Provides functionality to support data preparation and exploration for
  palaeobiological analyses, improving code reproducibility and accessibility. The
  wider aim of 'palaeoverse' is to bring the palaeobiological community together 
  to establish agreed standards. The package currently includes functionality for 
  data cleaning, binning (time and space), exploration, summarisation and 
  visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>)
  and auxiliary functions are also provided. Details can be found in:
  Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.

Implements sparse regression with paired covariates (Rauschenberger et al. 2020 <doi:10.1007/s11634-019-00375-6>). For the optional shrinkage, install ashr (<https://github.com/stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>) from GitHub (see README).

Implementation of the Partitioned Local Depth (PaLD) 
    approach which provides a measure of local depth and the cohesion of a point 
    to another which  (together with a universal threshold for distinguishing 
    strong and weak ties) may be used to reveal local and global structure in 
    data, based on methods described in Berenhaut, Moore, and Melvin (2022)
    <doi:10.1073/pnas.2003634119>. No extraneous inputs, distributional 
    assumptions, iterative procedures nor optimization criteria are employed. 
    This package includes functions for computing local depths and cohesion as
    well as flexible functions for plotting community networks and displays of 
    cohesion against distance.

Includes functions to wrap most endpoints of the 'PaleobioDB'
    API and functions to visualize and process the fossil data. The API
    documentation for the Paleobiology Database can be found at
    <https://paleobiodb.org/data1.2/>.

Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.