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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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2023-06-16 |
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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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2023-06-16 |
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r-propscrrand
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This package 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 this package only supports trials comparing two groups.
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2023-06-16 |
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r-proftools
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public |
Tools for examining Rprof profile output.
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2023-06-16 |
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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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2023-06-16 |
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r-powernormal
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Miscellaneous functions for a descriptive analysis and initial Bayesian and classical inference for the power parameter of the the Power Normal (PN) distribution. This miscellaneous will be extend for more distributions into the power family and the three-parameter model.
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2023-06-16 |
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r-portsort
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public |
Designed to aid both academic researchers and asset managers in conducting factor based portfolio sorts. Provides functionality to sort assets into portfolios for up to three factors via a conditional or unconditional sorting procedure.
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2023-06-16 |
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r-polytrend
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This algorithm classifies the trends into linear, quadratic, cubic, concealed and no-trend types. The "concealed trends" are those trends that possess quadratic or cubic forms, but the net change from the start of the time period to the end of the time period hasn't been significant. The "no-trend" category includes simple linear trends with statistically in-significant slope coefficient.
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2023-06-16 |
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r-plotcontour
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This function plots a contour line with a user-defined probability and tightness of fit.
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2023-06-16 |
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r-piper
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public |
Provides various styles of function chaining methods: Pipe operator, Pipe object, and pipeline function, each representing a distinct pipeline model yet sharing almost a common set of features: A value can be piped to the first unnamed argument of a function and to dot symbol in an enclosed expression. The syntax is designed to make the pipeline more readable and friendly to a wide range of operations.
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2023-06-16 |
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r-rzeit2
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Interface to gather newspaper articles from 'DIE ZEIT' and 'ZEIT ONLINE', based on a multilevel query <http://developer.zeit.de/>. A personal API key is required for usage.
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2023-06-16 |
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r-rxshrink
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public |
Identify and display TRACEs for a specified shrinkage path and determine the extent of shrinkage most likely, under normal distribution theory, to produce an optimal reduction in MSE Risk in estimates of regression (beta) coefficients. Alternative estimates are also provided when ill-conditioned (nearly multicollinear) models yield OLS estimates with "wrong" numerical signs.
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2023-06-16 |
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r-rtwalk
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The 't-walk' is a general-purpose MCMC sampler for arbitrary continuous distributions that requires no tuning.
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2023-06-16 |
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r-rtensor
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public |
A set of tools for creation, manipulation, and modeling of tensors with arbitrary number of modes. A tensor in the context of data analysis is a multidimensional array. rTensor does this by providing a S4 class 'Tensor' that wraps around the base 'array' class. rTensor provides common tensor operations as methods, including matrix unfolding, summing/averaging across modes, calculating the Frobenius norm, and taking the inner product between two tensors. Familiar array operations are overloaded, such as index subsetting via '[' and element-wise operations. rTensor also implements various tensor decomposition, including CP, GLRAM, MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements transpose, t-product, and t-SVD, as defined in Kilmer et al. (2013). Some auxiliary functions include the Khatri-Rao product, Kronecker product, and the Hamadard product for a list of matrices.
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2023-06-16 |
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r-rtauchen
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public |
Discretize AR(1) process following Tauchen (1986) <http://www.sciencedirect.com/science/article/pii/0165176586901680>. A discrete Markov chain that approximates in the sense of weak convergence a continuous-valued univariate Autoregressive process of first order is generated. It is a popular method used in economics and in finance.
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2023-06-16 |
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r-rsps
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public |
Provides functions for estimating power or sample size for RNA-Seq studies. Empirical approach is used and the data is assumed to be count in nature. The underlying distribution of data is assumed to be Poisson or negative binomial. The package contains 6 function; 4 functions provide estimates of sample size or power for Poisson and Negative Binomial distribution; 2 functions provide plots of power for given sample size or sample size for given power.
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2023-06-16 |
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r-rsoi
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public |
Downloads Southern Oscillation Index, Oceanic Nino Index, North Pacific Gyre Oscillation data, North Atlantic Oscillation and Arctic Oscillation. Data sources are described in the README file.
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2023-06-16 |
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r-rpaci
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public |
Analysis of corneal data obtained from a Placido disk corneal topographer with calculation of irregularity indices. A corneal topographer is an ophthalmic clinical device that obtains measurements in the cornea (the anterior part of the eye). A Placido disk corneal topographer makes use of the Placido disk (Rowsey et al. (1981), <doi:10.1001/archopht.1981.03930011093022>, Rand et al. (1997), <doi:10.1016/S0886-3350(99)00355-7>), which produce a circular pattern of measurement nodes. The raw information measured by such a topographer is used by practitioners to analyze curvatures, to study optical aberrations, or to diagnose specific conditions of the eye. The rPACI package allows the calculation of the corneal irregularity indices described in Ramos-Lopez et al. (2013), <doi:10.1097/OPX.0b013e3182843f2a>, and that were firstly introduced in Ramos-Lopez et al. (2011), <doi:10.1097/OPX.0b013e3182843f2a>. It provides a simple interface to read corneal topography data files as exported by a typical Placido disk topographer, to compute the irregularity indices mentioned before, and to display summary plots that are easy to interpret for a clinician.
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2023-06-16 |
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r-rowr
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public |
Provides utilities which interact with all R objects as if they were arranged in rows. It allows more consistent and predictable output to common functions, and generalizes a number of utility functions to to be failsafe with any number and type of input objects.
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2023-06-16 |
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r-rotationforest
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Fit and deploy rotation forest models ("Rodriguez, J.J., Kuncheva, L.I., 2006. Rotation forest: A new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28, 1619-1630 <doi:10.1109/TPAMI.2006.211>") for binary classification. Rotation forest is an ensemble method where each base classifier (tree) is fit on the principal components of the variables of random partitions of the feature set.
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2023-06-16 |
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r-rodm
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This package implements an interface to Oracle Data Mining (ODM). It provides an ideal environment for rapid development of demos and proof of concept data mining studies. It facilitates the prototyping of vertical applications and makes ODM and the RDBMS environment easily accessible to statisticians and data analysts familiar with R but not fluent in SQL or familiar with the database environment. It also facilitates the benchmarking and testing of ODM functionality including the production of summary statistics, performance metrics and graphics. It enables the scripting and control of production data mining methodologies from a high-level environment. Oracle Data Mining (ODM) is an option of Oracle Relational Database Management System (RDBMS) Enterprise Edition (EE). It contains several data mining and data analysis algorithms for classification, prediction, regression, clustering, associations, feature selection, anomaly detection, feature extraction, and specialized analytics. It provides means for the creation, management and operational deployment of data mining models inside the database environment. For more information consult the entry for "Oracle Data Mining" in Wikipedia (en.wikipedia.org).
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2023-06-16 |
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r-robustrankaggreg
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public |
Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation (Kolde et. al in preparation) and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
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2023-06-16 |
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r-rnentropy
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An implementation of a method based on information theory devised for the identification of genes showing a significant variation of expression across multiple conditions. Given expression estimates from any number of RNA-Seq samples and conditions it identifies genes or transcripts with a significant variation of expression across all the conditions studied, together with the samples in which they are over- or under-expressed. Zambelli et al. (2018) <doi:10.1093/nar/gky055>.
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2023-06-16 |
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r-rkum
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public |
Robust kernel center matrix, robust kernel cross-covariance operator for kernel unsupervised methods, kernel canonical correlation analysis, influence function of identifying significant outliers or atypical objects from multimodal datasets. Alam, M. A, Fukumizu, K., Wang Y.-P. (2018) <doi:10.1016/j.neucom.2018.04.008>. Alam, M. A, Calhoun, C. D., Wang Y.-P. (2018) <doi:10.1016/j.csda.2018.03.013>.
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2023-06-16 |
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r-rgift
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public |
This package provides some functions to create quizzes in the GIFT format. This format is used by several Virtual Learning Environments such as Moodle.
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2023-06-16 |
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r-rfordummies
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Contains all the code examples in the book "R for Dummies" (2nd edition) by Andrie de Vries and Joris Meys. You can view the table of contents as well as the sample code for each chapter.
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2023-06-16 |
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r-rforcecom
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public |
Insert, update, retrieve, delete and bulk operate datasets with a SaaS based CRM Salesforce.com and a PaaS based application platform Force.com from R.
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2023-06-16 |
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r-rflptools
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public |
RFLPtools provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).
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2023-06-16 |
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r-repo
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public |
A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with rich annotations, including corresponding code chunks, and easily searched and retrieved.
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2023-06-16 |
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r-records
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public |
Functions for generating k-record values and k-record times
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2023-06-16 |
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r-reat
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public |
Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
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2023-06-16 |
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r-rearrangement
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The rearrangement operator (Hardy, Littlewood, and Polya 1952) for univariate, bivariate, and trivariate point estimates of monotonic functions. The package additionally provides a function that creates simultaneous confidence intervals for univariate functions and applies the rearrangement operator to these confidence intervals.
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2023-06-16 |
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r-readoffice
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Reads in text from 'unstructured' modern Microsoft Office files (XML based files) such as Word and PowerPoint. This does not read in structured data (from Excel or Access) as there are many other great packages to that do so already.
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2023-06-16 |
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r-rclipboard
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Leverages the functionality of 'clipboard.js', a JavaScript library for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com> for more information), and provides a reactive copy-to-clipboard UI button component, called 'rclipButton', for 'shiny' R applications.
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2023-06-16 |
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r-rclean
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public |
To create clearer, more concise code provides this toolbox helps coders to isolate the essential parts of a script that produces a chosen result, such as an object, tables and figures written to disk and even warnings and errors. This work was funded by US National Science Foundation grant SSI-1450277 for applications of End-to-End Data Provenance.
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2023-06-16 |
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r-rcheology
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public |
Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
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2023-06-16 |
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r-rbtc
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public |
Implementation of the RPC-JSON API for Bitcoin and utility functions for address creation and content analysis of the blockchain.
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2023-06-16 |
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r-rap
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public |
To find the reversal association between variables.
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2023-06-16 |
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r-rankresponse
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public |
Methods for ranking responses of a single response question or a multiple response question
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2023-06-16 |
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r-rampath
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public |
We rewrite of RAMpath software developed by John McArdle and Steven Boker as an R package. In addition to performing regular SEM analysis through the R package lavaan, RAMpath has unique features. First, it can generate path diagrams according to a given model. Second, it can display path tracing rules through path diagrams and decompose total effects into their respective direct and indirect effects as well as decompose variance and covariance into individual bridges. Furthermore, RAMpath can fit dynamic system models automatically based on latent change scores and generate vector field plots based upon results obtained from a bivariate dynamic system. Starting version 0.4, RAMpath can conduct power analysis for both univariate and bivariate latent change score models.
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2023-06-16 |
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r-radwords
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Aims at loading Google Adwords data into R. Adwords is an online advertising service that enables advertisers to display advertising copy to web users (see <https://developers.google.com/adwords/> for more information). Therefore the package implements three main features. First, the package provides an authentication process for R with the Google Adwords API (see <https://developers.google.com/adwords/api/> for more information) via OAUTH2. Second, the package offers an interface to apply the Adwords query language in R and query the Adwords API with ad-hoc reports. Third, the received data are transformed into suitable data formats for further data processing and data analysis.
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2023-06-16 |
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r-r2pmml
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public |
R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>, which converts R models to Predictive Model Markup Language (PMML).
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2023-06-16 |
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r-r2dgc
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public |
Provides functions for aligning 2D gas chromatography mass spectrometry derived metabolite peaks obtained from primary processing and generates an alignment table that allows for a comparison of common peaks across samples and metabolite identification. Publication describing the package in detail is available at the following citation: Ryne C. Ramaker, Emily Gordon, Sara J. Cooper (2017) <doi:10.1101/179168>.
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2023-06-16 |
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r-quantilegrader
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Implementation of the food safety restaurant grading system adopted by Public Health - Seattle & King County (see Ashwood, Z.C., Elias, B., and Ho. D.E. "Improving the Reliability of Food Safety Disclosure: A Quantile Adjusted Restaurant Grading System for Seattle-King County" (working paper)). As reported in the accompanying paper, this package allows jurisdictions to easily implement refinements that address common challenges with unadjusted grading systems. First, in contrast to unadjusted grading, where the most recent single routine inspection is the primary determinant of a grade, grading inputs are allowed to be flexible. For instance, it is straightforward to base the grade on average inspection scores across multiple inspection cycles. Second, the package can identify quantile cutoffs by inputting substantively meaningful regulatory thresholds (e.g., the proportion of establishments receiving sufficient violation points to warrant a return visit). Third, the quantile adjustment equalizes the proportion of establishments in a flexible number of grading categories (e.g., A/B/C) across areas (e.g., ZIP codes, inspector areas) to account for inspector differences. Fourth, the package implements a refined quantile adjustment that addresses two limitations with the stats::quantile() function when applied to inspection score datasets with large numbers of score ties. The quantile adjustment algorithm iterates over quantiles until, over all restaurants in all areas, grading proportions are within a tolerance of desired global proportions. In addition the package allows a modified definition of "quantile" from "Nearest Rank". Instead of requiring that at least p[1]% of restaurants receive the top grade and at least (p[1]+p[2])% of restaurants receive the top or second best grade for quantiles p, the algorithm searches for cutoffs so that as close as possible p[1]% of restaurants receive the top grade, and as close as possible to p[2]% of restaurants receive the second top grade.
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2023-06-16 |
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r-qrmdata
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Various data sets (stocks, stock indices, constituent data, FX, zero-coupon bond yield curves, volatility, commodities) for Quantitative Risk Management practice.
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2023-06-16 |
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r-qlearning
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Implements Q-Learning, a model-free form of reinforcement learning, described in work by Strehl, Li, Wiewiora, Langford & Littman (2006) <doi:10.1145/1143844.1143955>.
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2023-06-16 |
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r-qdcomparison
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Allows practitioners to determine (i) if two univariate distributions (which can be continuous, discrete, or even mixed) are equal, (ii) how two distributions differ (shape differences, e.g., location, scale, etc.), and (iii) where two distributions differ (at which quantiles), all using nonparametric LP statistics. The primary reference is Jungreis, D. (2019, Technical Report).
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2023-06-16 |
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r-pumilior
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R package to query and get data out of a Pumilio sound archive system (http://ljvillanueva.github.io/pumilio/).
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2023-06-16 |
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r-pte
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We provide inference for personalized medicine models. Namely, we answer the questions: (1) how much better does a purported personalized recommendation engine for treatments do over a business-as-usual approach and (2) is that difference statistically significant?
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2023-06-16 |
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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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2023-06-16 |
