The algorithm of semi-supervised learning based on finite Gaussian mixture models with a missing-data mechanism is designed for a fitting g-class Gaussian mixture model via maximum likelihood (ML). It is proposed to treat the labels of the unclassified features as missing-data and to introduce a framework for their missing as in the pioneering work of Rubin (1976) for missing in incomplete data analysis. This dependency in the missingness pattern can be leveraged to provide additional information about the optimal classifier as specified by Bayesâ rule.

In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.

Fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. Loos, M., Gerber, C., Corona, F., Hollender, J., Singer, H. (2015) <doi:10.1021/acs.analchem.5b00941>.

This package provides tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.

This package provides functions for easy building of error correction models (ECM) for time series regression.

This package provides functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.

The nonparametric trend and its derivatives in equidistant time series (TS) with long-memory errors can be estimated. The estimation is conducted via local polynomial regression using an automatically selected bandwidth obtained by a built-in iterative plug-in algorithm or a bandwidth fixed by the user. The smoothing methods of the package are described in Letmathe, S., Beran, J. and Feng, Y., (2023) <doi:10.1080/03610926.2023.2276049>.

This package provides tools for accessing and analyzing eBird Status and Trends Data Products (<https://science.ebird.org/en/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by member of the public. eBird Status and Trends uses these data to model global bird distributions, abundances, and population trends at a high spatial and temporal resolution.

Processing tools to create emissions for use in numerical air quality models. Emissions can be calculated both using emission factors and activity data (Schuch et al 2018) <doi:10.21105/joss.00662> or using pollutant inventories (Schuch et al., 2018) <doi:10.30564/jasr.v1i1.347>. Functions to process individual point emissions, line emissions and area emissions of pollutants are available as well as methods to incorporate alternative data for Spatial distribution of emissions such as satellite images (Gavidia-Calderon et. al, 2018) <doi:10.1016/j.atmosenv.2018.09.026> or openstreetmap data (Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.

This package provides tools to download data from the Eurostat database <https://ec.europa.eu/eurostat> together with search and manipulation utilities.

Fits Leroux model in spectral domain to estimate causal spatial effect as detailed in Guan, Y; Page, G.L.; Reich, B.J.; Ventrucci, M.; Yang, S; (2020) <arXiv:2012.11767>. Both the parametric and semi-parametric models are available. The semi-parametric model relies on INLA'. The INLA package can be obtained from <https://www.r-inla.org/>.

Fits a state-space mass-balance model for marine ecosystems, which implements dynamics derived from Ecopath with Ecosim ('EwE') <https://ecopath.org/> while fitting to time-series of fishery catch, biomass indices, age-composition samples, and weight-at-age data. Ecostate fits biological parameters (e.g., equilibrium mass) and measurement parameters (e.g., catchability coefficients) jointly with residual variation in process errors, and can include Bayesian priors for parameters.

An extension of knitr that adds flexibility in several ways. One common source of frustration with knitr is that it assumes the directory where the source file lives should be the working directory, which is often not true. ezknitr addresses this problem by giving you complete control over where all the inputs and outputs are, and adds several other convenient features to make rendering markdown/HTML documents easier.

Deliver the full functionality of ECharts with minimal overhead. echarty users build R lists for ECharts API. Lean set of powerful commands.

Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.

An implementation of extended state-space SIR models developed by Song Lab at UM school of Public Health. There are several functions available by 1) including a time-varying transmission modifier, 2) adding a time-dependent quarantine compartment, 3) adding a time-dependent antibody-immunization compartment. Wang L. (2020) <doi:10.6339/JDS.202007_18(3).0003>.

Fit and plot some nonlinear models.

An interface to the Python InterpretML framework for fitting explainable boosting machines (EBMs); see Nori et al. (2019) <doi:10.48550/arXiv.1909.09223> for details. EBMs are a modern type of generalized additive model that use tree-based, cyclic gradient boosting with automatic interaction detection. They are often as accurate as state-of-the-art blackbox models while remaining completely interpretable.

Fitting and testing multi-attribute probabilistic choice models, especially the Bradley-Terry-Luce (BTL) model (Bradley & Terry, 1952 <doi:10.1093/biomet/39.3-4.324>; Luce, 1959), elimination-by-aspects (EBA) models (Tversky, 1972 <doi:10.1037/h0032955>), and preference tree (Pretree) models (Tversky & Sattath, 1979 <doi:10.1037/0033-295X.86.6.542>).

Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM). Includes functions to conduct mediation and moderation analyses and to diagnose multicollinearity. URL: <https://github.com/sduxbury/ergMargins>. BugReports: <https://github.com/sduxbury/ergMargins/issues>. Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>. Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>. Mize, Trenton D. (2019) <doi:10.15195/v6.a4>. Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>. Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>. Duxbury, Scott W, Jenna Wertsching (2023) <doi:10.1016/j.socnet.2023.02.003>. Huang, Peng, Carter Butts (2023) <doi:10.1016/j.socnet.2023.07.001>.

Create encrypted html files that are fully self contained and do not require any additional software. Using the package you can encrypt arbitrary html files and also directly create encrypted rmarkdown html reports.

This package provides a system for importing electrophysiological signal, based on the Waveform Database (WFDB) software package, written by Moody et al 2022 <doi:10.13026/gjvw-1m31>. A R-based system to utilize WFDB functions for reading and writing signal data, as well as functions for visualization and analysis are provided. A stable and broadly compatible class for working with signal data, supporting the reading in of cardiac electrophysiological files such as intracardiac electrograms, is introduced.

By using a multispectral image and ESRI shapefile (Point/ Line/ Polygon), a data table will be generated for classification, regression or other processing. The data table will be contained by band wise raster values and shapefile ids (User Defined).

This package implements the hybrid framework for event prediction described in Fang & Zheng (2011, <doi:10.1016/j.cct.2011.05.013>). To estimate the survival function the event prediction is based on, a piecewise exponential hazard function is fit to the time-to-event data to infer the potential change points. Prior to the last identified change point, the survival function is estimated using Kaplan-Meier, and the tail after the change point is fit using piecewise exponential.