README.md
In Acanthiza/envImport: Combine Disparate Data Sources


  library(envReport)
  library(envImport)
  library(magrittr)

envImport

The goal of envImport is to obtain, and make seamlessly useable, environmental data from disparate data sources, for a geographic area of interest.

You can install the development version of envImport from GitHub with:

# install.packages("devtools")
devtools::install_github("Acanthiza/envImport")

data_name = 'data source'. Data sources are (usually) obvious sources of data. Examples are the Global Biodiversity Infrastructure Facility (GBIF), Atlas of Living Australia (ALA) or Terrestrial Ecosystems Network (TERN). There are 11 data sources currently supported (also see envImport::data_map):

bdbsa: Biological databases of South Australia
egis: Occurrence datasets from the environmental databases of South Australia (e.g. supertables)
havplot: Harmonised Australian Vegetation Plot dataset
tern: Terrestrial ecosystem network
alis: Arid lands information system
bcm: Bushland condition monitoring
ptp: Paddock tree project
nvb: DEW Native Vegetation Branch
other: Other private datasets: SA Bird Atlas (UOA/Birds SA), Birdlife Australia Birdata portal, MLR Extra Bandicoot data, KI Post Fire Bird Monitoring, SA Seed Conservation Centre
galah: Atlas of Living Australia
gbif: Global biodiversity information facility

Four of these sources are publicly available (GBIF, ALA, HAVPlot and TERN).

`data_map`

The data_map (see table below) provides a mapping from original data sources to the desired columns in the assembled data set.

Table: Data map of desired columns in the assembled data (col) and names of columns in the original data. Where a column name from the original data source does not match columns in the original data source, the get_x function has usually created a new column to better meet the requirements of the final combined data set

|col |gbif |:--------------|:--- |data_name |gbif |epsg |4326 |site |gbifID |date |eventDate |lat |long |original_name |scientificName |common |NA |nsx |NA |occ_derivation |occurrenceStatus |quantity |survey_nr |NA |survey |NA |ind |NA |rel_metres |sens |NA |lifeform |NA |lifespan |NA |cover |NA |cover_code |NA |height |NA |quad_metres |NA |epbc_status |NA |npw_status |NA |method |obs |recordedBy |denatured |kingdom |kingdom |desc |data_name_use |GBIF |url |order |11 |tern |galah |havplot | -------------------------------------|:-----------------------------|:-----------------------------|:------------------------------------------------------------------------------------| |tern |galah |havplot | |4326 |4326 |4326 | |site_unique |locationID |plotName | |visit_start_date |eventDate |obsStartDate | |decimalLatitude |latitude |decimalLatitude |decimalLatitude | |decimalLongitude |longitude |decimalLongitude |decimalLongitude | |species |scientificName |scientificName | |NA |vernacularName |NA | |NA |organismID |NA | |NA |occurrenceStatus |abundanceValue | |organismQuantity |NA |organismQuantity |abundanceValue | |NA |NA |NA | |NA |datasetName |projectID | |NA |NA |NA | |coordinateUncertaintyInMeters |NA |coordinateUncertaintyInMeters |coordinateUncertaintyInMetres | |NA |NA |NA | |lifeform |NA |NA | |NA |NA |NA | |cover |NA |cover | |NA |NA |NA | |height |NA |NA | |quad_metres |NA |quad_metres | |NA |NA |NA | |NA |NA |NA | |samplingProtocol |NA |samplingProtocol |abundanceMethod | |observer_veg |recordedBy |individualName | |informationWithheld |NA |generalisationInMetres |NA | |kingdom |kingdom |kingdom | |Global biodiversity information facility |Terrestrial ecosystem network |Atlas of Living Australia |Harmonised Australian Vegetation Plot dataset | |TERN |ALA |HAVPlot | |https://www.gbif.org/ |https://www.tern.org.au/ |https://www.ala.org.au/ |https://researchdata.edu.au/harmonised-australian-vegetation-dataset-havplot/1950860 | |4 |10 |3 |

`get_x`

get_x functions get data from the data source x. Results are always saved to disk (as getting data can be slow). When run again, they load from the saved file by default. If available, get_x functions use any R packages and functions provided by the data source (e.g. TERN provides ausplotsR [@]). The first arguments to get_x functions are always:

aoi: an area of interest, provided as simple feature (see sf::sf())
save_dir: a directory to save the results to. The default (NULL) leads to the file here::here("out", "ds", "x.rds") being created and used as save_file. ds is for 'data source'. While the saved file is usually x.rds, in some instances it follows the format and naming of the download from x (e.g. GBIF data comes in a .zip file named by the corresponding download key)
get_new: an override to force get_x to requery the data source, even if save_file already exists
...: the dots are passed to any underlying 'native' function, such as rgbif::occ_download(), galah::galah_call() or ausplotsR::get_ausplots()

Only the get_x functions for publicly available data are available within envImport.

Within get_x functions the following steps are taken:

query the data source for data within the area of interest
- possibly including other criteria to limit the results
adjust the results, if required, to better integrate with other data sources
rename the columns to a common standard (via the data_map)
- possibly adding some commonly desired fields at this step: occ (is this a presence [1] or absence [0] record?), month and year
save the results, usually as .parquet

get_x functions can be run from get_data.

No specific functions are provided for combining data. The following are possible (assuming 'files' is a vector of file names resulting from get_x):

purrr::map_dfr(files, \(x) rio::import(x, setclass = "tibble")
arrow::open_dataset(files, unify_schema = TRUE) %>% dplyr::collect()

rio::import is possibly more robust to differences in schema when importing files (based on observation - needs testing).

Cleaning

envImport does not clean data. Any combined dataset is likely to contain all sorts of duplication and other spurious records. For help cleaning data, see, for example: