Datasets for 'spatstat' Family

Contains all the datasets for the 'spatstat' family of packages.

Epigenome-Wide Mediation Analysis Study

DNA methylation is essential for human, and environment can change the DNA methylation and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide. For more information on the methods we used, please see the following references: Tingley, D. (2014) , Turner, S. D. (2018) , Rosseel, D. (2012) .

Waiting List Metrics Using Queuing Theory

Waiting list management using queuing theory to analyse, predict and manage queues, based on the approach described in Fong et al. (2022) . Aimed at UK National Health Service (NHS) applications, waiting list summary statistics, target-value calculations, waiting list simulation, and scheduling functions are included.

Draw XmR Charts for NHS 'Making Data Count' Programme

Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHS 'Making Data Count' programme, and allows users to draw XmR charts, use change points and apply rules with summary indicators for when rules are breached.

Toolkit for Reduced Form and Structural Smooth Transition Vector Autoregressive Models

Penalized and non-penalized maximum likelihood estimation of smooth transition vector autoregressive models with various types of transition weight functions, conditional distributions, and identification methods. Constrained estimation with various types of constraints is available. Residual based model diagnostics, forecasting, simulations, counterfactual analysis, and computation of impulse response functions, generalized impulse response functions, generalized forecast error variance decompositions, as well as historical decompositions. See Heather Anderson, Farshid Vahid (1998) , Helmut Lütkepohl, Aleksei Netšunajev (2017) , Markku Lanne, Savi Virolainen (2025) , Savi Virolainen (2025) .

Compare Two Data Frames and Summarise the Difference

Easy comparison of two tabular data objects in R. Specifically designed to show differences between two sets of data in a useful way that should make it easier to understand the differences, and if necessary, help you work out how to remedy them. Aims to offer a more useful output than all.equal() when your two data sets do not match, but isn't intended to replace all.equal() as a way to test for equality.

A Calculator for Melting Temperature of Nucleic Acid Sequences

A comprehensive R package for calculating melting temperatures of nucleic acid sequences. Implements three calculation methods: 1. Wallace rule (Thein & Wallace, 1986) 2. Empirical formulas based on GC content (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001) 3. Nearest neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; Santalucia, 2005) Includes corrections for: - Salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) - Chemical compounds (dimethyl sulfoxide, formamide) Supports both direct sequence input and FASTA file input.

Species Sensitivity Distributions

Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) . The ssdtools package uses Maximum Likelihood to fit distributions such as the gamma, log-logistic, log-normal and log-normal log-normal mixture. Multiple distributions can be averaged using Akaike Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by bootstrapping.

Data Visualisation Functions for Epidemiological Data Science Products

Tools for making epidemiological reporting easier with consistent static and dynamic charts and maps. Builds on 'ggplot2' for static visualizations as described in Wickham (2016) and 'plotly' for interactive visualizations as described in Sievert (2020) .

Tools for Handling Spatial Objects

Please note that 'maptools' will be retired during October 2023, plan transition at your earliest convenience (see < https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance); some functionality will be moved to 'sp'. Set of tools for manipulating geographic data. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat.geom', 'maps', and others.