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r-noncompart
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Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) Use of CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
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2023-06-16 |
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r-phylotate
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public |
Functions to read and write APE-compatible phylogenetic trees in NEXUS and Newick formats, while preserving annotations.
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2023-06-16 |
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r-periodictable
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Provides a dataset containing properties for chemical elements. Helper functions are also provided to access some atomic properties.
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2023-06-16 |
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r-pearsonica
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The Pearson-ICA algorithm is a mutual information-based method for blind separation of statistically independent source signals. It has been shown that the minimization of mutual information leads to iterative use of score functions, i.e. derivatives of log densities. The Pearson system allows adaptive modeling of score functions. The flexibility of the Pearson system makes it possible to model a wide range of source distributions including asymmetric distributions. The algorithm is designed especially for problems with asymmetric sources but it works for symmetric sources as well.
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2023-06-16 |
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r-pcsinr
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Parallel Constraint Satisfaction (PCS) models are an increasingly common class of models in Psychology, with applications to reading and word recognition (McClelland & Rumelhart, 1981), judgment and decision making (Glöckner & Betsch, 2008; Glöckner, Hilbig, & Jekel, 2014), and several other fields (e.g. Read, Vanman, & Miller, 1997). In each of these fields, they provide a quantitative model of psychological phenomena, with precise predictions regarding choice probabilities, decision times, and often the degree of confidence. This package provides the necessary functions to create and simulate basic Parallel Constraint Satisfaction networks within R.
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2023-06-16 |
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r-patternator
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Provides a set of functions to efficiently recognize and clean the continuous dorsal pattern of a female brown anole lizard (Anolis sagrei) traced from 'ImageJ', an open platform for scientific image analysis (see <https://imagej.net> for more information), and extract common features such as the pattern sinuosity indices, coefficient of variation, and max-min width.
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2023-06-16 |
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r-parallelsvm
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By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
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2023-06-16 |
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r-palettetown
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Use Pokemon(R) inspired palettes with additional 'ggplot2' scales. Palettes are the colours in each Pokemon's sprite, ordered by how common they are in the image. The first 386 Pokemon are currently provided.
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2023-06-16 |
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r-paleobiodb
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Includes 19 functions to wrap each endpoint of the PaleobioDB API, plus 8 functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found in <http://paleobiodb.org/data1.1/>.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-phyloclim
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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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2023-06-16 |
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r-persiandictionary
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Translate words from English to Persian (Over 67,000 words)
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2023-06-16 |
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r-peerperformance
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Provides functions to perform the peer performance analysis of funds' returns as described in Ardia and Boudt (2018) <doi:10.1016/j.jbankfin.2017.10.014>.
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2023-06-16 |
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r-paneldata
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Linear models for panel data: the fixed effect model and the random effect model
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2023-06-16 |
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r-palettesforr
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A set of palettes imported from 'Gimp' distributed under GPL3 (<https://www.gimp.org/about/COPYING>), and 'Inkscape' distributed under GPL2 (<https://inkscape.org/about/license/>).
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2023-06-16 |
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r-paleomorph
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Fill missing symmetrical data with mirroring, calculate Procrustes alignments with or without scaling, and compute standard or vector correlation and covariance matrices (congruence coefficients) of 3D landmarks. Tolerates missing data for all analyses.
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2023-06-16 |
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r-pakpmics2014wm
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Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2014 Women (age 15-49 years) questionnaire data for Punjab, Pakistan (<http://www.mics.unicef.org/surveys>).
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2023-06-16 |
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r-pack
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public |
Functions to easily convert data to binary formats other programs/machines can understand.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-ordinallbm
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It implements functions for simulation and estimation of the ordinal latent block model (OLBM), as described in Corneli, Bouveyron and Latouche (2019).
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2023-06-16 |
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r-orddisp
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Estimate location-shift models or rating-scale models accounting for response styles (RSRS) for the regression analysis of ordinal responses.
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2023-06-16 |
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r-optimbase
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Provides a set of commands to manage an abstract optimization method. The goal is to provide a building block for a large class of specialized optimization methods. This package manages: the number of variables, the minimum and maximum bounds, the number of non linear inequality constraints, the cost function, the logging system, various termination criteria, etc...
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2023-06-16 |
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r-optextras
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Tools to assist in safely applying user generated objective and derivative function to optimization programs. These are primarily function minimization methods with at most bounds and masks on the parameters. Provides a way to check the basic computation of objective functions that the user provides, along with proposed gradient and Hessian functions, as well as to wrap such functions to avoid failures when inadmissible parameters are provided. Check bounds and masks. Check scaling or optimality conditions. Perform an axial search to seek lower points on the objective function surface. Includes forward, central and backward gradient approximation codes.
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2023-06-16 |
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r-ontologyindex
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Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017 <doi:10.1093/bioinformatics/btw763>.
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2023-06-16 |
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r-omisc
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Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi.org/10.1037/1082-989X.12.4.414>.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
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r-pdshiny
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Interactive shiny application for working with Probability Distributions. Calculations and Graphs are provided.
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2023-06-16 |
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r-pcensmix
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Functions for generating progressively Type-II censored data in a mixture structure and fitting models using a constrained EM algorithm. It can also create a progressive Type-II censored version of a given real dataset to be considered for model fitting.
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2023-06-16 |
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r-pbo
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Following the method of Bailey et al., computes for a collection of candidate models the probability of backtest overfitting, the performance degradation and probability of loss, and the stochastic dominance.
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2023-06-16 |
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r-pathlibr
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An OO Interface for path manipulation, emulating pythons "pathlib".
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2023-06-16 |
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r-patentsview
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Provides functions to simplify the 'PatentsView' API (<http://www.patentsview.org/api/doc.html>) query language, send GET and POST requests to the API's seven endpoints, and parse the data that comes back.
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2023-06-16 |
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r-partdsa
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A novel tool for generating a piecewise constant estimation list of increasingly complex predictors based on an intensive and comprehensive search over the entire covariate space.
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2023-06-16 |
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r-parentoffspring
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Conduct the Parent-Offspring Test Using Monomorphic SNP Markers. The similarity to the parents is computed for each offspring, and a plot of similarity for all offspring is produced. One can keep the offspring above some threshold for the similarity for further studies.
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2023-06-16 |
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r-parallelml
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By sampling your data, running the provided classifier on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular machine learning algorithm and possibly even more accurate predictions.
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2023-06-16 |
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r-parallelmap
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Unified parallelization framework for multiple back-end, designed for internal package and interactive usage. The main operation is parallel mapping over lists. Supports 'local', 'multicore', 'mpi' and 'BatchJobs' mode. Allows tagging of the parallel operation with a level name that can be later selected by the user to switch on parallel execution for exactly this operation.
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2023-06-16 |
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r-pakpmics2014hl
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Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2014 Household Listing questionnaire data for Punjab, Pakistan (<http://www.mics.unicef.org/surveys>).
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2023-06-16 |
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r-pairwised
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Pairing observations according to a chosen formula and facilitates bilateral analysis of the panel data. Paring is possible for observations, as well as for vectors of observations ordered with respect to time.
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2023-06-16 |
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r-pade
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Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
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2023-06-16 |
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r-packclassic
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This package comes to illustrate the book "Petit Manuel de Programmation Orientee Objet sous R"
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2023-06-16 |
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r-pacbpred
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This package is intended to perform estimation and prediction in high-dimensional additive models, using a sparse PAC-Bayesian point of view and a MCMC algorithm. The method is fully described in Guedj and Alquier (2013), 'PAC-Bayesian Estimation and Prediction in Sparse Additive Models', Electronic Journal of Statistics, 7, 264--291.
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2023-06-16 |
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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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2023-06-16 |
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r-ordfacreg
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In biomedical studies, researchers are often interested in assessing the association between one or more ordinal explanatory variables and an outcome variable, at the same time adjusting for covariates of any type. The outcome variable may be continuous, binary, or represent censored survival times. In the absence of a precise knowledge of the response function, using monotonicity constraints on the ordinal variables improves efficiency in estimating parameters, especially when sample sizes are small. This package implements an active set algorithm that efficiently computes such estimators.
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2023-06-16 |
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r-odr
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Calculate the optimal sample allocation that minimizes the variance of treatment effect in multilevel randomized trials under fixed budget and cost structure, perform power analyses with and without accommodating costs and budget. The references for proposed methods are: (1) Shen, Z. (in progress). Using optimal sample allocation to improve statistical precision and design efficiency for multilevel randomized trials. (unpublished doctoral dissertation). University of Cincinnati, Cincinnati, OH. (2) Shen, Z., & Kelcey, B. (revise & resubmit). Optimal sample allocation accounts for the full variation of sampling costs in cluster-randomized trials. Journal of Educational and Behavioral Statistics. (3) Shen, Z., & Kelcey, B. (2018, April). Optimal design of cluster randomized trials under condition- and unit-specific cost structures. Roundtable discussion presented at American Educational Research Association (AERA) annual conference. (4) Champely., S. (2018). pwr: Basic functions for power analysis (Version 1.2-2) [Software]. Available from <https://CRAN.R-project.org/package=pwr>.
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2023-06-16 |
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r-occ
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Generic function for estimating positron emission tomography (PET) neuroreceptor occupancies from the total volumes of distribution of a set of regions of interest. Fittings methods include the simple 'reference region' and 'ordinary least squares' (sometimes known as occupancy plot) methods, as well as the more efficient 'restricted maximum likelihood estimation'.
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2023-06-16 |
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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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2023-06-16 |
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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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2023-06-16 |
