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

r-clues | public | 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. | 2019-07-21 |

r-circular | public | Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific. | 2019-07-21 |

r-ccapp | public | Canonical correlation analysis and maximum correlation via projection pursuit, as well as fast implementations of correlation estimators, with a focus on robust and non-parametric methods. | 2019-07-21 |

r-cghflasso | public | Spatial smoothing and hot spot detection using the fused lasso regression | 2019-07-21 |

r-blockmodeling | public | This is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted: Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, Žiberna (2008)<doi:10.1080/00222500701790207>, Žiberna (2014)<doi:10.1016/j.socnet.2014.04.002>. | 2019-07-21 |

r-boolnet | public | Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks. | 2019-07-21 |

r-cairo | public | R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported. | 2019-07-21 |

r-bma | public | Package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression). | 2019-07-21 |

r-bootstrap | public | Software (bootstrap, cross-validation, jackknife) and data for the book "An Introduction to the Bootstrap" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided for projects already based on it, and for support of the book. New projects should preferentially use the recommended package "boot". | 2019-07-21 |

r-compute.es | public | This package contains several functions for calculating the most widely used effect sizes (ES), along with their variances, confidence intervals and p-values. The output includes ES's of d (mean difference), g (unbiased estimate of d), r (correlation coefficient), z' (Fisher's z), and OR (odds ratio and log odds ratio). In addition, NNT (number needed to treat), U3, CLES (Common Language Effect Size) and Cliff's Delta are computed. This package uses recommended formulas as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009). | 2019-07-21 |

r-colortools | public | R package with handy functions to help users select and play with color schemes in an HSV color model | 2019-07-21 |

r-cnogpro | public | Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms. | 2019-07-21 |

r-castor | public | Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>. | 2019-07-21 |

r-checkpoint | public | The goal of checkpoint is to solve the problem of package reproducibility in R. Specifically, checkpoint allows you to install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine. To achieve reproducibility, the checkpoint() function installs the packages required or called by your project and scripts to a local library exactly as they existed at the specified point in time. Only those packages are available to your project, thereby avoiding any package updates that came later and may have altered your results. In this way, anyone using checkpoint's checkpoint() can ensure the reproducibility of your scripts or projects at any time. To create the snapshot archives, once a day (at midnight UTC) Microsoft refreshes the Austria CRAN mirror on the "Microsoft R Archived Network" server (<https://mran.microsoft.com/>). Immediately after completion of the rsync mirror process, the process takes a snapshot, thus creating the archive. Snapshot archives exist starting from 2014-09-17. | 2019-07-21 |

r-ccremover | public | Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi | 2019-07-21 |

r-calibrate | public | Package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots. | 2019-07-21 |

r-caroline | public | The caroline R library contains dozens of functions useful for: database migration (dbWriteTable2), database style joins & aggregation (nerge, groupBy & bestBy), data structure conversion (nv, tab2df), legend table making (sstable & leghead), plot annotation (labsegs & mvlabs), data visualization (violins, pies & raPlot), character string manipulation (m & pad), file I/O (write.delim), batch scripting and more. The package's greatest contributions lie in the database style merge, aggregation and interface functions as well as in it's extensive use and propagation of row, column and vector names in most functions. | 2019-07-21 |

r-biwt | public | Compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator. | 2019-07-21 |

r-catnet | public | 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. | 2019-07-21 |

r-cba | public | Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation. | 2019-07-21 |

r-bioset | public | Functions to help dealing with raw data from measurements, like reading and transforming raw values organized in matrices, calculating and converting concentrations and calculating precision of duplicates / triplicates / ... . It is compatible with and building on top of some 'tidyverse'-packages. | 2019-07-21 |

r-blogdown | public | Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>). | 2019-07-21 |

r-bpca | public | Implements biplot (2d and 3d) of multivariate data based on principal components analysis and diagnostic tools of the quality of the reduction. | 2019-07-21 |

r-boruta | public | An all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes importance with importance achievable at random, estimated using their permuted copies (shadows). | 2019-07-21 |

r-bs4dash | public | Make 'Bootstrap 4' dashboards. Use the full power of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4' <https://github.com/almasaeed2010/AdminLTE/tree/v3-dev>. | 2019-07-21 |

r-bradleyterry2 | public | Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage. | 2019-07-21 |

r-c3net | public | This package allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET. | 2019-07-21 |

r-caper | public | Functions for performing phylogenetic comparative analyses. | 2019-07-21 |

r-captioner | public | 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. | 2019-07-21 |

r-ccp | public | Significance tests for canonical correlation analysis, including asymptotic tests and a Monte Carlo method | 2019-07-21 |

r-cdft | public | This package proposes a statistical downscaling method for cumulative distribution functions (CDF), as well as the computation of the Cram\`er-von Mises statistics U, and the Kolmogorov-Smirnov statistics KS. | 2019-07-21 |

r-cobs | public | Qualitatively Constrained (Regression) Smoothing Splines via Linear Programming and Sparse Matrices. | 2019-07-21 |

r-collapsibletree | public | Interactive Reingold-Tilford tree diagrams created using 'D3.js', where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame. See 'collapsibleTree' website for more information and examples. | 2019-07-21 |

r-collateral | public | The purrr package allows you to capture the side effects (errors, warning, messages and other output) of functions using safely() and quietly(). Using collateral, you can quickly see which elements of a list (or list-column) returned results, which threw errors and which returned warnings or other output. | 2019-07-21 |

r-chemometricswithr | public | 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. | 2019-07-21 |

r-conicfit | public | Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin. | 2019-07-21 |

r-clustermq | public | Evaluate arbitrary function calls using workers on HPC schedulers in single line of code. All processing is done on the network without accessing the file system. Remote schedulers are supported via SSH. | 2019-07-21 |

r-chemometrics | public | R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009). | 2019-07-21 |

r-clusterr | public | Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>. | 2019-07-21 |

r-cometexacttest | public | An algorithm for identifying combinations of mutually exclusive alterations in cancer genomes. CoMEt represents the mutations in a set M of k genes with a 2^k dimensional contingency table, and then computes the tail probability of observing T(M) exclusive alterations using an exact statistical test. | 2019-07-21 |

r-clustersim | public | Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>). | 2019-07-21 |

r-changepoint | public | Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean(), cpt.var(), cpt.meanvar() functions should be your first point of call. | 2019-07-21 |

r-clustercrit | public | Compute clustering validation indices. | 2019-07-21 |

r-clusterses | public | Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller (2010) <DOI:10.1198/jbes.2009.08046>, pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller (2008) <DOI:10.1162/rest.90.3.414>. Procedures are included for use with GLM, ivreg, plm (pooling or fixed effects), and mlogit models. | 2019-07-21 |

r-chemospec | public | A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available. | 2019-07-21 |

r-cgdsr | public | 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>. | 2019-07-21 |

r-clustergeneration | public | We developed the clusterGeneration package to provide functions for generating random clusters, generating random covariance/correlation matrices, calculating a separation index (data and population version) for pairs of clusters or cluster distributions, and 1-D and 2-D projection plots to visualize clusters. The package also contains a function to generate random clusters based on factorial designs with factors such as degree of separation, number of clusters, number of variables, number of noisy variables. | 2019-07-21 |

r-conflicted | public | R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use. | 2019-07-21 |

r-compare | public | Functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical. | 2019-07-21 |

r-ddrtree | public | No Summary | 2019-07-21 |

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