Package Name | Access | Summary | Updated |
---|---|---|---|

r-copula | public | Classes (S4) of commonly used elliptical, Archimedean, extreme value and some more copula families. Methods for density, distribution, random number generation, bivariate dependence measures, perspective and contour plots. Fitting copula models including variance estimates. | 2019-07-21 |

r-cooccur | public | This R package applies the probabilistic model of species co-occurrence (Veech 2013) to a set of species distributed among a set of survey or sampling sites. The algorithm calculates the observed and expected frequencies of co-occurrence between each pair of species. The expected frequency is based on the distribution of each species being random and independent of the other species. The analysis returns the probabilities that a more extreme (either low or high) value of co-occurrence could have been obtained by chance. The package also includes functions for visualizing species co-occurrence results and preparing data for downstream analyses. | 2019-07-21 |

r-coxphf | public | Implements Firth's penalized maximum likelihood bias reduction method for Cox regression which has been shown to provide a solution in case of monotone likelihood (nonconvergence of likelihood function). The program fits profile penalized likelihood confidence intervals which were proved to outperform Wald confidence intervals. | 2019-07-21 |

r-coxboost | public | This package provides routines for fitting Cox models by likelihood based boosting for a single endpoint or in presence of competing risks | 2019-07-21 |

r-coxme | public | Cox proportional hazards models containing Gaussian random effects, also known as frailty models. | 2019-07-21 |

r-cvxbiclustr | public | An iterative algorithm for solving a convex formulation of the biclustering problem. | 2019-07-21 |

r-crf | public | Implements modeling and computational tools for conditional random fields (CRF) model as well as other probabilistic undirected graphical models of discrete data with pairwise and unary potentials. | 2019-07-21 |

r-contrast | public | One degree of freedom contrasts for lm, glm, gls, and geese objects. | 2019-07-21 |

r-corrr | public | A tool for exploring correlations. It makes it possible to easily perform routine tasks when exploring correlation matrices such as ignoring the diagonal, focusing on the correlations of certain variables against others, or rearranging and visualising the matrix in terms of the strength of the correlations. | 2019-07-21 |

r-corrgram | public | Calculates correlation of variables and displays the results graphically. Included panel functions can display points, shading, ellipses, and correlation values with confidence intervals. See Friendly (2002) <doi:10.1198/000313002533>. | 2019-07-21 |

r-corrplot | public | A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. | 2019-07-21 |

r-ddpcr | public | An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R. | 2019-07-21 |

r-dbplot | public | Leverages 'dplyr' to process the calculations of a plot inside a database. This package provides helper functions that abstract the work at three levels: outputs a 'ggplot', outputs the calculations, outputs the formula needed to calculate bins. | 2019-07-21 |

r-d3heatmap | public | Create interactive heat maps that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a cell to show details, drag a rectangle to zoom, and click row/column labels to highlight. | 2019-07-21 |

r-ctv | public | Infrastructure for task views to CRAN-style repositories: Querying task views and installing the associated packages (client-side tools), generating HTML pages and storing task view information in the repository (server-side tools). | 2019-07-21 |

r-demerelate | public | Functions to calculate pairwise relatedness on diploid genetic datasets. Different estimators for relatedness can be combined with information on geographical distances. Information on heterozygosity, allele- and genotype diversity as well as genetic F-statistics are provided for each population. | 2019-07-21 |

r-dendsort | public | An implementation of functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization. | 2019-07-21 |

r-default | public | A simple syntax to change the default values for function arguments, whether they are in packages or defined locally. | 2019-07-21 |

libgdal | public | The Geospatial Data Abstraction Library (GDAL) | 2019-07-21 |

r-dendroextras | public | Provides extra functions to manipulate dendrograms that build on the base functions provided by the 'stats' package. The main functionality it is designed to add is the ability to colour all the edges in an object of class 'dendrogram' according to cluster membership i.e. each subtree is coloured, not just the terminal leaves. In addition it provides some utility functions to cut 'dendrogram' and 'hclust' objects and to set/get labels. | 2019-07-21 |

r-desctools | public | A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well. | 2019-07-21 |

r-dismo | public | Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites and the environment at these sites. | 2019-07-21 |

r-densityclust | public | An improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100, 000 samples) very efficiently. It was initially implemented by Thomas Lin Pedersen, with inputs from Sean Hughes and later improved by Xiaojie Qiu to handle large datasets with kNNs. | 2019-07-21 |

r-diffusr | public | Implementation of network diffusion algorithms such as heat diffusion or Markov random walks. Network diffusion algorithms generally spread information in the form of node weights along the edges of a graph to other nodes. These weights can for example be interpreted as temperature, an initial amount of water, the activation of neurons in the brain, or the location of a random surfer in the internet. The information (node weights) is iteratively propagated to other nodes until a equilibrium state or stop criterion occurs. | 2019-07-21 |

r-dppackage | public | Functions to perform inference via simulation from the posterior distributions for Bayesian nonparametric and semiparametric models. Although the name of the package was motivated by the Dirichlet Process prior, the package considers and will consider other priors on functional spaces. So far, DPpackage includes models considering Dirichlet Processes, Dependent Dirichlet Processes, Dependent Poisson- Dirichlet Processes, Hierarchical Dirichlet Processes, Polya Trees, Linear Dependent Tailfree Processes, Mixtures of Triangular distributions, Random Bernstein polynomials priors and Dependent Bernstein Polynomials. The package also includes models considering Penalized B-Splines. Includes semiparametric models for marginal and conditional density estimation, ROC curve analysis, interval censored data, binary regression models, generalized linear mixed models, IRT type models, and generalized additive models. Also contains functions to compute Pseudo-Bayes factors for model comparison, and to elicitate the precision parameter of the Dirichlet Process. To maximize computational efficiency, the actual sampling for each model is done in compiled FORTRAN. The functions return objects which can be subsequently analyzed with functions provided in the 'coda' package. | 2019-07-21 |

r-distrex | public | Extends package 'distr' by functionals, distances, and conditional distributions. | 2019-07-21 |

r-depmixs4 | public | Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models. | 2019-07-21 |

r-divemove | public | Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided. | 2019-07-21 |

r-distances | public | Provides tools for constructing, manipulating and using distance metrics. | 2019-07-21 |

r-diffusionmap | public | Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model. | 2019-07-21 |

r-diffr | public | An R interface to the 'codediff' JavaScript library (a copy of which is included in the package, see <https | 2019-07-21 |

r-dosnow | public | Provides a parallel backend for the %dopar% function using Luke Tierney's snow package. | 2019-07-21 |

r-discriminer | public | Functions for Discriminant Analysis and Classification purposes covering various methods such as descriptive, geometric, linear, quadratic, PLS, as well as qualitative discriminant analyses | 2019-07-21 |

r-dmt | public | Probabilistic dependency modeling toolkit. | 2019-07-21 |

r-docxtools | public | A set of helper functions for using R Markdown to create documents in docx format, especially documents for use in a classroom or workshop setting. | 2019-07-21 |

r-irkernel | public | The R kernel for the 'Jupyter' environment executes R code which the front-end ('Jupyter Notebook' or other front-ends) submits to the kernel via the network. | 2019-07-21 |

r-dmwr | public | This package includes functions and data accompanying the book "Data Mining with R, learning with case studies" by Luis Torgo, CRC Press 2010. | 2019-07-21 |

r-dofuture | public | Provides a '%dopar%' adapter such that any type of futures can be used as backends for the 'foreach' framework. | 2019-07-21 |

r-drc | public | Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions. | 2019-07-21 |

r-directlabels | public | An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method. | 2019-07-21 |

r-domc | public | Provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package. | 2019-07-21 |

r-drat | public | Creation and use of R Repositories via helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are support: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template. | 2019-07-21 |

websockets | public | A library for developing WebSocket servers and clients in Python. | 2019-07-21 |

r-extremes | public | Functions for performing extreme value analysis. | 2019-07-21 |

r-elpigraph.r | public | An R package to construct Elastic Principal Graphs | 2019-07-21 |

r-ecp | public | Implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and pruning, with no distributional assumptions other than the existence of certain absolute moments in one method. Hierarchical and exact search methods are included. All methods return the set of estimated change- points as well as other summary information. | 2019-07-21 |

r-envstats | public | Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. Major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. Numerous built-in data sets from regulatory guidance documents and environmental statistics literature. Includes scripts reproducing analyses presented in the book ""EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, <http://www.springer.com/book/9781461484554>). | 2019-07-21 |

r-ensurer | public | Add simple runtime contracts to R values. These ensure that values fulfil certain conditions and will raise appropriate errors if they do not. | 2019-07-21 |

r-emdbook | public | Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0). | 2019-07-21 |

r-emt | public | The package provides functions to carry out a Goodness-of-fit test for discrete multivariate data. It is tested if a given observation is likely to have occurred under the assumption of an ab-initio model. A p-value can be calculated using different distance measures between observed and expected frequencies. A Monte Carlo method is provided to make the package capable of solving high-dimensional problems. | 2019-07-21 |

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