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pracma:Practical Numerical Math Functions
Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Maintained by Hans W. Borchers. Last updated 1 years ago.
16.6 match 29 stars 12.34 score 6.6k scripts 931 dependentsfchamroukhi
samurais:Statistical Models for the Unsupervised Segmentation of Time-Series ('SaMUraiS')
Provides a variety of original and flexible user-friendly statistical latent variable models and unsupervised learning algorithms to segment and represent time-series data (univariate or multivariate), and more generally, longitudinal data, which include regime changes. 'samurais' is built upon the following packages, each of them is an autonomous time-series segmentation approach: Regression with Hidden Logistic Process ('RHLP'), Hidden Markov Model Regression ('HMMR'), Multivariate 'RHLP' ('MRHLP'), Multivariate 'HMMR' ('MHMMR'), Piece-Wise regression ('PWR'). For the advantages/differences of each of them, the user is referred to our mentioned paper references. These models are originally introduced and written in 'Matlab' by Faicel Chamroukhi <https://github.com/fchamroukhi?&tab=repositories&q=time-series&type=public&language=matlab>.
Maintained by Florian Lecocq. Last updated 5 years ago.
artificial-intelligencechange-point-detectiondata-sciencedynamic-programmingem-algorithmhidden-markov-modelshidden-process-regressionhuman-activity-recognitionlatent-variable-modelsmodel-selectionmultivariate-timeseriesnewton-raphsonpiecewise-regressionstatistical-inferencestatistical-learningtime-series-analysistime-series-clusteringopenblascpp
15.0 match 12 stars 6.18 score 28 scriptsyihui
animation:A Gallery of Animations in Statistics and Utilities to Create Animations
Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.
Maintained by Yihui Xie. Last updated 2 years ago.
animationstatistical-computingstatistical-graphicsstatistics
5.8 match 208 stars 12.08 score 2.5k scripts 29 dependentskkholst
lava:Latent Variable Models
A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.
Maintained by Klaus K. Holst. Last updated 2 months ago.
latent-variable-modelssimulationstatisticsstructural-equation-models
4.0 match 33 stars 12.85 score 610 scripts 476 dependentsfika-fianda
saebnocov:Small Area Estimation using Empirical Bayes without Auxiliary Variable
Estimates the parameter of small area in binary data without auxiliary variable using Empirical Bayes technique, mainly from Rao and Molina (2015,ISBN:9781118735787) with book entitled "Small Area Estimation Second Edition". This package provides another option of direct estimation using weight. This package also features alpha and beta parameter estimation on calculating process of small area. Those methods are Newton-Raphson and Moment which based on Wilcox (1979) <doi:10.1177/001316447903900302> and Kleinman (1973) <doi:10.1080/01621459.1973.10481332>.
Maintained by Siti Rafika Fiandasari. Last updated 3 years ago.
20.9 match 2.30 score 3 scriptsdcnorris
DTAT:Dose Titration Algorithm Tuning
Dose Titration Algorithm Tuning (DTAT) is a methodologic framework allowing dose individualization to be conceived as a continuous learning process that begins in early-phase clinical trials and continues throughout drug development, on into clinical practice. This package includes code that researchers may use to reproduce or extend key results of the DTAT research programme, plus tools for trialists to design and simulate a '3+3/PC' dose-finding study. Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and Norris (2017c) <doi:10.1101/240846>.
Maintained by David C. Norris. Last updated 10 months ago.
10.1 match 2.90 score 20 scriptscran
scam:Shape Constrained Additive Models
Generalized additive models under shape constraints on the component functions of the linear predictor. Models can include multiple shape-constrained (univariate and bivariate) and unconstrained terms. Routines of the package 'mgcv' are used to set up the model matrix, print, and plot the results. Multiple smoothing parameter estimation by the Generalized Cross Validation or similar. See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7> for an overview. A broad selection of shape-constrained smoothers, linear functionals of smooths with shape constraints, and Gaussian models with AR1 residuals.
Maintained by Natalya Pya. Last updated 2 months ago.
3.6 match 5 stars 7.17 score 388 scripts 23 dependentsmlysy
SuperGauss:Superfast Likelihood Inference for Stationary Gaussian Time Series
Likelihood evaluations for stationary Gaussian time series are typically obtained via the Durbin-Levinson algorithm, which scales as O(n^2) in the number of time series observations. This package provides a "superfast" O(n log^2 n) algorithm written in C++, crossing over with Durbin-Levinson around n = 300. Efficient implementations of the score and Hessian functions are also provided, leading to superfast versions of inference algorithms such as Newton-Raphson and Hamiltonian Monte Carlo. The C++ code provides a Toeplitz matrix class packaged as a header-only library, to simplify low-level usage in other packages and outside of R.
Maintained by Martin Lysy. Last updated 1 months ago.
3.7 match 2 stars 5.60 score 33 scripts 2 dependentsinlabru-org
dirinla:Hierarchical Bayesian Dirichlet regression models using Integrated Nested Laplace Approximation
The R-package dirinla allows the user to fit models in the compositional data context. In particular, it allows fit Dirichlet regression models using the Integrated Nested Laplace Approximation (INLA) methodology.
Maintained by Joaquín Martínez-Minaya. Last updated 4 months ago.
4.0 match 4 stars 3.89 score 13 scriptskarlines
rootSolve:Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE). Includes routines that: (1) generate gradient and jacobian matrices (full and banded), (2) find roots of non-linear equations by the 'Newton-Raphson' method, (3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the 'Newton-Raphson' method, or by dynamically running, (4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). Includes fortran code.
Maintained by Karline Soetaert. Last updated 1 years ago.
1.5 match 1 stars 9.61 score 1.2k scripts 216 dependentstabea17
noisySBM:Noisy Stochastic Block Mode: Graph Inference by Multiple Testing
Variational Expectation-Maximization algorithm to fit the noisy stochastic block model to an observed dense graph and to perform a node clustering. Moreover, a graph inference procedure to recover the underlying binary graph. This procedure comes with a control of the false discovery rate. The method is described in the article "Powerful graph inference with false discovery rate control" by T. Rebafka, E. Roquain, F. Villers (2020) <arXiv:1907.10176>.
Maintained by Tabea Rebafka. Last updated 4 years ago.
6.7 match 2.00 score 2 scriptscovaruber
sommer:Solving Mixed Model Equations in R
Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 21 days ago.
average-informationmixed-modelsrcpparmadilloopenblascppopenmp
1.0 match 43 stars 12.70 score 300 scripts 9 dependentslaurimeh
lmfor:Functions for Forest Biometrics
Functions for different purposes related to forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, modelling of diameter distributions and estimation off stand density using ITD. Several empirical datasets are also included.
Maintained by Lauri Mehtatalo. Last updated 3 years ago.
5.1 match 3 stars 2.42 score 29 scripts 1 dependentscran
spuRs:Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R"
Provides functions and datasets from Jones, O.D., R. Maillardet, and A.P. Robinson. 2014. An Introduction to Scientific Programming and Simulation, Using R. 2nd Ed. Chapman And Hall/CRC.
Maintained by Andrew Robinson. Last updated 7 years ago.
7.3 match 1 stars 1.66 score 46 scriptswahani
saeRobust:Robust Small Area Estimation
Methods to fit robust alternatives to commonly used models used in Small Area Estimation. The methods here used are based on best linear unbiased predictions and linear mixed models. At this time available models include area level models incorporating spatial and temporal correlation in the random effects.
Maintained by Sebastian Warnholz. Last updated 1 years ago.
2.4 match 1 stars 4.03 score 12 scripts 3 dependentscran
MultiGlarmaVarSel:Variable Selection in Sparse Multivariate GLARMA Models
Performs variable selection in high-dimensional sparse GLARMA models. For further details we refer the reader to the paper Gomtsyan et al. (2022), <arXiv:2208.14721>.
Maintained by Marina Gomtsyan. Last updated 3 years ago.
3.6 match 2.00 scorecran
GlarmaVarSel:Variable Selection in Sparse GLARMA Models
Performs variable selection in high-dimensional sparse GLARMA models. For further details we refer the reader to the paper Gomtsyan et al. (2020), <arXiv:2007.08623v1>.
Maintained by Marina Gomtsyan. Last updated 3 years ago.
3.6 match 2.00 score 2 scriptsmgomtsyan
NBtsVarSel:Variable Selection in a Specific Regression Time Series of Counts
Performs variable selection in sparse negative binomial GLARMA (Generalised Linear Autoregressive Moving Average) models. For further details we refer the reader to the paper Gomtsyan (2023), <arXiv:2307.00929>.
Maintained by Marina Gomtsyan. Last updated 2 years ago.
3.6 match 2.00 score 2 scriptsgarybaylor
mixR:Finite Mixture Modeling for Raw and Binned Data
Performs maximum likelihood estimation for finite mixture models for families including Normal, Weibull, Gamma and Lognormal by using EM algorithm, together with Newton-Raphson algorithm or bisection method when necessary. It also conducts mixture model selection by using information criteria or bootstrap likelihood ratio test. The data used for mixture model fitting can be raw data or binned data. The model fitting process is accelerated by using R package 'Rcpp'.
Maintained by Youjiao Yu. Last updated 5 months ago.
1.0 match 8 stars 5.66 score 95 scripts 1 dependentsbioc
fmrs:Variable Selection in Finite Mixture of AFT Regression and FMR Models
The package obtains parameter estimation, i.e., maximum likelihood estimators (MLE), via the Expectation-Maximization (EM) algorithm for the Finite Mixture of Regression (FMR) models with Normal distribution, and MLE for the Finite Mixture of Accelerated Failure Time Regression (FMAFTR) subject to right censoring with Log-Normal and Weibull distributions via the EM algorithm and the Newton-Raphson algorithm (for Weibull distribution). More importantly, the package obtains the maximum penalized likelihood (MPLE) for both FMR and FMAFTR models (collectively called FMRs). A component-wise tuning parameter selection based on a component-wise BIC is implemented in the package. Furthermore, this package provides Ridge Regression and Elastic Net.
Maintained by Farhad Shokoohi. Last updated 5 months ago.
survivalregressiondimensionreduction
1.0 match 3 stars 5.00 score 55 scripts 1 dependentscran
Copula.Markov:Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series
Estimation and statistical process control are performed under copula-based time-series models. Available are statistical methods in Long and Emura (2014 JCSA), Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>, Huang and Emura (2021 Commun Stat-Simul) <DOI:10.1080/03610918.2019.1602647>, Lin et al. (2021 Comm Stat-Simul) <DOI:10.1080/03610918.2019.1652318>, Sun et al. (2020 JSS Series in Statistics)<DOI:10.1007/978-981-15-4998-4>, and Huang and Emura (2021, in revision).
Maintained by Takeshi Emura. Last updated 3 years ago.
3.3 match 3 stars 1.48 scorejuhkim111
MGLM:Multivariate Response Generalized Linear Models
Provides functions that (1) fit multivariate discrete distributions, (2) generate random numbers from multivariate discrete distributions, and (3) run regression and penalized regression on the multivariate categorical response data. Implemented models include: multinomial logit model, Dirichlet multinomial model, generalized Dirichlet multinomial model, and negative multinomial model. Making the best of the minorization-maximization (MM) algorithm and Newton-Raphson method, we derive and implement stable and efficient algorithms to find the maximum likelihood estimates. On a multi-core machine, multi-threading is supported.
Maintained by Juhyun Kim. Last updated 3 years ago.
1.0 match 4 stars 4.65 score 53 scripts 1 dependentsjinhuasu
SemiEstimate:Solve Semi-Parametric Estimation by Implicit Profiling
Semi-parametric estimation problem can be solved by two-step Newton-Raphson iteration. The implicit profiling method<arXiv:2108.07928> is an improved method of two-step NR iteration especially for the implicit-bundled type of the parametric part and non-parametric part. This package provides a function semislv() supporting the above two methods and numeric derivative approximation for unprovided Jacobian matrix.
Maintained by Jinhua Su. Last updated 3 years ago.
1.0 match 3.70 score 3 scriptsbeanb2
intkrige:A Numerical Implementation of Interval-Valued Kriging
An interval-valued extension of ordinary and simple kriging. Optimization of the function is based on a generalized interval distance. This creates a non-differentiable cost function that requires a differentiable approximation to the absolute value function. This differentiable approximation is optimized using a Newton-Raphson algorithm with a penalty function to impose the constraints. Analyses in the package are driven by the 'intsp' and 'intgrd' classes, which are interval-valued extensions of 'SpatialPointsDataFrame' and 'SpatialPixelsDataFrame' respectively. The package includes several wrappers to functions in the 'gstat' and 'sp' packages.
Maintained by Brennan Bean. Last updated 4 years ago.
1.0 match 3.70 score 6 scriptscran
glmglrt:GLRT P-Values in Generalized Linear Models
Provides functions to compute Generalized Likelihood Ratio Tests (GLRT) also known as Likelihood Ratio Tests (LRT) and Rao's score tests of simple and complex contrasts of Generalized Linear Models (GLMs). It provides the same interface as summary.glm(), adding GLRT P-values, less biased than Wald's P-values and consistent with profile-likelihood confidence interval generated by confint(). See Wilks (1938) <doi:10.1214/aoms/1177732360> for the LRT chi-square approximation. See Rao (1948) <doi:10.1017/S0305004100023987> for Rao's score test. See Wald (1943) <doi:10.2307/1990256> for Wald's test.
Maintained by André GILLIBERT. Last updated 5 years ago.
3.3 match 1.00 scoresangkyustat
EMSS:Some EM-Type Estimation Methods for the Heckman Selection Model
Some EM-type algorithms to estimate parameters for the well-known Heckman selection model are provided in the package. Such algorithms are as follow: ECM(Expectation/Conditional Maximization), ECM(NR)(the Newton-Raphson method is adapted to the ECM) and ECME(Expectation/Conditional Maximization Either). Since the algorithms are based on the EM algorithm, they also have EM’s main advantages, namely, stability and ease of implementation. Further details and explanations of the algorithms can be found in Zhao et al. (2020) <doi: 10.1016/j.csda.2020.106930>.
Maintained by Sang Kyu Lee. Last updated 3 years ago.
1.0 match 2.48 score 1 scriptsnovacta
nprotreg:Nonparametric Rotations for Sphere-Sphere Regression
Fits sphere-sphere regression models by estimating locally weighted rotations. Simulation of sphere-sphere data according to non-rigid rotation models. Provides methods for bias reduction applying iterative procedures within a Newton-Raphson learning scheme. Cross-validation is exploited to select smoothing parameters. See Marco Di Marzio, Agnese Panzera & Charles C. Taylor (2018) <doi:10.1080/01621459.2017.1421542>.
Maintained by Giovanni Lafratta. Last updated 1 years ago.
1.0 match 1 stars 2.34 score 44 scriptsklauschn
fastM:Fast Computation of Multivariate M-Estimators
Implements the new algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators. The algorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) <doi:10.1016/j.jmva.2015.11.009>.
Maintained by Klaus Nordhausen. Last updated 7 years ago.
1.0 match 1.00 score 5 scripts