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

vaex-hdf5 | public | hdf5 file support for vaex | 2019-07-20 |

r-rpostgres | public | Fully 'DBI'-compliant 'Rcpp'-backed interface to 'PostgreSQL' <https://www.postgresql.org/>, an open-source relational database. | 2019-07-20 |

r-modeldb | public | Uses 'dplyr' and 'tidyeval' to fit statistical models inside the database. It currently supports KMeans and linear regression models. | 2019-07-20 |

r-stm | public | The Structural Topic Model (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions. Methods developed in Roberts et al (2014) <doi:10.1111/ajps.12103> and Roberts et al (2016) <doi:10.1080/01621459.2016.1141684>. | 2019-07-20 |

r-shinyhelper | public | Creates a lightweight way to add markdown helpfiles to 'shiny' apps, using modal dialog boxes, with no need to observe each help button separately. | 2019-07-20 |

r-sdmtools | public | This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.. This package was made possible in part by financial support from the Australian Research Council & ARC Research Network for Earth System Science. | 2019-07-20 |

r-softimpute | public | Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an "EM" flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components) | 2019-07-20 |

r-snftool | public | Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification. | 2019-07-20 |

r-weatherdata | public | No Summary | 2019-07-20 |

r-smvar | public | Implements the structural model for variances in order to detect differentially expressed genes from gene expression data | 2019-07-20 |

r-smoothwin | public | The main function in the package utilizes a windowing function in the form of an exponential weighting function to linear models. The bandwidth and sharpness of the window are controlled by two parameters. Then, a series of tests are used to identify the right parameters of the window (see Charles Kervrann (2004) <doi:10.1007/978-3-540-24672-5_11>). | 2019-07-20 |

r-tkrplot | public | Simple mechanism for placing R graphics in a Tk widget. | 2019-07-20 |

r-snpls | public | Tools for performing variable selection in three-way data using N-PLS in combination with L1 penalization. The N-PLS model (Rasmus Bro, 1996 <DOI:10.1002/(SICI)1099-128X(199601)10:1%3C47::AID-CEM400%3E3.0.CO;2-C>) is the natural extension of PLS (Partial Least Squares) to N-way structures, and tries to maximize the covariance between X and Y data arrays. The package also adds variable selection through L1 penalization. | 2019-07-20 |

r-tidyxl | public | Imports non-tabular from Excel files into R. Exposes cell content, position and formatting in a tidy structure for further manipulation. Tokenizes Excel formulas. Supports '.xlsx' and '.xlsm' via the embedded 'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Does not support '.xlsb' or '.xls'. | 2019-07-20 |

r-snpassoc | public | This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. | 2019-07-20 |

r-solarius | public | SOLAR is the standard software program to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. This package allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. See <http | 2019-07-20 |

r-timsac | public | Functions for statistical analysis, prediction and control of time series based mainly on Akaike and Nakagawa (1988) <ISBN 978-90-277-2786-2>. | 2019-07-20 |

r-soniclength | public | Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance. | 2019-07-20 |

r-shinybusy | public | Add a global indicator (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy. | 2019-07-20 |

r-shinydashboardplus | public | Extend 'shinydashboard' with 'AdminLTE2' components. 'AdminLTE2' is a free 'Bootstrap 3' dashboard template available at <https://adminlte.io>. Customize boxes, add timelines and a lot more. | 2019-07-20 |

r-shinylp | public | Provides functions that wrap HTML Bootstrap components code to enable the design and layout of informative landing home pages for Shiny applications. This can lead to a better user experience for the users and writing less HTML for the developer. | 2019-07-20 |

r-soildb | public | A collection of functions for reading data from USDA-NCSS soil databases. | 2019-07-20 |

r-shinycssloaders | public | Create a lightweight Shiny wrapper for the css-loaders created by Luke Hass <https://github.com/lukehaas/css-loaders>. Wrapping a Shiny output will automatically show a loader when the output is (re)calculating. | 2019-07-20 |

r-sentimentr | public | Calculate text polarity sentiment at the sentence level and optionally aggregate by rows or grouping variable(s). | 2019-07-20 |

r-shinyeffects | public | Add fancy CSS effects to your 'shinydashboards' or 'shiny' apps. 100% compatible with 'shinydashboardPlus' and 'bs4Dash'. | 2019-07-20 |

r-shinyalert | public | Easily create pretty popup messages (modals) in 'Shiny'. A modal can contain text, images, OK/Cancel buttons, an input to get a response from the user, and many more customizable options. | 2019-07-20 |

r-shiny.semantic | public | Creating a great user interface for your Shiny apps can be a hassle, especially if you want to work purely in R and don't want to use, for instance HTML templates. This package adds support for a powerful UI library Semantic UI - <http://semantic-ui.com/>. It also supports universal UI input binding that works with various DOM elements. | 2019-07-20 |

r-sparseinv | public | Creates a wrapper for the 'SuiteSparse' routines that execute the Takahashi equations. These equations compute the elements of the inverse of a sparse matrix at locations where the its Cholesky factor is structurally non-zero. The resulting matrix is known as a sparse inverse subset. Some helper functions are also implemented. Support for spam matrices is currently limited and will be implemented in the future. See Rue and Martino (2007) <doi:10.1016/j.jspi.2006.07.016> and Zammit-Mangion and Rougier (2018) <doi:10.1016/j.csda.2018.02.001> for the application of these equations to statistics. | 2019-07-20 |

r-servr | public | Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory. | 2019-07-20 |

r-spatialextremes | public | Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>. | 2019-07-20 |

r-shadowtext | public | Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'. These functions create/draw text grob with background shadow. | 2019-07-20 |

r-seacarb | public | Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments. | 2019-07-20 |

r-sparktf | public | A 'sparklyr' extension that enables reading and writing 'TensorFlow' TFRecord files via 'Apache Spark'. | 2019-07-20 |

r-survivalroc | public | Compute time-dependent ROC curve from censored survival data using Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344) | 2019-07-20 |

r-segregation | public | Computes entropy-based segregation indices, as developed by Theil (1971) <isbn:978-0471858454>, with a focus on the Mutual Information Index (M) and Theil's Information Index (H). The M, further described by Mora and Ruiz-Castillo (2011) <doi:10.1111/j.1467-9531.2011.01237.x> and Frankel and Volij (2011) <doi:10.1016/j.jet.2010.10.008>, is a measure of segregation that is highly decomposable. The package provides tools to decompose the index by units and groups (local segregation), and by within and between terms. Includes standard error estimation by bootstrapping. | 2019-07-20 |

r-adgoftest | public | No Summary | 2019-07-20 |

r-rrblup | public | Software for genomic prediction with the RR-BLUP mixed model (Endelman 2011, <doi:10.3835/plantgenome2011.08.0024>). One application is to estimate marker effects by ridge regression; alternatively, BLUPs can be calculated based on an additive relationship matrix or a Gaussian kernel. | 2019-07-20 |

r-shinyjqui | public | An extension to shiny that brings interactions and animation effects from 'jQuery UI' library. | 2019-07-20 |

r-shinysky | public | No Summary | 2019-07-20 |

r-rsnns | public | The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the 'RSNNS' low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R. | 2019-07-20 |

r-venn | public | Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set intersections. | 2019-07-20 |

r-xtensor | public | R bindings for xtensor, the C++ tensor algebra library | 2019-07-20 |

r-sctransform | public | A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija 2019 <doi:10.1101/576827> for more details. | 2019-07-20 |

r-workflowr | public | Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results. | 2019-07-20 |

r-ruv | public | Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms. | 2019-07-20 |

r-sampling | public | Functions for drawing and calibrating samples. | 2019-07-20 |

r-scrm | public | A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences. | 2019-07-20 |

r-waterfall | public | Provides support for creating waterfall charts in R using both traditional base and lattice graphics. | 2019-07-20 |

r-tidymodels | public | The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse. | 2019-07-20 |

r-waterfalls | public | A not uncommon task for quants is to create 'waterfall charts'. There seems to be no simple way to do this in 'ggplot2' currently. This package contains a single function (waterfall) that simply draws a waterfall chart in a 'ggplot2' object. Some flexibility is provided, though often the object created will need to be modified through a theme. | 2019-07-20 |

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