The proposed method aims at predicting the longitudinal mean response trajectory by a kernel-based estimator. The kernel estimator is constructed by imposing weights based on subject-wise similarity on L2 metric space between predictor trajectories as well as time proximity. Users could also perform variable selections to derive functional predictors with predictive significance by the proposed multiplicative model with multivariate Gaussian kernels.

Detects and suggests fixes for semantic inconsistencies in data frames by calling large language models (LLMs) through a unified, provider-agnostic interface. Supported providers include OpenAI ('GPT-4o', GPT-4o-mini') <https://platform.openai.com>, Anthropic ('Claude') <https://www.anthropic.com>, Google ('Gemini') <https://ai.google.dev>, Groq (free-tier LLaMA and Mixtral') <https://groq.com>, and local Ollama models <https://ollama.com>. The package identifies issues that rule-based tools cannot detect: abbreviation variants, typographic errors, case inconsistencies, and malformed values. Results are returned as tidy data frames with column, row index, detected value, issue type, suggested fix, and confidence score. An offline fallback using statistical and fuzzy-matching methods is provided for use without any application programming interface (API) key. Interactive fix application with human review is supported via apply_fixes()'. Methods follow de Jonge and van der Loo (2013) <https://cran.r-project.org/doc/contrib/de_Jonge+van_der_Loo-Introduction_to_data_cleaning_with_R.pdf> and Chaudhuri et al. (2003) <doi:10.1145/872757.872796>.

Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) <doi:10.1111/1755-0998.13349> and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.

Includes some procedures for latent variable modeling with a particular focus on multilevel data. The LAM package contains mean and covariance structure modelling for multivariate normally distributed data (mlnormal(); Longford, 1987; <doi:10.1093/biomet/74.4.817>), a general Metropolis-Hastings algorithm (amh(); Roberts & Rosenthal, 2001, <doi:10.1214/ss/1015346320>) and penalized maximum likelihood estimation (pmle(); Cole, Chu & Greenland, 2014; <doi:10.1093/aje/kwt245>).

Density, distribution function, quantile function and random generation for the L-Logistic distribution with parameters m and phi. The parameter m is the median of the distribution.

This package contains functions to estimate a penalized regression model using 3CoSE algorithm, see Weber, Striaukas, Schumacher Binder (2018) <doi:10.2139/ssrn.3211163>.

This package provides lightweight, dependency-minimal implementations of Langevin diffusion based Markov chain Monte Carlo samplers, including the Unadjusted Langevin Algorithm (ULA) and the Metropolis-Adjusted Langevin Algorithm (MALA). The core sampling loops are written in C++ via Rcpp and RcppArmadillo for performance, while exposing a simple R-level interface where the user supplies the gradient of the negative log-density (and, for MALA, the negative log-density itself). Intended as a building block for Bayesian inference and stochastic optimization rather than a full probabilistic programming framework. Methods follow Roberts and Tweedie (1996) <doi:10.2307/3318418> and Roberts and Rosenthal (1998) <doi:10.1111/1467-9868.00123>.

Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.

Interpretable nonparametric modeling of longitudinal data using additive Gaussian process regression. Contains functionality for inferring covariate effects and assessing covariate relevances. Models are specified using a convenient formula syntax, and can include shared, group-specific, non-stationary, heterogeneous and temporally uncertain effects. Bayesian inference for model parameters is performed using Stan'. The modeling approach and methods are described in detail in Timonen et al. (2021) <doi:10.1093/bioinformatics/btab021>.

This package contains functions for a flexible varying-coefficient landmark model by incorporating multiple short-term events into the prediction of long-term survival probability. For more information about landmark prediction please see Li, W., Ning, J., Zhang, J., Li, Z., Savitz, S.I., Tahanan, A., Rahbar.M.H., (2023+). "Enhancing Long-term Survival Prediction with Multiple Short-term Events: Landmarking with A Flexible Varying Coefficient Model".

Estimates lacunarity and generalized lacunarity for unidimensional binary time series. The lacunarity index summarizes the similarity of parts from different regions of a series at a given scale by averaging the behavior of variable size structures of zeros and ones. The generalized lacunarity concept provides an enhanced measure of the organization of the gaps over all measured scales and over the different arrangements of smaller and larger gaps in the series.

Simplex optimization algorithms as firstly proposed by Spendley et al. (1962) <doi:10.1080/00401706.1962.10490033> and later modified by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> for laboratory and manufacturing processes. The package also provides tools for graphical representation of the simplexes and some example response surfaces that are useful in illustrating the optimization process.

This package provides a bridge between the loon and ggplot2 packages. Extends the grammar of ggplot to add clauses to create interactive loon plots. Existing ggplot(s) can be turned into interactive loon plots and loon plots into static ggplot(s); the function loon.ggplot() is the bridge from one plot structure to the other.

It uses phenological and productivity-related variables derived from time series of vegetation indexes, such as the Normalized Difference Vegetation Index, to assess ecosystem dynamics and change, which eventually might drive to land degradation. The final result of the Land Productivity Dynamics indicator is a categorical map with 5 classes of land productivity dynamics, ranging from declining to increasing productivity. See www.sciencedirect.com/science/article/pii/S1470160X21010517/ for a description of the methods used in the package to calculate the indicator.

Routines for fitting Logic Regression models. Logic Regression is described in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005) <DOI:10.1002/gepi.20042>.

Insieme di funzioni di supporto al volume "Laboratorio di Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia, 2006. This package contains sets of functions defined in "Laboratorio di Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia, 2006. Function names and docs are in italian as well.

Read, register and compare point sets from single molecule localization microscopy.

Implementation of the methods described in Holzmann, Klar (2024) <doi: 10.1111/sjos.12733>. Lancaster correlation is a correlation coefficient which equals the absolute value of the Pearson correlation for the bivariate normal distribution, and is equal to or slightly less than the maximum correlation coefficient for a variety of bivariate distributions. Rank and moment-based estimators and corresponding confidence intervals are implemented, as well as independence tests based on these statistics.

Calculates landscape metrics for categorical landscape patterns in a tidy workflow. landscapemetrics reimplements the most common metrics from FRAGSTATS (<https://www.fragstats.org/>) and new ones from the current literature on landscape metrics. This package supports terra SpatRaster objects as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.

Alternate font rendering is useful when rendering text to novel graphics outputs where modern font rendering is not available or where bespoke text positioning is required. Bitmap and vector fonts allow for custom layout and rendering using pixel coordinates and line drawing. Formatted text is created as a data.frame of pixel coordinates (for bitmap fonts) or stroke coordinates (for vector fonts). All text can be easily previewed as a matrix or raster image. A selection of fonts is included with this package.

Estimate the slope and intercept of a bivariate linear relationship by calculating a posterior density that is invariant to interchange and scaling of the coordinates.

An RStudio addin that integrates large language model (LLM) assistance directly into the code-editing workflow. Features include: (1) generate R code from inline comments; (2) obtain LLM-assisted fixes for console errors; (3) insert plain-English explanations of selected code blocks; (4) a multi-turn Chat Panel with session-context awareness (loaded packages, global objects, source editor contents, console history). Supports OpenAI', Anthropic (Claude), DeepSeek', Groq', Together AI', OpenRouter', Ollama (fully local, no API key required), and any OpenAI'-compatible custom endpoint (e.g. LM Studio', vLLM', llama.cpp').

This package provides a toolbox for R arrays. Flexibly split, bind, reshape, modify, subset and name arrays.

This package provides the method for computing the local partial autocorrelation function for locally stationary wavelet time series from Killick, Knight, Nason, Eckley (2020) <doi:10.1214/20-EJS1748>.