Contains utilities for the analysis of post-translational modifications (PTMs) in proteins, 
    with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download, 
    filter and analyze data from the sulfoxidation database 'MetOSite'. Utilities to search and characterize S-aromatic motifs in proteins are also provided. 
    In addition, functions to analyze sequence environments around modifiable residues in proteins can be found. 
    For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable 
    residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
    these differential sequence environments are also implemented. 
    Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).

Fits the Poisson-Tweedie generalized linear mixed model
    described in Signorelli et al. (2021, <doi:10.1177/1471082X20936017>).
    Likelihood approximation based on adaptive Gauss Hermite quadrature
    rule.

Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.

Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".

Utility functions produced specifically for (but not limited
    to) working with 'ProjectTemplate' data pipelines. This package helps
    to quickly create and manage sequentially numbered scripts, quickly
    set up logging with 'log4r' and functions to help debug and monitor
    procedures.