Micro-Macro Analysis for Social Networks

Estimates micro effects on macro structures (MEMS) and average micro mediated effects (AMME). URL: < https://github.com/sduxbury/netmediate>. BugReports: < https://github.com/sduxbury/netmediate/issues>. Robins, Garry, Phillipa Pattison, and Jodie Woolcock (2005) . Snijders, Tom A. B., and Christian E. G. Steglich (2015) . Imai, Kosuke, Luke Keele, and Dustin Tingley (2010) . Duxbury, Scott (2023) . Duxbury, Scott (2024) .

Generalized Path Analysis for Social Networks

The social network literature features numerous methods for assigning value to paths as a function of their ties. 'gretel' systemizes these approaches, casting them as instances of a generalized path value function indexed by a penalty parameter. The package also calculates probabilistic path value and identifies optimal paths in either value framework. Finally, proximity matrices can be generated in these frameworks that capture high-order connections overlooked in primitive adjacency sociomatrices. Novel methods are described in Buch (2019) < https://davidbuch.github.io/analyzing-networks-with-gretel.html>. More traditional methods are also implemented, as described in Yang, Knoke (2001) .

Identification and Analysis of Co-Occurrence Networks

Implementation of the NetCutter algorithm described in Müller and Mancuso (2008) . The package identifies co-occurring terms in a list of containers. For example, it may be used to detect genes that co-occur across genomes.

Network Meta-Analysis Based on Multivariate Meta-Analysis Models

Network meta-analysis tools based on contrast-based approach using the multivariate meta-analysis and meta-regression models (Noma et al. (2023) ). Standard analysis tools for network meta-analysis and meta-regression (e.g., synthesis analysis, ranking analysis, and creating league table) are available by simple commands. For inconsistency analyses, the local and global inconsistency tests based on the Higgins' design-by-treatment interaction model can be applied. Also, the side-splitting and the Jackson's random inconsistency model are available. Standard graphical tools for network meta-analysis (e.g., network plot, ranked forest plot, and transitivity analysis) can also be utilized. For the synthesis analyses, the Noma-Hamura's improved REML (restricted maximum likelihood)-based methods (Noma et al. (2023) ) are adopted as the default methods.

Pathway Enrichment Analysis Based on Bayesian Network

Maleknia et al. (2020) . A novel pathway enrichment analysis package based on Bayesian network to investigate the topology features of the pathways. firstly, 187 kyoto encyclopedia of genes and genomes (KEGG) human non-metabolic pathways which their cycles were eliminated by biological approach, enter in analysis as Bayesian network structures. The constructed Bayesian network were optimized by the Least Absolute Shrinkage Selector Operator (lasso) and the parameters were learned based on gene expression data. Finally, the impacted pathways were enriched by Fisher’s Exact Test on significant parameters.

Thresholds and Invariant Intervals for Network Meta-Analysis

Calculation and presentation of decision-invariant bias adjustment thresholds and intervals for Network Meta-Analysis, as described by Phillippo et al. (2018) . These describe the smallest changes to the data that would result in a change of decision.

The Plate Plot for Network Meta-Analysis Results

A graphical display of results from network meta-analysis (NMA). It is suitable for outcomes like odds ratio (OR), risk ratio (RR), risk difference (RD) and standardized mean difference (SMD). It also has an option to visually display and compare the surface under the cumulative ranking (SUCRA) of different treatments.

Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Bayesian Network Meta-Analysis with Missing Participants

A comprehensive suite of functions to perform and visualise pairwise and network meta-analysis with aggregate binary or continuous missing participant outcome data. The package covers core Bayesian one-stage models implemented in a systematic review with multiple interventions, including fixed-effect and random-effects network meta-analysis, meta-regression, evaluation of the consistency assumption via the node-splitting approach and the unrelated mean effects model (original and revised model proposed by Spineli, (2022) ), and sensitivity analysis (see Spineli et al., (2021) ). Missing participant outcome data are addressed in all models of the package (see Spineli, (2019) , Spineli et al., (2019) , Spineli, (2019) , and Spineli et al., (2021) ). The robustness to primary analysis results can also be investigated using a novel intuitive index (see Spineli et al., (2021) ). Methods to evaluate the transitivity assumption using trial dissimilarities and hierarchical clustering are provided (see Spineli, (2024) , and Spineli et al., (2025) ). A novel index to facilitate interpretation of local inconsistency is also available (see Spineli, (2024) ) The package also offers a rich, user-friendly visualisation toolkit that aids in appraising and interpreting the results thoroughly and preparing the manuscript for journal submission. The visualisation tools comprise the network plot, forest plots, panel of diagnostic plots, heatmaps on the extent of missing participant outcome data in the network, league heatmaps on estimation and prediction, rankograms, Bland-Altman plot, leverage plot, deviance scatterplot, heatmap of robustness, barplot of Kullback-Leibler divergence, heatmap of comparison dissimilarities and dendrogram of comparison clustering. The package also allows the user to export the results to an Excel file at the working directory.

Bayesian Spatio-Temporal Analysis in Stream Networks

Fits Bayesian spatio-temporal models and makes predictions on stream networks using the approach by Santos-Fernandez, Edgar, et al. (2022)."Bayesian spatio-temporal models for stream networks". . In these models, spatial dependence is captured using stream distance and flow connectivity, while temporal autocorrelation is modelled using vector autoregression methods.