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r-cdrom
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Classification is based on the recently developed phylogenetic approach by Assis and Bachtrog (2013). The method classifies the evolutionary mechanisms retaining pairs of duplicate genes (conservation, neofunctionalization, subfunctionalization, or specialization) by comparing gene expression profiles of duplicate genes in one species to those of their single- copy ancestral genes in a sister species.
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2023-06-16 |
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r-cdlasso
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Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Regression
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2023-06-16 |
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r-cbird
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The clustering of binary data with reducing the dimensionality (CLUSBIRD) proposed by Yamamoto and Hayashi (2015) <doi:10.1016/j.patcog.2015.05.026>.
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2023-06-16 |
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r-cin
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Many experiments in neuroscience involve randomized and fast stimulation while the continuous outcome measures respond at much slower time scale, for example event-related fMRI. This package provide valid statistical tools with causal interpretation under these challenging settings, without imposing model assumptions.
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2023-06-16 |
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r-cec2005benchmark
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This package is a wrapper for the C implementation of the 25 benchmark functions for the CEC 2005 Special Session on Real-Parameter Optimization. The original C code by Santosh Tiwari and related documentation are available at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC-05/CEC05.htm.
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2023-06-16 |
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r-cityplot
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Input: a csv-file for each database table and a controlfile describing relations between tables. Output: An extended ER diagram
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2023-06-16 |
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r-cdvine
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Functions for statistical inference of canonical vine (C-vine) and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate as well as vine copula selection are provided. Models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are also included. Data is assumed to lie in the unit hypercube (so-called copula data).
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2023-06-16 |
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r-changepointshd
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This implements the methods developed in, L. Bybee and Y. Atchade. (2018). Contains a series of methods for estimating change-points given user specified black-box models. The methods include binary segmentation for multiple change-point estimation. For estimating each individual change-point the package includes simulated annealing, brute force, and, for Gaussian graphical models, an applications specific rank-one update implementation. Additionally, code for estimating Gaussian graphical models is included. The goal of this package is to allow for the efficient estimation of change-points in complicated models with high dimensional data.
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2023-06-16 |
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r-cdb
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A constant database is a data structure created by Daniel J. Bernstein in his cdb package. Its format consists on a sequence of (key,value)-pairs. This R package replicates the basic utilities for reading (cdbget) and writing (cdbdump) constant databases.
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2023-06-16 |
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r-care1
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The R package CARE1, the first part of the program CARE (Capture-Recapture) in http://chao.stat.nthu.edu.tw/softwareCE.html, can be used to analyze epidemiological data via sample coverage approach (Chao et al. 2001a). Based on the input of records from several incomplete lists (or samples) of individuals, the R package CARE1 provides output of population size estimate and related statistics.
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2023-06-16 |
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r-clrdag
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Provides MLEdag() for constrained maximum likelihood estimation and likelihood ratio test of a large directed acyclic graph. The algorithms are described in the paper by Li, Shen, and Pan (2019) <doi:10.1080/01621459.2019.1623042>.
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2023-06-16 |
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r-censregmod
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Fits univariate censored linear regression model under Normal or Student-t distribution
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2023-06-16 |
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r-ccchooser
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ccChooser can be used to developing and evaluation of core collections for germplasm collections (entire collection). This package used to develop a core collection for biological resources like genbanks. A core collection is defined as a sample of accessions that represent, with the lowest possible level of redundancy, the genetic diversity (the richness of gene or genotype categories) of the entire collection. The establishing a core collection that represents genetic diversity of the entire collection with minimum loss of its original diversity and minimum redundancies is an important problem for gene-banks curators and crop breeders. ccChooser establish core collection base on phenotypic data (agronomic, morphological, phenological).
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2023-06-16 |
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r-censnid
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Implements AS138, AS139.
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2023-06-16 |
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r-chemometricswithr
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Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011). Data used in the package are available from github.
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2023-06-16 |
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r-cgh
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Functions to analyze microarray comparative genome hybridization data using the Smith-Waterman algorithm
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2023-06-16 |
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r-clsocp
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This package provides and implementation of a one step smoothing newton method for the solution of second order cone programming problems, originally described by Xiaoni Chi and Sanyang Liu.
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2023-06-16 |
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r-cld3
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Google's Compact Language Detector 3 is a neural network model for language identification and the successor of 'cld2' (available from CRAN). The algorithm is still experimental and takes a novel approach to language detection with different properties and outcomes. It can be useful to combine this with the Bayesian classifier results from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
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2023-06-16 |
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r-cheb
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Discrete Linear Chebyshev Approximation
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2023-06-16 |
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r-cbsem
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The composites are linear combinations of their indicators in composite based structural equation models. Structural models are considered consisting of two blocks. The indicators of the exogenous composites are named by X, the indicators of the endogenous by Y. Reflective relations are given by arrows pointing from the composite to their indicators. Their values are called loadings. In a reflective-reflective scenario all indicators have loadings. Arrows are pointing to their indicators only from the endogenous composites in the formative-reflective scenario. There are no loadings at all in the formative-formative scenario. The covariance matrices are computed for these three scenarios. They can be used to simulate these models. These models can also be estimated and a segmentation procedure is included as well.
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2023-06-16 |
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r-carlit
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Functions to calculate and plot ecological quality ratios (EQR) as specified by Ballesteros et al. 2007.
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2023-06-16 |
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r-cents
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Fit censored time series
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2023-06-16 |
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r-cec2013
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This package provides R wrappers for the C implementation of 28 benchmark functions defined for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013. The focus of this package is to provide an open-source and multi-platform implementation of the CEC2013 benchmark functions, in order to make easier for researchers to test the performance of new optimization algorithms in a reproducible way. The original C code (Windows only) was provided by Jane Jing Liang, while GNU/Linux comments were made by Janez Brest. This package was gently authorised for publication on CRAN by Ponnuthurai Nagaratnam Suganthan. The official documentation is available at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC2013/CEC2013.htm. Bugs reports/comments/questions are very welcomed (in English, Spanish or Italian).
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2023-06-16 |
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r-cgraph
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Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various operations including basic arithmetic, trigonometry operations, and linear algebra operations. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
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2023-06-16 |
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r-censys
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The 'Censys' public search engine enables researchers to quickly ask questions about the hosts and networks that compose the Internet. Details on how 'Censys' was designed and how it is operated are available at <https://www.censys.io/about>. Both basic and extended research access queries are made available. More information on the SQL dialect used by the 'Censys' engine can be found at <https://cloud.google.com/bigquery/docs/reference/legacy-sql>.
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2023-06-16 |
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r-capwire
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Fits models from Miller et al. 2005 to estimate population sizes from natural populations. Several models are implemented. Package also includes functions to perform a likelihood ratio test to choose between models, perform parametric bootstrapping to obtain confidence intervals and multiple functions to simulate data.
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2023-06-16 |
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r-causalmgm
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Allows users to learn undirected and directed (causal) graphs over mixed data types (i.e., continuous and discrete variables). To learn a directed graph over mixed data, it first calculates the undirected graph (Sedgewick et al, 2016) and then it uses local search strategies to prune-and-orient this graph (Sedgewick et al, 2017). AJ Sedgewick, I Shi, RM Donovan, PV Benos (2016) <doi:10.1186/s12859-016-1039-0>. AJ Sedgewick, JD Ramsey, P Spirtes, C Glymour, PV Benos (2017) <arXiv:1704.02621>.
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2023-06-16 |
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r-catspec
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`ctab' creates (multiway) percentage tables. `sqtab' contains a set of functions for estimating models for square tables such as quasi-independence, symmetry, uniform association. Examples show how to use these models in a loglinear model using glm or in a multinomial logistic model using mlogit or clogit
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2023-06-16 |
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r-catchr
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R has a unique way of dealing with warnings, errors, messages, and other conditions, but it can often be troublesome to users coming from different programming backgrounds. The purpose of this package is to provide flexible and useful tools for handling R conditions with less hassle. In order to lower the barrier of entry, keep code clean and readable, and reduce the amount of typing required, `catchr` uses a very simple domain-specific language that simplifies things on the front-end. This package aims to maintain a continuous learning curve that lets new users jump straight in to condition-handling, while simultaneously offering depth and complexity for more advanced users.
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2023-06-16 |
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r-chi2x3way
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Provides two index partitions for three-way contingency tables: partition of the association measure chi-squared and of the predictability index tau under several representative hypotheses about the expected frequencies (hypothesized probabilities).
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2023-06-16 |
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r-cgdsr
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Provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC) at <www.cbioportal.org>.
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2023-06-16 |
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r-cblasr
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Provides the 'cblas.h' header file as C interface to the underlying internal 'BLAS' library in R. 'CBLAS' <https://www.netlib.org/blas/cblas.h> is a collection of wrappers originally written by Keita Teranishi and provides a C interface to the FORTRAN 'BLAS' library <https://www.netlib.org/blas/>. Note that as internal 'BLAS' library provided by R <https://svn.r-project.org/R/trunk/src/include/R_ext/BLAS.h> is used and only the double precision / double complex 'BLAS' routines are supported.
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2023-06-16 |
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r-citccmst
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This package implements the approach to assign tumor gene expression dataset to the 6 CIT Colon Cancer Molecular Subtypes described in Marisa et al 2013.
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2023-06-16 |
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r-cfestimatequantiles
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Estimate quantiles using formula (18) from http://www.jaschke-net.de/papers/CoFi.pdf (Yaschke; 2001)
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2023-06-16 |
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r-ccagfa
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Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
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2023-06-16 |
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r-captioner
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Provides a method for automatically numbering figures, tables, or other objects. Captions can be displayed in full, or as citations. This is especially useful for adding figures and tables to R markdown documents without having to numbering them manually.
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2023-06-16 |
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r-catnet
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Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
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2023-06-16 |
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r-citbcmst
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This package implements the approach to assign tumor gene expression dataset to the 6 CIT Breast Cancer Molecular Subtypes described in Guedj et al 2012.
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2023-06-16 |
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r-clues
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We developed the clues R package to provide functions for automatically estimating the number of clusters and getting the final cluster partition without any input parameter except the stopping rule for convergence. The package also provides functions to evaluate and compare the performances of partitions of a data set both numerically and graphically.
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2023-06-16 |
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r-chargetransport
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This package provides functions to compute Marcus, Marcus-Levich-Jortner or Landau-Zener charge transfer rates. These rates can then be used to perform kinetic Monte Carlo simulations to estimate charge carrier mobilities in molecular materials. The preparation of this package was supported by the the Fondazione Cariplo (PLENOS project, ref. 2011-0349).
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2023-06-16 |
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r-cernn
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An implementation of the covariance estimation method proposed in Chi and Lange (2014), "Stable estimation of a covariance matrix guided by nuclear norm penalties," Computational Statistics and Data Analysis 80:117-128.
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2023-06-16 |
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r-ccpop
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Tests of association between SNPs or pairs of SNPs and binary phenotypes, in case-control / case-population / case-control-population studies.
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2023-06-16 |
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r-cardiomodel
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Includes over 100 mixed-effects model structures describing the relationship between drug concentration and QT interval, heart rate/pulse rate or blood pressure. Given an exposure-response dataset, the tool fits each model structure to the observed data.
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2023-06-16 |
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r-cleanerr
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How to deal with missing data?Based on the concept of almost functional dependencies, a method is proposed to fill missing data, as well as help you see what data is missing. The user can specify a measure of error and how many combinations he wish to test the dependencies against, the closer to the length of the dataset, the more precise. But the higher the number, the more time it will take for the process to finish. If the program cannot predict with the accuracy determined by the user it shall not fill the data, the user then can choose to increase the error or deal with the data another way.
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2023-06-16 |
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r-cateselection
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A multi-factor dimensionality reduction based forward selection method for genetic association mapping.
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2023-06-16 |
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r-bioftf
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The main drawback of the most common biodiversity indices is that different measures may lead to different rankings among communities. This instrument overcomes this limit using some functional tools with the diversity profiles. In particular, the derivatives, the curvature, the radius of curvature, the arc length, and the surface area are proposed. The goal of this method is to interpret in detail the diversity profiles and obtain an ordering between different ecological communities on the basis of diversity. In contrast to the typical indices of diversity, the proposed method is able to capture the multidimensional aspect of biodiversity, because it takes into account both the evenness and the richness of the species present in an ecological community.
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2023-06-16 |
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r-blatr
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A wrapper around the 'Blat' command line SMTP mailer for Windows. 'Blat' is public domain software, but be sure to read the license before use. It can be found at the Blat website http://www.blat.net.
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2023-06-16 |
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r-bvenn
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This package implements a simple alternative to the traditional Venn diagram. It depicts each overlap as a separate bubble with area proportional to the overlap size. Relation of the bubbles to input sets is shown by their their arrangement.
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2023-06-16 |
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r-boottol
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Used to create bootstrap tolerance levels for the Kolmogorov-Smirnov (KS) statistic, the area under receiver operator characteristic curve (AUROC) statistic, and the Gini coefficient for each score cutoff. Also provides a bootstrap alternative to the Vasicek test.
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2023-06-16 |
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r-boostr
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boostr provides a modular framework that return the focus of ensemble learning back to 'learning' (instead of programming).
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2023-06-16 |
