A mathematical optimization procedure in combination with statistical bootstrap for the estimation of the latent signals (sometimes called scores) informing the global consensus ranking (often named aggregation ranking). To solve mid/large-scale problems, users should install the 'gurobi' optimiser (available from <https://www.gurobi.com/>).

A toolkit for calculating topographic distances and identifying and plotting topographic paths. Topographic distances can be calculated along shortest topographic paths (Wang (2009) <doi:10.1111/j.1365-294X.2009.04338.x>), weighted topographic paths (Zhan et al. (1993) <doi:10.1007/3-540-57207-4_29>), and topographic least cost paths (Wang and Summers (2010) <doi:10.1111/j.1365-294X.2009.04465.x>). Functions can map topographic paths on colored or hill shade maps and plot topographic cross sections (elevation profiles) for the paths.

Using Gaussian graphical models we propose a novel approach to
             perform pathway analysis using gene expression. Given the
             structure of a graph (a pathway) we introduce two statistical
             tests to compare the mean and the concentration matrices between
             two groups. Specifically, these tests can be performed on the
             graph and on its connected components (cliques). The package is
             based on the method described in Massa M.S., Chiogna M., Romualdi
             C. (2010) <doi:10.1186/1752-0509-4-121>.

Topological data analysis methods based on graph-theoretic
    approaches for discovering topological structures in data. Constructs
    topological spaces from graphs following Nada et al. (2018)
    <doi:10.1002/mma.4726>, with visibility graph construction for time
    series following Lacasa et al. (2008) <doi:10.1073/pnas.0709247105>.
    Supports directed visibility graphs for bitopological analysis of
    temporal irreversibility (Kelly, 1963), and Alexandrov topology
    construction from reachability preorders.

A tool to analyze and visualize toponym distributions. This package is intended as an interface to the GeoNames data. A regular expression filters data and in a second step a map is created displaying all locations in the filtered data set. The functions make data and plots available for further analysis—either within R or in a chosen directory. Users can select regions within countries, provide coordinates to define regions, or specify a region within the package to restrict the data selection to that region or compare regions with the remainder of countries. This package relies on the R packages 'geodata' for map data and 'ggplot2' for plotting purposes. For more information on the study of toponyms, see Wichmann & Chevallier (2025) <doi:10.5195/names.2025.2616>.