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hib_update_db: Update an existing HibDatabase with further data

Source: R/hib_update_db.R
hib_update_db.Rd

This function updates an existing HibDatabase, for example by adding the 2022 version of the PREDICTS data to the 2016 version.

Usage

hib_update_db(obj, path_species, path_sites = "", dataset_name = "")

Arguments

obj

A HibDatabase object.

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

The updated HibDatabase object, with the supplied dataset added to its site and species data.

Details

Newly provided data (from files) will be appended to the previously created HibDatabase. Species data will be added to the species data.frame, and site data to the site data.frame. Meta-data/descriptors in the HibDatabase will be updated to reflect the additions. Note: Prior filtering/processing of the initial HibDatabase will not be applied to the newly provided data. Please load all data of interest into the HibDatabase prior to further processing.

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, "predicts_2016")
  path_species_upd <- "rawdata/PREDICTS/2022/database2ndrelease.rds"
  hibDB <- update_hib(hibDB, path_species_upd, "", "predicts_2022")
  hibDB
} # }