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hib_create_db: Create a HibDatabase object from input files

Source: R/hib_create_db.R
hib_create_db.Rd

This function creates an R6 HibDatabase object containing the loaded PREDICTS-like database.

Usage

hib_create_db(path_species, path_sites = "", dataset_name = "")

Arguments

path_species

A character pointing to a PREDICTS formatted abundance/ occurrence database.

path_sites

Optional character argument, pointing to a PREDICTS formatted site database. Default value is "". If "" is provided, site data will be generated from the species data.

dataset_name

A character indicating the dataset used to create the HibDatabase. Default is "". If "" is supplied, the parameter will be internally updated to the filename associated with path_species.

Value

An object of class HibDatabase, containing site and species information which can be further modified for subsequent ecological analysis.

Details

This function assumes that a species database file is explicitly provided, with a site database file being optional. Provided file paths are expected to include a '.rds' extension.
All files are loaded and compiled into a single database object that can be stored for future use (see hib_save()). This object is then used in other functions of this package to prepare or filter the database and enable ecological impact analyses.

References

    1. Hudson, L.N., Newbold, T., Contu, S., Hill, S.L.L., Lysenko, I., De Palma, A., Phillips, H.R.P., Senior, R.A., Bennett, D.J., Booth, H., et al. (2014). The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts. Ecol. Evol. 4, 4701–4735. 10.1002/ece3.1303.

    1. Hudson, L.N., Newbold, T., Contu, S., Hill, S.L.L., Lysenko, I., De Palma, A., Phillips, H.R.P., Alhusseini, T.I., Bedford, F.E., Bennett, D.J., et al. (2017). The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project. Ecol. Evol. 7, 145–188. 10.1002/ece3.2579.

    1. Lawrence Hudson; Tim Newbold; Sara Contu; Samantha L L Hill et al. (2023). The 2016 release of the PREDICTS database V1.1. Natural History Museum. https://doi.org/10.5519/j4sh7e0w

    1. Sara Contu; Adriana De Palma; Rachel Bates; Jessica Borer et al. (2022). Release of data added to the PREDICTS database (November 2022). Natural History Museum. https://doi.org/10.5519/jg7i52dg

Examples

if (FALSE) { # \dontrun{
  path_species <- "rawdata/PREDICTS/2016/database.rds"
  path_sites <- "rawdata/PREDICTS/2016/sites.rds"
  hibDB <- hib_create_db(path_species, path_sites)
  hibDB
} # }