Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

This package provides functions to estimate the parameters of the generalized Poisson distribution with or without covariates using maximum likelihood. The references include Nikoloulopoulos A.K. & Karlis D. (2008). "On modeling count data: a comparison of some well-known discrete distributions". Journal of Statistical Computation and Simulation, 78(3): 437--457, <doi:10.1080/10629360601010760> and Consul P.C. & Famoye F. (1992). "Generalized Poisson regression model". Communications in Statistics - Theory and Methods, 21(1): 89--109, <doi:10.1080/03610929208830766>.

Streamline the creation of common charts by taking care of a lot of data preprocessing and plot customization for the user. Provides a high-level interface to create plots using ggplot2'.

Read and manipulate landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

Extremely efficient procedures for fitting regularization path with l0, l1, and truncated lasso penalty for linear regression and logistic regression models. This version is a completely new version compared with our previous version, which was mainly based on R. New core algorithms are developed and are now written in C++ and highly optimized.

Likelihood ratio tests for genome-wide association and genome-wide linkage analysis under heterogeneity.

Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, calculating inbreeding coefficients (Meuwissen & Luo, 1992 <doi:10.1186/1297-9686-24-4-305>), as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.

This package provides methods for dividing data into groups. Create balanced partitions and cross-validation folds. Perform time series windowing and general grouping and splitting of data. Balance existing groups with up- and downsampling or collapse them to fewer groups.

This package provides a suite of function-building tools centered around a (forward) composition operator, %>>>%, which extends the semantics of the magrittr %>% operator and supports Tidyverse quasiquotation. It enables you to construct composite functions that can be inspected and transformed as list-like objects. In conjunction with %>>>%, a compact function constructor, fn(), and a partial-application constructor, partial(), are also provided; both support quasiquotation.

Efficient algorithms for fitting the regularization path of linear regression, GLM, and Cox regression models with grouped penalties. This includes group selection methods such as group lasso, group MCP, and group SCAD as well as bi-level selection methods such as the group exponential lasso, the composite MCP, and the group bridge. For more information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>, Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang (2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015) <doi:10.1111/biom.12300>, or visit the package homepage <https://pbreheny.github.io/grpreg/>.

Helper to add insets based on geom_sf() from ggplot2'. This package gives you a drop-in replacement for geom_sf() that supports adding a zoomed inset map without having to create and embed a separate plot.

This package implements the Gaussian Kernel Robust Regression (GKRReg / GKRR) method proposed by De Carvalho, Lima Neto and Ferreira (2017) <doi:10.1016/j.neucom.2016.12.035>. The method re-weights observations iteratively using the Gaussian kernel so that poorly-fitted observations (outliers, leverage points) receive small weights, yielding resistance to Y-space outliers, X-space outliers and leverage points. Convergence is guaranteed by Propositions 4.1 and 4.2 of the original paper. Three estimators for the kernel width hyper-parameter are provided (S1: Caputo, S2: pairwise median, S3: residual variance). Inference is provided via an analytic sandwich variance estimator (default) or via bootstrap (percentile, normal and BCa intervals with p-values) through gkrr_boot(). Six real datasets from the robust regression literature are included to facilitate reproducible comparisons.

Visualise overlapping time series lines as a heatmap of line density. Provides a ggplot2 statistic implementing the DenseLines algorithm, which "normalizes time series by the arc length to compute accurate densities" (Moritz and Fisher, 2018) <doi:10.48550/arXiv.1808.06019>.

The genetic algorithm can be used directly to find the similarity of users and more effectively to increase the efficiency of the collaborative filtering method. By identifying the nearest neighbors to the active user, before the genetic algorithm, and by identifying suitable starting points, an effective method for user-based collaborative filtering method has been developed. This package uses an optimization algorithm (continuous genetic algorithm) to directly find the optimal similarities between active users (users for whom current recommendations are made) and others. First, by determining the nearest neighbor and their number, the number of genes in a chromosome is determined. Each gene represents the neighbor's similarity to the active user. By estimating the starting points of the genetic algorithm, it quickly converges to the optimal solutions. The positive point is the independence of the genetic algorithm on the number of data that for big data is an effective help in solving the problem.

Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>. gambin is short for gamma-binomial'. The main function is fit_abundances(), which estimates the alpha parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.

Simple and user-friendly wrappers to the saemix package for performing linear and non-linear mixed-effects regression modeling for growth data to account for clustering or longitudinal analysis via repeated measurements. The package allows users to fit a variety of growth models, including linear, exponential, logistic, and Gompertz functions. For non-linear models, starting values are automatically calculated using initial least-squares estimates. The package includes functions for summarizing models, visualizing data and results, calculating doubling time and other key statistics, and generating model diagnostic plots and residual summary statistics. It also provides functions for generating publication-ready summary tables for reports. Additionally, users can fit linear and non-linear least-squares regression models if clustering is not applicable. The mixed-effects modeling methods in this package are based on Comets, Lavenu, and Lavielle (2017) <doi:10.18637/jss.v080.i03> as implemented in the saemix package. Please contact us at models@dfci.harvard.edu with any questions.

Using mixed effects models to analyse longitudinal gene expression can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, and are less optimal for analysing longitudinal data. This package provides negative binomial and Gaussian mixed effects models to fit gene expression and other biological data across repeated samples. This is particularly useful for investigating changes in RNA-Sequencing gene expression between groups of individuals over time, as described in: Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M. J., & Pitzalis, C. (2022) Nature medicine <doi:10.1038/s41591-022-01789-0>.

This package provides a ggplot2 based implementation of biplots, giving a representation of a dataset in a two dimensional space accounting for the greatest variance, together with variable vectors showing how the data variables relate to this space. It provides a replacement for stats::biplot(), but with many enhancements to control the analysis and graphical display. It implements biplot and scree plot methods which can be used with the results of prcomp(), princomp(), FactoMineR::PCA(), ade4::dudi.pca() or MASS::lda() and can be customized using ggplot2 techniques.

Palettes based on video games.

This package provides tools to download datasets of German elections covering local, state, federal, mayoral, European Parliament, and county (Kreistag) elections, with federal county-level coverage from 1953 and other families extending through 2025. The package supplies turnout, vote shares, and derived indicators at the municipal and county level, including geographically harmonized datasets that account for changes in municipal boundaries over time and incorporate mail-in voting districts. Bundled data includes county-level INKAR covariates (1995-2022) and municipality-level Zensus 2022 indicators. Data is sourced from <https://github.com/awiedem/german_election_data>.

Implementing generalized structured component analysis (GSCA) and its basic extensions, including constrained single and multiple group analysis, and second order latent variable modeling. For a comprehensive overview of GSCA, see Hwang & Takane (2014, ISBN: 9780367738754).

This package provides functions that automate downloading and importing University of East Anglia Climate Research Unit ('CRU') CL v. 2.0 climatology data, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a data.table object or a terra SpatRaster object. CRU CL v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arc minutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.

Wrapper ggplot2 functions for publication-quality visualisation. Aligned with ggplot2 and tidyverse'. Covers much of what ggplot2 does.

Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.