, such as ToppNet <https://toppgene.cchmc.org>. In this study, a candidate gene prioritization method was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease PPI networks with weights for nodes and edges based on functional information.
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2023-06-16 |
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r-pooledmeangroup
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Calculates the pooled mean group (PMG) estimator for dynamic panel data models, as described by Pesaran, Shin and Smith (1999) <doi:10.1080/01621459.1999.10474156>.
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2023-06-16 |
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r-polysegratio
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Perform classic chi-squared tests and Ripol et al(1999) binomial confidence interval approach for autopolyploid dominant markers. Also, dominant markers may be generated for families of offspring where either one or both of the parents possess the marker. Missing values and misclassified markers may be generated at random.
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2023-06-16 |
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r-polynom
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A collection of functions to implement a class for univariate polynomial manipulations.
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2023-06-16 |
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r-polyaaeppli
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Functions for evaluating the mass density, cumulative distribution function, quantile function and random variate generation for the Polya-Aeppli distribution, also known as the geometric compound Poisson distribution.
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2023-06-16 |
