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r-pstat
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Calculating Pst values to assess differentiation among populations from a set of quantitative traits is the primary purpose of such a package. The bootstrap method provides confidence intervals and distribution histograms of Pst. Variations of Pst in function of the parameter c/h^2 are studied as well. Finally, the package proposes different transformations especially to eliminate any variation resulting from allometric growth (calculation of residuals from linear regressions, Reist standardizations or Aitchison transformation).
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2025-03-25 |
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r-psoptim
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Particle swarm optimization - a basic variant.
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2025-03-25 |
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r-pso
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Provides an implementation of particle swarm optimisation consistent with the standard PSO 2007/2011 by Maurice Clerc. Additionally a number of ancillary routines are provided for easy testing and graphics.
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2025-03-25 |
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r-psi
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public |
This package contains functions to calculate the Specificity Index statistic, which can be used for comparative quantitative analysis to identify genes enriched in specific cell populations across a large number of profiles, as well as perform numerous post-processing operations. NOTE:Supplementary data (human & mouse expression sets, calculated pSI datasets, etc.) can be found in pSI.data package located at the following URL: http://genetics.wustl.edu/jdlab/psi_package/
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2025-03-25 |
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r-pseval
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Contains the core methods for the evaluation of principal surrogates in a single clinical trial. Provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation summary methods are provided, including print, summary, plot, and testing.
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2025-03-25 |
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r-psagraphics
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A collection of functions that primarily produce graphics to aid in a Propensity Score Analysis (PSA). Functions include: cat.psa and box.psa to test balance within strata of categorical and quantitative covariates, circ.psa for a representation of the estimated effect size by stratum, loess.psa that provides a graphic and loess based effect size estimate, and various balance functions that provide measures of the balance achieved via a PSA in a categorical covariate.
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2025-03-25 |
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r-prroc
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Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.
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2025-03-25 |
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r-provviz
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Displays provenance graphically for provenance collected by the 'rdt' or 'rdtLite' packages, or other tools providing compatible PROV JSON output. The exact format of the JSON created by 'rdt' and 'rdtLite' is described in <https://github.com/End-to-end-provenance/ExtendedProvJson>. More information about rdtLite and associated tools is available at <https://github.com/End-to-end-provenance/> and Barbara Lerner, Emery Boose, and Luis Perez (2018), Using Introspection to Collect Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
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2025-03-25 |
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r-provparser
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R functions to access provenance information collected by 'rdt' or 'rdtLite'. The information is stored inside a 'ProvInfo' object and can be accessed through a collection of functions that will return the requested data. The exact format of the JSON created by 'rdt' and 'rdtLite' is described in <https://github.com/End-to-end-provenance/ExtendedProvJson>.
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2025-03-25 |
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r-protr
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public |
Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download> for more information.
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2025-03-25 |
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r-proton
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'The Proton Game' is a console-based data-crunching game for younger and older data scientists. Act as a data-hacker and find Slawomir Pietraszko's credentials to the Proton server. You have to solve four data-based puzzles to find the login and password. There are many ways to solve these puzzles. You may use loops, data filtering, ordering, aggregation or other tools. Only basics knowledge of R is required to play the game, yet the more functions you know, the more approaches you can try. The knowledge of dplyr is not required but may be very helpful. This game is linked with the ,,Pietraszko's Cave'' story available at http://biecek.pl/BetaBit/Warsaw. It's a part of Beta and Bit series. You will find more about the Beta and Bit series at http://biecek.pl/BetaBit.
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2025-03-25 |
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r-protolidar
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PROTOLIDAR package contains functions for analyze the LIDAR scan of plants (grapevine) and make 3D maps in GRASS GIS.
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2025-03-25 |
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r-protoclass
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public |
Greedy algorithm described in Bien and Tibshirani (2011) Prototype Selection for Interpretable Classification. Annals of Applied Statistics. 5(4). 2403-2424
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2025-03-25 |
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r-proteomicdesign
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This package provides functions to identify the optimal solution that maximizes numbers of detectable differentiated proteins from a multi-stage clinical proteomic study.
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2025-03-25 |
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r-proteindescriptors
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An implementation of protein descriptors in R. These descriptors combine the advantages of being fixed length and including partial sequential effect: Various length of protein sequences are described with fixed length vectors that are suitable for machine learning algorithms, and still includes partial sequential effect.
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2025-03-25 |
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r-prosper
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An environment to simulate the development of annual plant populations with regard to population dynamics and genetics, especially herbicide resistance. It combines genetics on the individual level (Renton et al. 2011) with a stochastic development on the population level (Daedlow, 2015). Renton, M, Diggle, A, Manalil, S and Powles, S (2011) <doi:10.1016/j.jtbi.2011.05.010> Daedlow, Daniel (2015, doctoral dissertation: University of Rostock, Faculty of Agriculture and Environmental Sciences.)
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2025-03-25 |
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r-proscorertools
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Provides a reliable and flexible toolbox to score patient-reported outcome (PRO), Quality of Life (QOL), and other psychometric measures. The guiding philosophy is that scoring errors can be eliminated by using a limited number of well-tested, well-behaved functions to score PRO-like measures. The workhorse of the package is the 'scoreScale' function, which can be used to score most single-scale measures. It can reverse code items that need to be reversed before scoring and pro-rate scores for missing item data. Currently, three different types of scores can be output: summed item scores, mean item scores, and scores scaled to range from 0 to 100. The 'PROscorerTools' functions can be used to write new functions that score more complex measures. In fact, 'PROscorerTools' functions are the building blocks of the scoring functions in the 'PROscorer' package (which is a repository of functions that score specific commonly-used instruments). Users are encouraged to use 'PROscorerTools' to write scoring functions for their favorite PRO-like instruments, and to submit these functions for inclusion in 'PROscorer' (a tutorial vignette will be added soon). The long-term vision for the 'PROscorerTools' and 'PROscorer' packages is to provide an easy-to-use system to facilitate the incorporation of PRO measures into research studies in a scientifically rigorous and reproducible manner. These packages and their vignettes are intended to help establish and promote "best practices" for scoring and describing PRO-like measures in research.
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2025-03-25 |
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r-propscrrand
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Contains functions to run propensity-biased allocation to balance covariate distributions in sequential trials and propensity-constrained randomization to balance covariate distributions in trials with known baseline covariates at time of randomization. Currently only supports trials comparing two groups.
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2025-03-25 |
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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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2025-03-25 |
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r-propcis
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Computes two-sample confidence intervals for single, paired and independent proportions.
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2025-03-25 |
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r-promote
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public |
Deploy, maintain, and invoke predictive models using the 'Alteryx Promote' REST API. 'Alteryx Promote' is available at the URL: <https://www.alteryx.com/products/alteryx-promote>.
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2025-03-25 |
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r-promethee
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public |
Functions which can be used to support the Multicriteria Decision Analysis (MCDA) process involving multiple criteria, by PROMETHEE (Preference Ranking Organization METHod for Enrichment of Evaluations).
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2025-03-25 |
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r-proliferativeindex
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Provides functions for calculating and analyzing the proliferative index (PI) from an RNA-seq dataset. As described in Ramaker & Lasseigne, et al. bioRxiv, 2016 <doi:10.1101/063057>.
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2025-03-25 |
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r-projmgr
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public |
Provides programmatic access to 'GitHub' API with a focus on project management. Key functionality includes setting up issues and milestones from R objects or 'YAML' configurations, querying outstanding or completed tasks, and generating progress updates in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal, professional, or academic settings with an emphasis on streamlining the workflow of data analysis projects.
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2025-03-25 |
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r-projecttemplate
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Provides functions to automatically build a directory structure for a new R project. Using this structure, 'ProjectTemplate' automates data loading, preprocessing, library importing and unit testing.
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2025-03-25 |
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r-prognosticroc
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Prognostic ROC curve is an alternative graphical approach to represent the discriminative capacity of the marker: a receiver operating characteristic (ROC) curve by plotting 1 minus the survival in the high-risk group against 1 minus the survival in the low-risk group. This package contains functions to assess prognostic ROC curve. The user can enter the survival according to a model previously estimated or the user can also enter individual survival data for estimating the prognostic ROC curve by using Kaplan-Meier estimator. The area under the curve (AUC) corresponds to the probability that a patient in the low-risk group has a longer lifetime than a patient in the high-risk group. The prognostic ROC curve provides complementary information compared to survival curves. The AUC is assessed by using the trapezoidal rules. When survival curves do not reach 0, the prognostic ROC curve is incomplete and the extrapolations of the AUC are performed by assuming pessimist, optimist and non-informative situations.
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2025-03-25 |
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r-proftools
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public |
Tools for examining Rprof profile output.
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2025-03-25 |
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r-profr
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An alternative data structure and visual rendering for the profiling information generated by Rprof.
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2025-03-25 |
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r-profmem
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public |
A simple and light-weight API for memory profiling of R expressions. The profiling is built on top of R's built-in memory profiler ('utils::Rprofmem()'), which records every memory allocation done by R (also native code).
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2025-03-25 |
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r-profilelikelihood
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Provides profile likelihoods for a parameter of interest in commonly used statistical models. The models include linear models, generalized linear models, proportional odds models, linear mixed-effects models, and linear models for longitudinal responses fitted by generalized least squares. The package also provides plots for normalized profile likelihoods as well as the maximum profile likelihood estimates and the kth likelihood support intervals.
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2025-03-25 |
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r-prodigenr
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Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).
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2025-03-25 |
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r-processcontrol
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public |
Generate time series chart for individual values with mean and +/- 3 standard deviation lines and the corresponding mR chart with the upper control limit. Also execute the 8 Shewhart stability run tests and display the violations.
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2025-03-25 |
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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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2025-03-25 |
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r-probsvm
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This package provides multiclass conditional probability estimation for the SVM, which is distributional assumption free.
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2025-03-25 |
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r-probhat
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Computes nonparametric probability distributions (probability density functions, cumulative distribution functions and quantile functions) using kernel smoothing. Supports univariate, multivariate and conditional distributions, and weighted data (possibly useful mixed with fuzzy clustering or frequency data). Also, supports empirical continuous cumulative distribution functions and their inverses, and random number generation.
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2025-03-25 |
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r-probfda
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Probabilistic Fisher discriminant analysis (pFDA) is a probabilistic version of the popular and powerful Fisher linear discriminant analysis for dimensionality reduction and classification.
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2025-03-25 |
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r-probemod
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Contains functions that are useful for probing moderation effects (or interactions) including techniques such as pick-a-point (also known as spotlight analysis) and Johnson-Neyman (also known as floodlight analysis). Plot function is also provided to facilitate visualization of results from each of these techniques.
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2025-03-25 |
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r-pro
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Optogenetics is a new tool to study neuronal circuits that have been genetically modified to allow stimulation by flashes of light. This package implements the methodological framework, Point-process Response model for Optogenetics (PRO), for analyzing data from these experiments. This method provides explicit nonlinear transformations to link the flash point-process with the spiking point-process. Such response functions can be used to provide important and interpretable scientific insights into the properties of the biophysical process that governs neural spiking in response to optogenetic stimulation.
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2025-03-25 |
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r-prnsamplr
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Survey sampling using permanent random numbers (PRN's). A solution to the problem of unknown overlap between survey samples, which leads to a low precision in estimates when the survey is repeated or combined with other surveys. The PRN solution is to supply the U(0, 1) random numbers to the sampling procedure, instead of having the sampling procedure generate them. In Lindblom (2014) <doi:10.2478/jos-2014-0047>, and therein cited articles, it is shown how this is carried out and how it improves the estimates. This package supports two common fixed-size sampling procedures (simple random sampling and probability-proportional-to-size sampling) and includes a function for transforming the PRN's in order to control the sample overlap.
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2025-03-25 |
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r-privatelr
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Implements two differentially private algorithms for estimating L2-regularized logistic regression coefficients. A randomized algorithm F is epsilon-differentially private (C. Dwork, Differential Privacy, ICALP 2006 <DOI:10.1007/11681878_14>), if |log(P(F(D) in S)) - log(P(F(D') in S))| <= epsilon for any pair D, D' of datasets that differ in exactly one record, any measurable set S, and the randomness is taken over the choices F makes.
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2025-03-25 |
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r-prithulib
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Enables user to perform the following: 1. Roll 'n' number of die/dice (roll()). 2. Toss 'n' number of coin(s) (toss()). 3. Play the game of Rock, Paper, Scissors. 4. Choose 'n' number of card(s) from a pack of 52 playing cards (Joker optional).
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2025-03-25 |
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r-prism.forecast
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Implements Penalized Regression with Inferred Seasonality Module (PRISM) to generate forecast estimation of weekly unemployment initial claims using 'Google Trends' data. It includes required data and tools for backtesting the performance in 2007-2020.
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2025-03-25 |
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r-prioritylasso
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Fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block. Also offers options to deal with block-wise missingness in multi-omics data.
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2025-03-25 |
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r-prioritizrdata
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Conservation planning datasets for learning how to use the 'prioritizr' package <https://CRAN.R-project.org/package=prioritizr>.
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2025-03-25 |
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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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2025-03-25 |
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r-printr
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Extends the S3 generic function knit_print() in 'knitr' to automatically print some objects using an appropriate format such as Markdown or LaTeX. For example, data frames are automatically printed as tables, and the help() pages can also be rendered in 'knitr' documents.
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2025-03-25 |
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r-prinsimp
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Provides capabilities beyond principal components analysis to focus on finding structure in low variability subspaces. Constructs and plots simple basis vectors for pre-defined and user-defined measures of simplicity.
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2025-03-25 |
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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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2025-03-25 |
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r-prevederer
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Easy and efficient access to the API provided by 'Prevedere', an industry insights and predictive analytics company. Query and download indicators, models and workbenches built with 'Prevedere' for further analysis and reporting <https://www.prevedere.com/>.
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2025-03-25 |
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r-prettyr
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Functions for conventionally formatting descriptive stats, reshaping data frames and formatting R output as HTML.
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2025-03-25 |
