Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.

This package provides row-level data provenance tracking for analytical pipelines. Tags datasets with unique lineage identifiers that persist through filter, join, and derive operations. Requires documented reasons for every row exclusion, capturing who was removed, why, and at which pipeline stage. Variable derivations are registered as structured specifications linking output variables back to their source. Any row in any downstream dataset can be traced back to its origin via lg_trace(). Generates structured HTML provenance reports suitable for regulatory submissions, internal audit, or analytical documentation. General-purpose: works for clinical data, machine learning pipelines, financial modelling, epidemiology, or any workflow where row-level accountability matters. Optional features support pharmaceutical users including population flag definitions, source-to-analysis variable mapping, and Reviewer's Guide-aligned report output. Complements the regulog package for tamper-evident session-level audit logging. For more details see <https://reprostats.org/lineager/>.

This package provides a shiny application to construct age-specific life tables and fertility schedules from individual female daily egg records. The application computes age-specific survival and fertility functions and estimates key demographic parameters including the net reproductive rate, mean generation time, intrinsic rate of increase, finite rate of increase and doubling time. Optional confidence intervals can be obtained using percentile bootstrap or delete-1 jackknife resampling at the female level. Methods and definitions follow Stevens (2009) <doi:10.1007/978-0-387-89882-7> and Rossini et al. (2024) <doi:10.1371/journal.pone.0299598>.

This package provides methods for estimation and statistical inference on directional and fluctuating selection in age-structured populations.

Flexible procedures to compute local density-based outlier scores for ranking outliers. Both exact and approximate nearest neighbor search can be implemented, while also accommodating multiple neighborhood sizes and four different local density-based methods. It allows for referencing a random subsample of the input data or a user specified reference data set to compute outlier scores against, so both unsupervised and semi-supervised outlier detection can be implemented.

This package provides a suite of tools for literature-based discovery in biomedical research. Provides functions for retrieving scientific articles from PubMed and other NCBI databases, extracting biomedical entities (diseases, drugs, genes, etc.), building co-occurrence networks, and applying various discovery models including ABC', AnC', LSI', and BITOLA'. The package also includes visualization tools for exploring discovered connections.

This package provides 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.

This package provides a suite of tools to use the eBird database (<https://ebird.org/home/>) and APIs to compare users species lists to recent observations and create a report of the top sites to visit to see new species.

Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.

Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (D. Robelin, S. Déjean, S. Mercier (2025) <doi:10.24072/pcjournal.650> ; S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://pmc.ncbi.nlm.nih.gov/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).

This package provides flexible but lightweight logging facilities for R scripts. Supports priority levels for logs and messages, flagging messages, capturing script output, switching logs, and logging to files or connections.

Facilitates access to the Comparative Legislators Database (CLD). The CLD includes political, sociodemographic, career, online presence, public attention, and visual information for over 67,000 contemporary and historical politicians from 16 countries.

Large language model agents as governed research instruments, built on LLMR'. The package supports designed conversations and factorial experiments with declared tools and budgets. Each run produces an inspectable record that can be archived and checked.

Non-parametric estimators for casual effects based on longitudinal modified treatment policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment, and traditional longitudinal effects. Continuous, binary, categorical treatments, and multivariate treatments are allowed as well are censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects can be calculated and relative risks and odds ratios may be calculated for binary outcomes. Supports survival outcomes with competing risks (Diaz, Hoffman, and Hejazi; <doi:10.1007/s10985-023-09606-7>).

Profiles political leaders at a distance from text data such as speeches, interviews, press conferences, and other public statements. Computes Leadership Trait Analysis scores for seven personality traits -- including need for power, conceptual complexity, and self-confidence -- and classifies leaders into one of eight leadership styles. Also computes Operational Code Analysis scores summarising a leader's beliefs about politics and the use of power.

Dimensionality reduction techniques for binary data including logistic PCA.

Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop. This is a derived work from the later package aiming to reduce the number of dependencies.

Extensive functions for Lmoments (LMs) and probability-weighted moments (PWMs), distribution parameter estimation, LMs for distributions, LM ratio diagrams, multivariate Lcomoments, and asymmetric (asy) trimmed LMs (TLMs). Maximum likelihood and maximum product spacings estimation are available. Right-tail and left-tail LM censoring by threshold or indicator variable are available. LMs of residual (resid) and reversed (rev) residual life are implemented along with 13 quantile operators for reliability analyses. Exact analytical bootstrap estimates of order statistics, LMs, and LM var-covars are available. Harri-Coble Tau34-squared Normality Test is available. Distributions with L, TL, and added (+) support for right-tail censoring (RC) encompass: Asy Exponential (Exp) Power [L], Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp Poisson [L], Gen Extreme Value [L], Gen Lambda [L, TL], Gen Logistic [L], Gen Normal [L], Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3p log-Normal [L], Pearson Type III [L], Polynomial Density-Quantile 3 and 4 [L], Rayleigh [L], Rev-Gumbel [L+RC], Rice [L], Singh Maddala [L], Slash [TL], 3p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].

Life and Fertility Tables are appropriate to study the dynamics of arthropods populations. This package provides utilities for constructing Life Tables and Fertility Tables, related demographic parameters, and some simple graphs of interest. It also offers functions to transform the obtained data into a known format for better manipulation. In addition, two methods for obtaining the confidence interval are included.

This package provides functions implementing multivariate state space models for purposes of time series analysis and forecasting. The focus of the package is on multivariate models, such as Vector Exponential Smoothing, Vector ETS (Error-Trend-Seasonal model) etc. It currently includes Vector Exponential Smoothing (VES, de Silva et al., 2010, <doi:10.1177/1471082X0901000401>), Vector ETS (Svetunkov et al., 2023, <doi:10.1016/j.ejor.2022.04.040>) and simulation function for VES.

This package contains a suite of shiny applications meant to explore linear model inference feature through simulation and games.

Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.

Bayesian Survival models via the mixture of Log-Normal distribution extends the well-known survival models and accommodates different behaviour over time and considers higher censored survival times. The proposal combines mixture distributions Fruhwirth-Schnatter(2006) <doi:10.1007/s11336-009-9121-4>, and data augmentation techniques Tanner and Wong (1987) <doi:10.1080/01621459.1987.10478458>.

The goal of LCMSQA is to make it easy to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments using a shiny application. This package provides interactive data visualizations for quality control (QC) samples, including total ion current chromatogram (TIC), base peak chromatogram (BPC), mass spectrum, extracted ion chromatogram (XIC), and feature detection results from internal standards or known metabolites.