Spider Knowledge Online

Allows the user to connect with the World Spider Catalogue (WSC; < https://wsc.nmbe.ch/>) and the World Spider Trait (WST; < https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; < https://www.gbif.org/>), and mapping.

Spatial Interpolation of Genetic Data

The spatial interpolation of genetic distances between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.

Bayesian LDA for Mixed-Membership Clustering Analysis

Estimates the Bayesian LDA model for mixed-membership clustering based on different types of data (i.e., Multinomial, Bernoulli, and Binomial entries). Albuquerque, Valle and Li (2019) .

Calculate the NLTT Statistic

Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.

Research Assessment Tools

Includes algorithms to assess research productivity and patterns, such as the h-index and i-index. Cardoso et al. (2022) Cardoso, P., Fukushima, C.S. & Mammola, S. (2022) Quantifying the internationalization and representativeness in research. Trends in Ecology and Evolution, 37: 725-728.

Spatial Regression Analysis

A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) . The models are further described by 'Anselin' (1988) . Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) and (1999) are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximum likelihood and MCMC fitting are compared by 'Bivand et al.' (2013) , and model fitting methods by 'Bivand' and 'Piras' (2015) ; both of these articles include extensive lists of references. A recent review is provided by 'Bivand', 'Millo' and 'Piras' (2021) . 'spatialreg' >= 1.1-* corresponded to 'spdep' >= 1.1-1, in which the model fitting functions were deprecated and passed through to 'spatialreg', but masked those in 'spatialreg'. From versions 1.2-*, the functions have been made defunct in 'spdep'. From version 1.3-6, add Anselin-Kelejian (1997) test to `stsls` for residual spatial autocorrelation .

High Dimensional Discriminant Analysis

Performs linear discriminant analysis in high dimensional problems based on reliable covariance estimators for problems with (many) more variables than observations. Includes routines for classifier training, prediction, cross-validation and variable selection.

R as a Plotting Engine

Generate basic charts either by custom applications, or from a small script launched from the system console, or within the R console. Two ASCII text files are necessary: (1) The graph parameters file, which name is passed to the function 'rplotengine()'. The user can specify the titles, choose the type of the graph, graph output formats (e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend, whether to show or not a grid at the background, etc. (2) The data to be plotted, which name is specified as a parameter ('data_filename') in the previous file. This data file has a tabulated format, with a single character (e.g. tab) between each column. Optionally, the file could include data columns for showing confidence intervals.

Test and Detection of Explosive Behaviors for Time Series

Provides the Augmented Dickey-Fuller test and its variations to check the existence of bubbles (explosive behavior) for time series, based on the article by Peter C. B. Phillips, Shuping Shi and Jun Yu (2015a) . Some functions may take a while depending on the size of the data used, or the number of Monte Carlo replications applied.

Efficient Estimation Under Staggered Treatment Timing

Efficiently estimates treatment effects in settings with randomized staggered rollouts, using tools proposed by Roth and Sant'Anna (2023) .