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r-derezende.ferreira
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public |
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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2025-04-22 |
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r-depthtools
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public |
depthTools is a package that implements different statistical tools for the description and analysis of gene expression data based on the concept of data depth, namely, the scale curves for visualizing the dispersion of one or various groups of samples (e.g. types of tumors), a rank test to decide whether two groups of samples come from a single distribution and two methods of supervised classification techniques, the DS and TAD methods. All these techniques are based on the Modified Band Depth, which is a recent notion of depth with a low computational cost, what renders it very appropriate for high dimensional data such as gene expression data.
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2025-04-22 |
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r-depth.plot
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public |
Could be used to obtain spatial depths, spatial ranks and outliers of multivariate random variables. Could also be used to visualize DD-plots (a multivariate generalization of QQ-plots).
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2025-04-22 |
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r-deplogo
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public |
Plots dependency logos from a set of input sequences.
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2025-04-22 |
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r-depend.truncation
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public |
Estimation and testing methods for dependently truncated data. Semi-parametric methods are based on Emura et al. (2011)<Stat Sinica 21:349-67>, Emura & Wang (2012)<doi:10.1016/j.jmva.2012.03.012>, and Emura & Murotani (2015)<doi:10.1007/s11749-015-0432-8>. Parametric approaches are based on Emura & Konno (2012)<doi:10.1007/s00362-014-0626-2> and Emura & Pan (2017)<doi:10.1007/s00362-017-0947-z>. A regression approach is based on Emura & Wang (2016)<doi:10.1007/s10463-015-0526-9>. Quasi-independence tests are based on Emura & Wang (2010)<doi:10.1016/j.jmva.2009.07.006>. Right-truncated data for Japanese male centenarians are given by Emura & Murotani (2015)<doi:10.1007/s11749-015-0432-8>.
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2025-04-22 |
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r-denvax
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public |
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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2025-04-22 |
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r-denstrip
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public |
Graphical methods for compactly illustrating probability distributions, including density strips, density regions, sectioned density plots and varying width strips.
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2025-04-22 |
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r-densratio
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public |
Density ratio estimation. The estimated density ratio function can be used in many applications such as anomaly detection, change-point detection, covariate shift adaptation. The implemented methods are uLSIF (Hido et al. (2011) <doi:10.1007/s10115-010-0283-2>), RuLSIF (Yamada et al. (2011) <doi:10.1162/NECO_a_00442>), and KLIEP (Sugiyama et al. (2007) <doi:10.1007/s10463-008-0197-x>).
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2025-04-22 |
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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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2025-04-22 |
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r-denseflmm
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public |
Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.
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2025-04-22 |
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r-denoiseq
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public |
Given count data from two conditions, it determines which transcripts are differentially expressed across the two conditions using Bayesian inference of the parameters of a bottom-up model for PCR amplification. This model is developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Friedman (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in a distribution for the counts that is a superposition of the binomial and negative binomial distribution.
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2025-04-22 |
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r-dendsort
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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.
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2025-04-22 |
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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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2025-04-22 |
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r-demova
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public |
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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2025-04-22 |
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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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2025-04-22 |
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r-demogr
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public |
Construction and analysis of matrix population models in R.
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2025-04-22 |
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r-deming
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public |
Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
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2025-04-22 |
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r-demetics
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This package allows to calculate the fixation index Gst (Nei, 1973) and the differentiation index D (Jost, 2008) pairwise between or averaged over several populations. P-values, stating the significance of differentiation, and 95 percent confidence intervals can be estimated using bootstrap resamplings. In the case that more than two populations are compared pairwise, the p-values are adjusted by bonferroni correction and in several other ways due to the multiple comparison from one data set.
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2025-04-22 |
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r-deltd
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It plots densities by using asymmetrical kernels which belong to life time distributions and calculate its related MSE. For details see Chen (2000), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
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2025-04-22 |
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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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2025-04-22 |
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r-delta
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Measure of agreement delta was originally by MartÃn & Femia (2004) <DOI:10.1348/000711004849268>. Since then has been considered as agreement measure for different fields, since their behavior is usually better than the usual kappa index by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta is that can not be computed by hand contrary to kappa. The current algorithm is based on the Version 5 of the delta windows program that can be found on <https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.
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2025-04-22 |
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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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2025-04-22 |
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r-deepnn
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Implementation of some Deep Learning methods. Includes multilayer perceptron, different activation functions, regularisation strategies, stochastic gradient descent and dropout. Thanks go to the following references for helping to inspire and develop the package: Ian Goodfellow, Yoshua Bengio, Aaron Courville, Francis Bach (2016, ISBN:978-0262035613) Deep Learning. Terrence J. Sejnowski (2018, ISBN:978-0262038034) The Deep Learning Revolution. Grant Sanderson (3brown1blue) <https://www.youtube.com/playlist?list=PLZHQObOWTQDNU6R1_67000Dx_ZCJB-3pi> Neural Networks YouTube playlist. Michael A. Nielsen <http://neuralnetworksanddeeplearning.com/> Neural Networks and Deep Learning.
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2025-04-22 |
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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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2025-04-22 |
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r-deepgmm
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public |
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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2025-04-22 |
