Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'.
  These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging.
  bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.

Flags and checks occurrence data that are in Darwin Core
    format.  The package includes generic functions and data as well as
    some that are specific to bees. This package is meant to build upon
    and be complimentary to other excellent occurrence cleaning packages,
    including 'bdc' and 'CoordinateCleaner'.  This package uses datasets
    from several sources and particularly from the Discover Life Website,
    created by Ascher and Pickering (2020).  For further information,
    please see the original publication and package website.  Publication
    - Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package
    website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.

Performs estimation of marginal treatment effects for binary 
  outcomes when using logistic regression working models with covariate 
  adjustment (see discussions in Magirr et al (2024) <https://osf.io/9mp58/>). 
  Implements the variance estimators of Ge et al (2011) <doi:10.1177/009286151104500409> 
  and Ye et al (2023) <doi:10.1080/24754269.2023.2205802>.

Tools to calibrate, validate, and make predictions with the
    General Unified Threshold model of Survival adapted for Bee species. The
    model is presented in the publication from Baas, J., Goussen, B., Miles, M.,
    Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and 
    Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G., 
    van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the 
    GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011) 
    <doi:10.1021/es103092a>.
    The authors are grateful to Bayer A.G. for its financial support.