% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/cograph-package.R
\docType{package}
\name{cograph-package}
\alias{cograph-package}
\title{cograph: Modern Network Visualization for R}
\description{
A modern, extensible network visualization package that provides high-quality
static network plots and ggplot2 conversions. cograph accepts adjacency
matrices, edge lists, or igraph objects and offers customizable layouts,
node shapes, edge styles, and themes.
}
\section{Main Functions}{

\itemize{
\item \code{\link{cograph}}: Main entry point for creating network visualizations
\item \code{\link{sn_layout}}: Apply layout algorithms
\item \code{\link{sn_nodes}}: Customize node aesthetics
\item \code{\link{sn_edges}}: Customize edge aesthetics
\item \code{\link{sn_theme}}: Apply visual themes
\item \code{\link{sn_render}}: Render to device
\item \code{\link{sn_ggplot}}: Convert to ggplot2 object
}
}

\section{Layouts}{

cograph provides several built-in layouts:
\itemize{
\item \code{circle}: Nodes arranged in a circle
\item \code{spring}: Fruchterman-Reingold force-directed layout
\item \code{groups}: Group-based circular layout
\item \code{custom}: User-provided coordinates
}
}

\section{Themes}{

Built-in themes include:
\itemize{
\item \code{classic}: Traditional network visualization style
\item \code{colorblind}: Accessible color scheme
\item \code{gray}: Grayscale theme
\item \code{dark}: Dark background theme
\item \code{minimal}: Clean, minimal style
\item \code{viridis}: Viridis-based colour theme
\item \code{nature}: Nature-inspired colour theme
}
}

\section{Weight conventions}{

cograph's analytic functions follow a single convention for edge weights:
\itemize{
\item \strong{Semantics.} A weight is a \emph{strength}: higher weight
means a stronger connection (larger transition probability, thicker
correlation, stronger tie). This matches the qgraph / \pkg{tna}
convention and the intuition of most user-facing inputs.
\item \strong{Path-based measures} (betweenness, closeness, harmonic,
eccentricity, stress, load, radiality, etc.) invert weights to
\emph{distances} via \code{1 / weight ^ alpha}. The \code{alpha}
argument (default 1) tunes how strongly weight differences compress
paths. Controlled by the \code{invert_weights} argument, which
auto-detects to \code{TRUE} for tna objects and \code{FALSE} for
matrices/igraph (matching native igraph / \pkg{sna} defaults).
\item \strong{Non-path measures} (degree, strength, eigenvector,
PageRank, transitivity, modularity, ...) use the raw weights as-is
without inversion.
\item \strong{Unweighted override.} Passing \code{weights = NA} to any
analytic function forces unweighted behavior regardless of what is
attached to the graph.
}
Individual functions may document exceptions in their own help pages.
Any deviation from this convention is a bug — please report.
}

\seealso{
Useful links:
\itemize{
  \item \url{https://sonsoles.me/cograph/}
  \item \url{https://github.com/sonsoleslp/cograph}
  \item Report bugs at \url{https://github.com/sonsoleslp/cograph/issues}
}

}
\author{
\strong{Maintainer}: Sonsoles López-Pernas \email{sonsoles.lopez@uef.fi} [copyright holder]

Authors:
\itemize{
  \item Mohammed Saqr [copyright holder]
}

}
\keyword{internal}
