|
r-plis
|
public |
PLIS is a multiple testing procedure for testing several groups of hypotheses. Linear dependency is expected from the hypotheses within the same group and is modeled by hidden Markov Models. It is noted that, for PLIS, a smaller p value does not necessarily imply more significance because of dependency among the hypotheses. A typical application of PLIS is to analyze genome wide association studies datasets, where SNPs from the same chromosome are treated as a group and exhibit strong linear genomic dependency.
|
2023-06-16 |
|
r-sabarsi
|
public |
Implements a new approach 'SABARSI' described in Wang et al., "A Statistical Approach of Background Removal and Spectrum Identification for SERS Data" (Unpublished). Sabarsi forms a pipeline for SERS (surface-enhanced Raman scattering) data analysis including background removal, signal detection, signal integration, and cross-experiment comparison. The background removal algorithm, the very first step of SERS data analysis, takes into account the change of background shape.
|
2023-06-16 |
|
r-rtype
|
public |
A strong type system for R which supports symbol declaration and assignment with type checking and condition checking.
|
2023-06-16 |
|
r-rtrim
|
public |
The TRIM model is widely used for estimating growth and decline of animal populations based on (possibly sparsely available) count data. The current package is a reimplementation of the original TRIM software developed at Statistics Netherlands by Jeroen Pannekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d> for more information about TRIM.
|
2023-06-16 |
|
r-rtape
|
public |
Storing huge data in RData format causes problems because of the necessity to load the whole file to the memory in order to access and manipulate objects inside such file; rtape is a simple solution to this problem. The package contains several wrappers of R built-in serialize/unserialize mechanism allowing user to quickly append objects to a tape-like file and later iterate over them requiring only one copy of each stored object to reside in memory a time.
|
2023-06-16 |
|
r-rpnf
|
public |
A set of functions to analyze and print the development of a commodity using the Point and Figure (P&F) approach. A P&F processor can be used to calculate daily statistics for the time series. These statistics can be used for deeper investigations as well as to create plots. Plots can be generated as well known X/O Plots in plain text format, and additionally in a more graphical format.
|
2023-06-16 |
|
r-roperators
|
public |
Provides string arithmetic, reassignment operators, logical operators that handle missing values, and extra logical operators such as floating point equality and all or nothing. The intent is to allow R users to write code that is easier to read, write, and maintain while providing a friendlier experience to new R users from other language backgrounds (such as 'Python') who are used to concepts such as x += 1 and 'foo' + 'bar'.
|
2023-06-16 |
|
r-robrsvd
|
public |
This package provides the function to calculate SVD, regularized SVD, robust SVD and robust regularized SVD method. The robust SVD methods use alternating iteratively reweighted least squares methods. The regularized SVD uses generalized cross validation to choose the optimal smoothing parameters.
|
2023-06-16 |
|
r-robcor
|
public |
Robust pairwise correlations based on estimates of scale, particularly on "FastQn" one-step M-estimate.
|
2023-06-16 |
|
r-rnpn
|
public |
Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.
|
2023-06-16 |
|
r-rmeta
|
public |
Functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. Draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.
|
2023-06-16 |
|
r-rmaf
|
public |
Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
|
2023-06-16 |
|
r-rlmdatadriven
|
public |
Data driven approach for robust regression estimation in homoscedastic and heteroscedastic context. See Wang et al. (2007), <doi:10.1198/106186007X180156> regarding homoscedastic framework.
|
2023-06-16 |
|
r-rleafangle
|
public |
Leaf angle distribution is described by a number of functions (e.g. ellipsoidal, Beta and rotated ellipsoidal). The parameters of leaf angle distributions functions are estimated through different empirical relationship. This package includes estimations of parameters of different leaf angle distribution function, plots and evaluates leaf angle distribution functions, calculates extinction coefficients given leaf angle distribution. Reference: Wang(2007)<doi:10.1016/j.agrformet.2006.12.003>.
|
2023-06-16 |
|
r-riverplot
|
public |
Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings.
|
2023-06-16 |
|
r-risksetroc
|
public |
Compute time-dependent Incident/dynamic accuracy measures (ROC curve, AUC, integrated AUC )from censored survival data under proportional or non-proportional hazard assumption of Heagerty & Zheng (Biometrics, Vol 61 No 1, 2005, PP 92-105).
|
2023-06-16 |
|
r-ridgefusion
|
public |
This package implements ridge fusion methodology for inverse covariance matrix estimation for use in quadratic discriminant analysis. The package also contains function for model based clustering using ridge fusion for inverse matrix estimation, as well as tuning parameter selection functions. We have also implemented QDA using joint inverse covariance estimation.
|
2023-06-16 |
|
r-rgrass7
|
public |
Interpreted interface between 'GRASS' 7 geographical information system and R, based on starting R from within the 'GRASS' 'GIS' environment, or running free-standing R in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the R command line. This package may not be used for 'GRASS' 6, for which 'spgrass6' should be used.
|
2023-06-16 |
|
r-rgoogleanalytics
|
public |
Provides functions for accessing and retrieving data from the Google Analytics API.
|
2023-06-16 |
|
r-rgammagamma
|
public |
This package implements a Gamma convolution model for background correction.
|
2023-06-16 |
|
r-ress
|
public |
Contains three functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.essentia' takes an Essentia script and captures the output csv data into R, where you can save the output to a dataframe or stream it directly into additional analysis. 'capture.essentia' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
|
2023-06-16 |
|
r-reliability
|
public |
Functions for estimating parameters in software reliability models. Only infinite failure models are implemented so far.
|
2023-06-16 |
|
r-relatable
|
public |
Functions to safely map from a vector of keys to a vector of values, determine properties of a given relation, or ensure a relation conforms to a given type, such as many-to-many, one-to-many, injective, surjective, or bijective. Permits default return values for use similar to a vectorised switch statement, as well as safely handling large vectors, NAs, and duplicate mappings.
|
2023-06-16 |
|
r-relabeloadings
|
public |
In confirmatory factor analysis (CFA), structural constraints typically ensure that the model is identified up to all possible reflections, i.e., column sign changes of the matrix of loadings. Such reflection invariance is problematic for Bayesian CFA when the reflection modes are not well separated in the posterior distribution. Imposing rotational constraints -- fixing some loadings to be zero or positive in order to pick a factor solution that corresponds to one reflection mode -- may not provide a satisfactory solution for Bayesian CFA. The function 'relabel' uses the relabeling algorithm of Erosheva and Curtis to correct for sign invariance in MCMC draws from CFA models. The MCMC draws should come from Bayesian CFA models that are fit without rotational constraints.
|
2023-06-16 |
|
r-refmanager
|
public |
Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.
|
2023-06-16 |
|
r-reffreeewas
|
public |
Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption. The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.
|
2023-06-16 |
|
r-reca
|
public |
Relevant Component Analysis (RCA) tries to find a linear transformation of the feature space such that the effect of irrelevant variability is reduced in the transformed space.
|
2023-06-16 |
|
r-read.gb
|
public |
Opens complete record(s) with .gb extension from the NCBI/GenBank Nucleotide database and returns a list containing shaped record(s). These kind of files contains detailed records of DNA samples (locus, organism, type of sequence, source of the sequence...). An example of record can be found at <https://www.ncbi.nlm.nih.gov/nuccore/HE799070>.
|
2023-06-16 |
|
r-rcreds
|
public |
Tools to write a list of credentials to an encrypted file and later read from that file into R. The goal is to have a useful alternative to including username/passwords as part of a script or even stored in the clear in a separate text file. Additional tools provided which are specific for connecting to a database.
|
2023-06-16 |
|
r-rcppxptrutils
|
public |
Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
|
2023-06-16 |
|
r-rconics
|
public |
Solve some conic related problems (intersection of conics with lines and conics, arc length of an ellipse, polar lines, etc.).
|
2023-06-16 |
|
r-rcarto
|
public |
This package makes some maps using shapefiles and dataframes. Five kinds of maps are available : proportionnal circles, proportionnal circles colored by a discretized quantitative variable, proportionnal circles colored by the modalities of a qualitative variable, choropleth and typology.
|
2023-06-16 |
|
r-rca
|
public |
Relational Class Analysis (RCA) is a method for detecting heterogeneity in attitudinal data (as described in Goldberg A., 2011, Am. J. Soc, 116(5)).
|
2023-06-16 |
|
r-rbenchmark
|
public |
rbenchmark is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.
|
2023-06-16 |
|
r-rateratio.test
|
public |
A function which performs exact rate ratio tests and returns an object of class htest.
|
2023-06-16 |
|
r-rainfallerosivityfactor
|
public |
Determination of rainfall-runoff erosivity factor.
|
2023-06-16 |
|
r-radjust
|
public |
Calculates adjusted p-values for the null hypothesis of no replicability across studies for two study designs: (i) a primary and follow-up study, where the features in the follow-up study are selected from the primary study, as described in Bogomolov and Heller (2013) <doi:10.1080/01621459.2013.829002> and Heller, Bogomolov and Benjamini (2014) <doi:10.1073/pnas.1314814111>; (ii) two independent studies, where the features for replicability are first selected in each study separately, as described in Bogomolov and Heller (2018) <doi:10.1093/biomet/asy029>. The latter design is the one encountered in a typical meta-analysis of two studies, but the inference is for replicability rather than for identifying the features that are non-null in at least one study.
|
2023-06-16 |
|
r-radarchart
|
public |
Create interactive radar charts using the 'Chart.js' 'JavaScript' library and the 'htmlwidgets' package. 'Chart.js' <http://www.chartjs.org/> is a lightweight library that supports several types of simple chart using the 'HTML5' canvas element. This package provides an R interface specifically to the radar chart, sometimes called a spider chart, for visualising multivariate data.
|
2023-06-16 |
|
r-qdapregex
|
public |
A collection of regular expression tools associated with the 'qdap' package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.
|
2023-06-16 |
|
r-qcv
|
public |
Primarily, the 'qcv' package computes key indices related to the Quantifying Construct Validity procedure (QCV; Westen & Rosenthal, 2003 <doi:10.1037/0022-3514.84.3.608>; see also Furr & Heuckeroth, in press). The qcv() function is the heart of the 'qcv' package, but additional functions in the package provide useful ancillary information related to the QCV procedure.
|
2023-06-16 |
|
r-purging
|
public |
Simple method of purging independent variables of mediating effects. First, regress the direct variable on the indirect variable. Then, used the stored residuals as the new purged (direct) variable in the updated specification. This purging process allows for use of a new direct variable uncorrelated with the indirect variable. Please cite the method and/or package using Waggoner, Philip D. (2018) <doi:10.1177/1532673X18759644>.
|
2023-06-16 |
|
r-provparser
|
public |
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>.
|
2023-06-16 |
|
r-prosper
|
public |
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.)
|
2023-06-16 |
|
r-promethee
|
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).
|
2023-06-16 |
|
r-projmgr
|
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.
|
2023-06-16 |
|
r-probhat
|
public |
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.
|
2023-06-16 |
|
r-prnsamplr
|
public |
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.
|
2023-06-16 |
|
r-prioritizrdata
|
public |
Conservation planning data sets for learning how to use the 'prioritizr' package <https://CRAN.R-project.org/package=prioritizr>.
|
2023-06-16 |
|
r-prettygraphs
|
public |
Simple and crisp publication-quality graphics for the ExPosition family of packages. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.
|
2023-06-16 |
|
r-pracma
|
public |
Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
|
2023-06-16 |
