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r-doubcens
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Contains the discrete nonparametric survivor function estimation algorithm of De Gruttola and Lagakos for doubly interval-censored failure time data and the discrete nonparametric survivor function estimation algorithm of Sun for doubly interval-censored left-truncated failure time data [Victor De Gruttola & Stephen W. Lagakos (1989) <doi:10.2307/2532030>] [Jianguo Sun (1995) <doi:10.2307/2533008>].
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2023-06-16 |
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r-doestrare
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Rare variant association test integrating variant position information. It aims to identify the presence of clusters of disease-risk variants in specific gene regions. For more details, please read the publication from Persyn et al. (2017) <doi:10.1371/journal.pone.0179364>.
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2023-06-16 |
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r-dint
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S3 classes and methods to create and work with year-quarter, year-month and year-isoweek vectors. Basic arithmetic operations (such as adding and subtracting) are supported, as well as formatting and converting to and from standard R date types.
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2023-06-16 |
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r-difconet
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Estimation of DIFferential COexpressed NETworks using diverse and user metrics. This package is basically used for three functions related to the estimation of differential coexpression. First, to estimate differential coexpression where the coexpression is estimated, by default, by Spearman correlation. For this, a metric to compare two correlation distributions is needed. The package includes 6 metrics. Some of them needs a threshold. A new metric can also be specified as a user function with specific parameters (see difconet.run). The significance is be estimated by permutations. Second, to generate datasets with controlled differential correlation data. This is done by either adding noise, or adding specific correlation structure. Third, to show the results of differential correlation analyses. Please see <http://bioinformatica.mty.itesm.mx/difconet> for further information.
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2023-06-16 |
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r-dielectric
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Physical constants. Gold, silver and glass permittivities, together with spline interpolation functions.
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2023-06-16 |
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r-diagonals
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Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
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2023-06-16 |
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r-dgodata
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Provides data used by package 'dgo' in examples and vignettes.
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2023-06-16 |
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r-devore7
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Data sets and sample analyses from Jay L. Devore (2008), "Probability and Statistics for Engineering and the Sciences (7th ed)", Thomson.
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2023-06-16 |
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r-densparcorr
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Provide a Dens-based method for estimating functional connection in large scale brain networks using partial correlation.
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2023-06-16 |
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r-demokde
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public |
Demonstration code showing how (univariate) kernel density estimates are computed, at least conceptually, and allowing users to experiment with different kernels, should they so wish. NOTE: the density function in the stats package should be used for computational efficiency.
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2023-06-16 |
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r-deepnet
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Implement some deep learning architectures and neural network algorithms, including BP,RBM,DBN,Deep autoencoder and so on.
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2023-06-16 |
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r-direct
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public |
A Bayesian clustering method for replicated time series or replicated measurements from multiple experimental conditions, e.g., time-course gene expression data. It estimates the number of clusters directly from the data using a Dirichlet-process prior. See Fu, A. Q., Russell, S., Bray, S. and Tavare, S. (2013) Bayesian clustering of replicated time-course gene expression data with weak signals. The Annals of Applied Statistics. 7(3) 1334-1361. <doi:10.1214/13-AOAS650>.
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2023-06-16 |
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r-depmix
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Fits (multigroup) mixtures of latent or hidden Markov models on mixed categorical and continuous (timeseries) data. The Rdonlp2 package can optionally be used for optimization of the log-likelihood and is available from R-forge.
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2023-06-16 |
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r-disclap
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Discrete Laplace exponential family for models such as a generalized linear model
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2023-06-16 |
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r-dialr
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Parse, format, and validate international phone numbers using Google's 'libphonenumber' java library, <https://github.com/googlei18n/libphonenumber>.
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2023-06-16 |
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r-bivarp
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Parameter estimation of bivariate distribution functions modeled as a Archimedean copula function. The input data may contain values from right censored. Used marginal distributions are two-parameter. Methods for density, distribution, survival, random sample generation.
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2023-06-16 |
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r-dkdna
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Compute diffusion kernels on DNA polymorphisms, including SNP and bi-allelic genotypes.
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2023-06-16 |
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r-diphiseq
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Implements the algorithm described in Jun Li and Alicia T. Lamere, "DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes" (Unpublished). Detects not only genes that show different average expressions ("differential expression", DE), but also genes that show different diversities of expressions in different groups ("differentially dispersed", DD). DD genes can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the quasi-likelihood function, and thus has superior robustness against outliers and other noise. Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi. (2) Added a function for estimating the proportion of outliers in the data. (3) Modified the input parameter names for clarity, and modified the output format for the main function.
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2023-06-16 |
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r-diaplt
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Visualize one-factor data frame. Beads plot consists of diamonds of each factor of each data series. A diamond indicates average and range. Look over a data frame with many numeric columns and a factor column.
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2023-06-16 |
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r-dfcrm
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Provides functions to run the CRM and TITE-CRM in phase I trials and calibration tools for trial planning purposes.
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2023-06-16 |
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r-dfadjust
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Computes small-sample degrees of freedom adjustment for heteroskedasticity robust standard errors, and for clustered standard errors in linear regression. See Imbens and Kolesár (1994) <doi:10.1162/REST_a_00552> for a discussion of these adjustments.
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2023-06-16 |
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r-det
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Builds both ROC (Receiver Operating Characteristic) and DET (Detection Error Tradeoff) curves from a set of predictors, which are the results of a binary classification system. The curves give a general vision of the performance of the classifier, and are useful for comparing performance of different systems.
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2023-06-16 |
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r-desnowball
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This package implements a statistical data mining method to compare whole genome gene expression profiles, with respect to the presence of a recurrent genetic disturbance event, to identify the affected target genes.
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2023-06-16 |
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r-derezende.ferreira
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Modeling the zero coupon yield curve using the dynamic De Rezende and Ferreira (2011) <doi:10.1002/for.1256> five factor model with variable or fixed decaying parameters. For explanatory purposes, the package also includes various short datasets of interest rates for the BRICS countries.
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2023-06-16 |
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r-denvax
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Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds" in <doi:10.1098/rsif.2019.0234>. Using the functions in the package, that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data using other functions in this package (as in the manuscript) or from some other source. The package provides a vignette which walks through the analysis in the publication, as well as a function to generate a project skeleton for such an analysis.
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2023-06-16 |
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r-dendroextras
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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.
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2023-06-16 |
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r-demova
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Tool for the development of multi-linear QSPR/QSAR models (Quantitative structure-property/activity relationship). Theses models are used in chemistry, biology and pharmacy to find a relationship between the structure of a molecule and its property (such as activity, toxicology but also physical properties). The various functions of this package allows: selection of descriptors based of variances, intercorrelation and user expertise; selection of the best multi-linear regression in terms of correlation and robustness; methods of internal validation (Leave-One-Out, Leave-Many-Out, Y-scrambling) and external using test sets.
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2023-06-16 |
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r-dhsic
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Contains an implementation of the d-variable Hilbert Schmidt independence criterion and several hypothesis tests based on it, as described in Pfister et al. (2017) <doi:10.1111/rssb.12235>.
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2023-06-16 |
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r-discfrail
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Functions for fitting Cox proportional hazards models for grouped time-to-event data, where the shared group-specific frailties have a discrete nonparametric distribution. The methods proposed in the package is described by Gasperoni, F., Ieva, F., Paganoni, A. M., Jackson, C. H., Sharples, L. (2018) <doi:10.1093/biostatistics/kxy071>. There are also functions for simulating from these models, with a nonparametric or a parametric baseline hazard function.
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2023-06-16 |
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r-dirmult
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Estimate parameters in Dirichlet-Multinomial and compute profile log-likelihoods.
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2023-06-16 |
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r-directlabels
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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.
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2023-06-16 |
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r-dotcall64
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Provides .C64(), which is an enhanced version of .C() and .Fortran() from the foreign function interface. .C64() supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.
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2023-06-16 |
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r-divdyn
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Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
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2023-06-16 |
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r-dfoptim
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Derivative-Free optimization algorithms. These algorithms do not require gradient information. More importantly, they can be used to solve non-smooth optimization problems.
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2023-06-16 |
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r-dendsort
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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.
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2023-06-16 |
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r-deltaplotr
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The deltaPlotR package implements Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported (Magis and Facon (2014) <doi:10.18637/jss.v059.c01>).
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2023-06-16 |
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r-default
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A simple syntax to change the default values for function arguments, whether they are in packages or defined locally.
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2023-06-16 |
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r-dparser
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A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita (1987) algorithm. (Paper can be found at <http://acl-arc.comp.nus.edu.sg/archives/acl-arc-090501d3/data/pdf/anthology-PDF/J/J87/J87-1004.pdf>). The original 'dparser' package documentation can be found at <http://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like RxODE's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use #include <dparser.h>. This also provides a R-based port of the make_dparser <http://dparser.sourceforge.net/d/make_dparser.cat> command called mkdparser(). Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar testing. The fastest parsing, of course, occurs at the C level, and is suggested.
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2023-06-16 |
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r-detestset
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Solvers and test set for stiff and non-stiff differential equations, and differential algebraic equations. 'Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 10.1016/j.cam.2012.03.014'.
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2023-06-16 |
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r-bitrina
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Provides methods for the binarization and trinarization of one-dimensional data and some visualization functions.
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2023-06-16 |
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r-des
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Discrete event simulation (DES) involves modeling of systems having discrete, i.e. abrupt, state changes. For instance, when a job arrives to a queue, the queue length abruptly increases by 1. This package is an R implementation of the event-oriented approach to DES; see the tutorial in Matloff (2008) <http://heather.cs.ucdavis.edu/~matloff/156/PLN/DESimIntro.pdf>.
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2023-06-16 |
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r-derivmkts
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A set of pricing and expository functions that should be useful in teaching a course on financial derivatives.
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2023-06-16 |
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r-deepgmm
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Deep Gaussian mixture models as proposed by Viroli and McLachlan (2019) <doi:10.1007/s11222-017-9793-z> provide a generalization of classical Gaussian mixtures to multiple layers. Each layer contains a set of latent variables that follow a mixture of Gaussian distributions. To avoid overparameterized solutions, dimension reduction is applied at each layer by way of factor models.
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2023-06-16 |
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r-devemf
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Output graphics to EMF+/EMF.
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2023-06-16 |
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r-descr
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Weighted frequency and contingency tables of categorical variables and of the comparison of the mean value of a numerical variable by the levels of a factor, and methods to produce xtable objects of the tables and to plot them. There are also functions to facilitate the character encoding conversion of objects, to quickly convert fixed width files into csv ones, and to export a data.frame to a text file with the necessary R and SPSS codes to reread the data.
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2023-06-16 |
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r-directeffects
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A set of functions to estimate the controlled direct effect of treatment fixing a potential mediator to a specific value. Implements the sequential g-estimation estimator described in Vansteelandt (2009) <doi:10.1097/EDE.0b013e3181b6f4c9> and Acharya, Blackwell, and Sen (2016) <doi:10.1017/S0003055416000216>.
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2023-06-16 |
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r-dng
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Provides density, distribution function, quantile function and random generation for the split normal and split-t distributions, and computes their mean, variance, skewness and kurtosis for the two distributions (Li, F, Villani, M. and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>).
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2023-06-16 |
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r-datautils
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Contains facilities such as getting the current timestamp in decimal seconds, computing interval w.r.t. a reference timestamp, and custom plotting with error bars.
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2023-06-16 |
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r-diezeit
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A wrapper for the ZEIT ONLINE Content API, available at <http://developer.zeit.de>. 'diezeit' gives access to articles and corresponding metadata from the ZEIT archive and from ZEIT ONLINE. A personal API key is required for usage.
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2023-06-16 |
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r-didacticboost
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A basic, clear implementation of tree-based gradient boosting designed to illustrate the core operation of boosting models. Tuning parameters (such as stochastic subsampling, modified learning rate, or regularization) are not implemented. The only adjustable parameter is the number of training rounds. If you are looking for a high performance boosting implementation with tuning parameters, consider the 'xgboost' package.
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2023-06-16 |
