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Spatial Network Analysis
Interface package for 'sala', the spatial network analysis library from the 'depthmapX' software application. The R parts of the code are based on the 'rdepthmap' package. Allows for the analysis of urban and building-scale networks and provides metrics and methods usually found within the Space Syntax domain. Methods in this package are described by K. Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax methodology", and also by A. Turner (2004) < https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's handbook".
Network Analysis and Visualization
Collection of functions for fast manipulation, handling, and analysis of large-scale networks based on family and social data. Functions are utility functions used to manipulate data in three "formats": sparse adjacency matrices, pedigree trio family data, and pedigree family data. When possible, the functions should be able to handle millions of data points quickly for use in combination with data from large public national registers and databases. Kenneth Lange (2003, ISBN:978-8181281135).
Epistemic Network Analysis
ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
Multilevel Networks Analysis
Analyze multilevel networks as described in Lazega et al (2008)
Bibliographic Network Analysis
Enables the user to build a citation network/graph from bibliographic data and, based on modularity and heterocitation metrics, assess the degree of awareness/cross-fertilization between two corpora/communities. This toolset is optimized for Scopus data.
Dyadic Network Analysis
Contains functions for the MCMC simulation of dyadic network models j2 (Zijlstra, 2017,
Network Analysis of Immune Repertoire
Pipelines for studying the adaptive immune repertoire of T cells
and B cells via network analysis based on receptor sequence similarity.
Relate clinical outcomes to immune repertoires based on their network
properties, or to particular clusters and clones within a repertoire.
Yang et al. (2023)
Network Analysis for Omics Data
Comprehensive network analysis package. Calculate correlation network fastly, accelerate lots of analysis by parallel computing. Support for multi-omics data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in each omics. Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize. Provide comprehensive topology indexes calculation, including ecological network stability.
Network Analysis and Community Detection
Features tools for the network data analysis and community detection.
Provides multiple methods for fitting, model selection and goodness-of-fit testing in degree-corrected stochastic blocks models.
Most of the computations are fast and scalable for sparse networks, esp. for Poisson versions of the models.
Implements the following:
Amini, Chen, Bickel and Levina (2013)
Transition Network Analysis (TNA)
Provides tools for performing Transition Network Analysis (TNA) to
study relational dynamics, including functions for building and plotting TNA
models, calculating centrality measures, and identifying dominant events and
patterns. TNA statistical techniques (e.g., bootstrapping and permutation
tests) ensure the reliability of observed insights and confirm that
identified dynamics are meaningful. See (Saqr et al., 2025)