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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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r-outrankingtools
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Functions to process ''outranking'' ELECTRE methods existing in the literature. See, e.g., <http://en.wikipedia.org/wiki/ELECTRE> about the outranking approach and the foundations of ELECTRE methods.
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2025-04-22 |
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r-outliers
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A collection of some tests commonly used for identifying outliers.
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2025-04-22 |
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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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2025-04-22 |
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r-outbreaks
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Empirical or simulated disease outbreak data, provided either as RData or as text files.
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2025-04-22 |
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r-otutable
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Analyses of OTU tables produced by 16S rRNA gene amplicon sequencing, as well as example data. It contains the data and scripts used in the paper Linz, et al. (2017) "Bacterial community composition and dynamics spanning five years in freshwater bog lakes," <doi: 10.1128/mSphere.00169-17>.
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2025-04-22 |
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r-otrselect
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A penalized regression framework that can simultaneously estimate the optimal treatment strategy and identify important variables. Appropriate for either censored or uncensored continuous response.
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2025-04-22 |
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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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2025-04-22 |
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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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2025-04-22 |
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r-osmose
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The multispecies and individual-based model (IBM) 'OSMOSE' (Shin and Curry (2001) <doi:10.1016/S0990-7440(01)01106-8> and Shin and Curry (2004) <doi:10.1139/f03-154>) focuses on fish species. This model assumes opportunistic predation based on spatial co-occurrence and size adequacy between a predator and its prey (size-based opportunistic predation). It represents fish individuals grouped into schools, which are characterized by their size, weight, age, taxonomy and geographical location (2D model), and which undergo major processes of fish life cycle (growth, explicit predation, natural and starvation mortalities, reproduction and migration) and fishing exploitation. The model needs basic biological parameters that are often available for a wide range of species, and which can be found in 'FishBase' for instance (see <http://www.fishbase.org/search.php>), and fish spatial distribution data. This package provides tools to build and run simulations using the 'OSMOSE' model.
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2025-04-22 |
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r-oshka
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Expands quoted language by recursively replacing any symbol that points to quoted language with the language it points to. The recursive process continues until only symbols that point to non-language objects remain. The resulting quoted language can then be evaluated normally. This differs from the traditional 'quote'/'eval' pattern because it resolves intermediate language objects that would interfere with evaluation.
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2025-04-22 |
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r-osdr
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Provides routines for finding an Optimal System of Distinct Representatives (OSDR), as defined by D.Gale (1968) <doi:10.1016/S0021-9800(68)80039-0>.
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2025-04-22 |
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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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2025-04-22 |
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r-orthopanels
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Implements the orthogonal reparameterization approach recommended by Lancaster (2002) to estimate dynamic panel models with fixed effects (and optionally: panel specific intercepts). The approach uses a likelihood-based estimator and produces estimates that are asymptotically unbiased as N goes to infinity, with a T as low as 2.
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2025-04-22 |
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r-orthogonalsplinebasis
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Represents the basis functions for B-splines in a simple matrix formulation that facilitates, taking integrals, derivatives, and making orthogonal the basis functions.
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2025-04-22 |
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r-orsifronts
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A data set package with the "Orsi" fronts as a 'SpatialLinesDataFrame' object. The Orsi et al. (1995) fronts are published at the Southern Ocean Atlas Database Page, please see package CITATION for details.
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2025-04-22 |
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r-orientlib
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Representations, conversions and display of orientation SO(3) data. See the orientlib help topic for details.
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2025-04-22 |
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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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2025-04-22 |
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r-orgmassspecr
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Organic/biological mass spectrometry data analysis.
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2025-04-22 |
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r-org
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A system to help you organize projects. Most analyses have three (or more) main sections: code, results, and data, each with different requirements (version control/sharing/encryption). You provide folder locations and 'org' helps you take care of the details.
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2025-04-22 |
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r-ores
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A connector to ORES (<http://ores.wmflabs.org/>), an AI project to provide edit scoring for content on Wikipedia and other Wikimedia projects. This lets a researcher identify if edits are likely to be reverted, damaging, or made in good faith.
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2025-04-22 |
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r-ordmonreg
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We consider the problem of estimating two isotonic regression curves g1* and g2* under the constraint that they are ordered, i.e. g1* <= g2*. Given two sets of n data points y_1, ..., y_n and z_1, ..., z_n that are observed at (the same) deterministic design points x_1, ..., x_n, the estimates are obtained by minimizing the Least Squares criterion L(a, b) = sum_{i=1}^n (y_i - a_i)^2 w1(x_i) + sum_{i=1}^n (z_i - b_i)^2 w2(x_i) over the class of pairs of vectors (a, b) such that a and b are isotonic and a_i <= b_i for all i = 1, ..., n. We offer two different approaches to compute the estimates: a projected subgradient algorithm where the projection is calculated using a PAVA as well as Dykstra's cyclical projection algorithm.
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2025-04-22 |
