Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation

Fork of qgraph - Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) .

Plotting Multi-Dimensional Data

Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.

Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations

Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE). Includes routines that: (1) generate gradient and jacobian matrices (full and banded), (2) find roots of non-linear equations by the 'Newton-Raphson' method, (3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the 'Newton-Raphson' method, or by dynamically running, (4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). Includes fortran code.

Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Alluvial Plots in 'ggplot2'

Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables; see Riehmann, Hanfler, and Froehlich (2005) and Rosvall and Bergstrom (2010) . Alluvial plots are statistical graphics in the sense of Wilkinson (2006) ; they share elements with Sankey diagrams and parallel sets plots but are uniquely determined from the data and a small set of parameters. This package extends Wickham's (2010) layered grammar of graphics to generate alluvial plots from tidy data.

Latent Variable Analysis

Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.

Fast, Dependency-Free Geodesic Distance Calculations

Dependency-free, ultra fast calculation of geodesic distances. Includes the reference nanometre-accuracy geodesic distances of Karney (2013) , as used by the 'sf' package, as well as Haversine and Vincenty distances. Default distance measure is the "Mapbox cheap ruler" which is generally more accurate than Haversine or Vincenty for distances out to a few hundred kilometres, and is considerably faster. The main function accepts one or two inputs in almost any generic rectangular form, and returns either matrices of pairwise distances, or vectors of sequential distances.

Generalized Estimation Equation Solver

Generalized Estimation Equation solver.

Markov Chain Monte Carlo (MCMC) Package

Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

Coordinate System Transformations for Generic Map Data

Transform coordinates from a specified source to a specified target map projection. This uses the 'PROJ' library directly, by wrapping the 'PROJ' package which leverages 'libproj', otherwise the 'proj4' package. The 'reproj()' function is generic, methods may be added to remove the need for an explicit source definition. If 'proj4' is in use 'reproj()' handles the requirement for conversion of angular units where necessary. This is for use primarily to transform generic data formats and direct leverage of the underlying 'PROJ' library. (There are transformations that aren't possible with 'PROJ' and that are provided by the 'GDAL' library, a limitation which users of this package should be aware of.) The 'PROJ' library is available at < https://proj.org/>.