An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.

This package provides functions for range estimation in birds based on Pennycuick (2008) and Pennycuick (1975), Flight program which compliments Pennycuick (2008) requires manual entry of birds which can be tedious when there are thousands of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975) and time-marching computation method "constant muscle mass" as in Pennycuick (1998). See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>, and Pennycuick (2008, ISBN:9780080557816).

This package provides a population genetic simulator, which is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst) as explained in Balding and Nichols (1995) <doi:10.1007/BF01441146>. This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.

It is known that current false discovery rate (FDR) procedures can be very conservative when applied to multiple testing in the discrete paradigm where p-values (and test statistics) have discrete and heterogeneous null distributions. This package implements more powerful weighted or adaptive FDR procedures for FDR control and estimation in the discrete paradigm. The package takes in the original data set rather than just the p-values in order to carry out the adjustments for discreteness and heterogeneity of p-value distributions. The package implements methods for two types of test statistics and their p-values: (a) binomial test on if two independent Poisson distributions have the same means, (b) Fisher's exact test on if the conditional distribution is the same as the marginal distribution for two binomial distributions, or on if two independent binomial distributions have the same probabilities of success.

Developed for the following tasks. 1 ) Computing the probability density function, cumulative distribution function, random generation, and estimating the parameters of the eleven mixture models. 2 ) Point estimation of the parameters of two - parameter Weibull distribution using twelve methods and three - parameter Weibull distribution using nine methods. 3 ) The Bayesian inference for the three - parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to grouped data using three methods including approximated maximum likelihood, expectation maximization, and maximum likelihood. 5 ) Estimating the parameters of the gamma, log-normal, and Weibull mixture models fitted to the grouped data through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve fitted to the height - diameter observation, 7 ) Estimating parameters, computing probability density function, cumulative distribution function, and generating realizations from gamma shape mixture model introduced by Venturini et al. (2008) <doi:10.1214/07-AOAS156> , 8 ) The Bayesian inference, computing probability density function, cumulative distribution function, and generating realizations from univariate and bivariate Johnson SB distribution, 9 ) Robust multiple linear regression analysis when error term follows skewed t distribution, 10 ) Estimating parameters of a given distribution fitted to grouped data using method of maximum likelihood, and 11 ) Estimating parameters of the Johnson SB distribution through the Bayesian, method of moment, conditional maximum likelihood, and two - percentile method.

Read and write PNG images with arrays, rasters, native rasters, numeric arrays, integer arrays, raw vectors and indexed values. This PNG encoder exposes configurable internal options enabling the user to select a speed-size tradeoff. For example, disabling compression can speed up writing PNG by a factor of 50. Multiple image formats are supported including raster, native rasters, and integer and numeric arrays at color depths of 1, 2, 3 or 4. 16-bit images are also supported. This implementation uses the libspng C library which is available from <https://github.com/randy408/libspng/>.

FS-DAM performs feature extraction through latent variables identification. Implementation is based on autoencoders with monotonicity and orthogonality constraints.

This package provides a collection of functions to manage, to investigate and to analyze data sets of financial assets from different points of view.

Multifactor nonparametric analysis of variance based on ranks. Builds on the Kruskal-Wallis H test and its 2x2 Scheirer-Ray-Hare extension to handle any factorial designs. Provides effect sizes, Dunn-Bonferroni pairwise-comparison matrices, and simple-effects analyses. Tailored for psychology and the social sciences, with beginner-friendly R syntax and outputs that can be dropped into journal reports. Includes helpers to export tab-separated results and compact tables of descriptive statistics (to APA-style reports).

This package provides a wrapper for the Filebin API. Filebin implements convenient file sharing on the web.

The algorithm assigns rareness/ outlierness score to every sample in voluminous datasets. The algorithm makes multiple estimations of the proximity between a pair of samples, in low-dimensional spaces. To compute proximity, FiRE uses Sketching, a variant of locality sensitive hashing. For more details: Jindal, A., Gupta, P., Jayadeva and Sengupta, D., 2018. Discovery of rare cells from voluminous single cell expression data. Nature Communications, 9(1), p.4719. <doi:10.1038/s41467-018-07234-6>.

Modelizations and previsions functions for Functional AutoRegressive processes using nonparametric methods: functional kernel, estimation of the covariance operator in a subspace, ...

This package implements the Mode Jumping Markov Chain Monte Carlo algorithm described in <doi:10.1016/j.csda.2018.05.020> and its Genetically Modified counterpart described in <doi:10.1613/jair.1.13047> as well as the sub-sampling versions described in <doi:10.1016/j.ijar.2022.08.018> for flexible Bayesian model selection and model averaging.

It offers comprehensive tools for the analysis of functional time series data, focusing on white noise hypothesis testing and goodness-of-fit evaluations, alongside functions for simulating data and advanced visualization techniques, such as 3D rainbow plots. These methods are described in Kokoszka, Rice, and Shang (2017) <doi:10.1016/j.jmva.2017.08.004>, Yeh, Rice, and Dubin (2023) <doi:10.1214/23-EJS2112>, Kim, Kokoszka, and Rice (2023) <doi:10.1214/23-ss143>, and Rice, Wirjanto, and Zhao (2020) <doi:10.1111/jtsa.12532>.

Computes unidimensional and multidimensional Reciprocity and Inaccuracy indices. These indices are applicable to common heterostylous populations and to any other type of stylar dimorphic and trimorphic populations, such as in enantiostylous and three-dimensional heterostylous plants. Simón-Porcar, V., A. J. Muñoz-Pajares, J. Arroyo, and S. D. Johnson. (in press) "FlowerMate: multidimensional reciprocity and inaccuracy indices for style-polymorphic plant populations.".

Finds the URL to the favicon for a website. This is useful if you want to display the favicon in an HTML document or web application, especially if the website is behind a firewall.

This package provides functionality to produce graphs of probability density functions and cumulative distribution functions with few keystrokes, allows shading under the curve of the probability density function to illustrate concepts such as p-values and critical values, and fits a simple linear regression line on a scatter plot with the equation as the main title.

Automated feature engineering functions tailored for credit scoring. It includes utilities for extracting structured features from timestamps, IP addresses, and email addresses, enabling enhanced predictive modeling for financial risk assessment.

This package contains functions for fitting shared frailty models with a semi-parametric baseline hazard with the Expectation-Maximization algorithm. Supported data formats include clustered failures with left truncation and recurrent events in gap-time or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable and the Power Variance Family are supported.

This package provides a tidy R interface for count time series analysis. It includes implementation of the INGARCH (Integer Generalized Autoregressive Conditional Heteroskedasticity) model from the tscount package and the GLARMA (Generalized Linear Autoregressive Moving Averages) model from the glarma package. Additionally, it offers automated parameter selection algorithms based on the minimization of a penalized likelihood.

This Rcpp'-based package implements highly efficient functions for the calculation of the Jonckheere-Terpstra statistic. It can be used for a variety of applications, including feature selection in machine learning problems, or to conduct genome-wide association studies (GWAS) with multiple quantitative phenotypes. The code leverages OpenMP directives for multi-core computing to reduce overall processing time.

Fit Elastic Net, Lasso, and Ridge regression and do cross-validation in a fast way. We build the algorithm based on Least Angle Regression by Bradley Efron, Trevor Hastie, Iain Johnstone, etc. (2004)(<doi:10.1214/009053604000000067 >) and some algorithms like Givens rotation and Forward/Back Substitution. In this way, many matrices to be computed are retained as triangular matrices which can eventually speed up the computation. The fitting algorithm for Elastic Net is written in C++ using Armadillo linear algebra library.

Package for parametric relative survival analyses. It allows to model non-linear and non-proportional effects and both non proportional and non linear effects, using splines (B-spline and truncated power basis), Weighted Cumulative Index of Exposure effect, with correction model for the life table. Both non proportional and non linear effects are described in Remontet, L. et al. (2007) <doi:10.1002/sim.2656> and Mahboubi, A. et al. (2011) <doi:10.1002/sim.4208>.

Fast censored linear regression for the accelerated failure time (AFT) model of Huang (2013) <doi:10.1111/sjos.12031>.