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Extracting the traits from the downloaded data.

Source: R/fw_fetchdata.R
fw_fetchdata.Rd

Extracting the traits from the downloaded data.

Usage

fw_fetchdata(
  data,
  organismgroup,
  ecoparams = NULL,
  taxalevel = "species",
  taxonomic_column = NULL,
  organismgroup_column = NULL,
  apikey = NULL,
  seed = 1134,
  secure = TRUE,
  percenterror = 80,
  errorness = 20,
  warn = FALSE,
  inform = FALSE,
  cachefolder = "cache",
  details = FALSE
)

Arguments

data

vector. The list or vector with species names for which ecological references needs to be extracted from the database.

organismgroup

string. The organism group to download from the platform. The allowed group includes "fi", "mi", "pp", "pb", "di","mp" for fishes, macroinvertebrates, phytoplankton, phytobenthos, diatoms, and macrophytes, respectively. Multiple groups allowed, such as 'pp', 'di'.

  • pp: Pytoplankton.

  • mp: Macrophytes

  • mi: Macroinvertebrates

  • fi: Fishes

  • di: Diatoms

  • pb: Phytobenthos without diatoms

ecoparams

vector. Selected traits that should be downloaded for a particular organism group. Check fw_dbguide for the allowed traits in the database.

taxalevel

string Allowed taxonomic levels at which data can be retrieved. Default is 'species' but data can also be downloaded at family, genus, and taxagroup level.

taxonomic_column

string. If the data is a dataframe, the species column is required and provided in this parameter. The column should have complete species name and not genus and species provided separately.

organismgroup_column

string If the data is a dataframe, and more than one taxonomic group exists in the data, the organismgroup_column is required to iterate over the taxonomic groups separately.

apikey

string. The API key is automatically loaded using the loadapikey() internal function.

seed

integer. An integer to help track the caching of the access token generated during data collation. If a user wants a new token, the seed should be changed.

secure

logical. If TRUE, the User will be prompted to set the API key in the .Renviron file by running the fw_setapikey function. The User must strictly type in API_KEY = 'api key', save, close the file and restart the R session or RStudio for the API_KEY environment to be captured. If FALSE, then the key will be entered directly in the API_KEY directly in the fw_token() function. This method is insecure, since other users can obtain the key from the codes.

percenterror

numeric. The number used as a cutoff to infer similarity of the user provided name and what is found in the database. The higher the percentage, the higher the similarity the species name provided by the user and the one in the database. percenterror ranges from 0 to 100 but the default is 80 to ensure that wrong names are not selected at low similarity percentage cutoff.

errorness

numeric Similar to percenterror, errorness parameter uses the distance differences between the user-provided names and all the taxa group species standard names. The lower the percentage error, the higher the similarity in the species names provided. Default is 20 and beyond 30, a warning is showed to avoid wrong species replace the user provided name, which leads to extracting wrong traits.

warn

logical To show species name warning checks and traits cleaning. Default FALSE.

inform

logical. This is to indicate if the token has been successfully generated. Default TRUE.

cachefolder

string. The root path were the cached data will be saved on the user PC. If the path is not provided, the cached information will be saved in the current working directly.

details

loical. Outputs the downloaded details including the organism groups considered by the user, the functional call, and whether some groups were successful in retrieving data.

Value

dataframe The output has four sections, including

  • ecodata, which is the complete dataframe with all the taxonomic names and ecological parameters. \ item taxasearch: is a table with the taxonomic names,both original and cleaned names.

  • fetch: an indication that data has been fetched from www.freshwaterecology.info.

  • fun_call: A functional call used internally to review the data cleaning process.

Examples


if (FALSE) { # \dontrun{

dfextract <- fw_fetchdata(data = "Abramis brama", organismgroup = 'fi', inform = TRUE,
                            ecoparams = 'migration', cachefolder = 'cache' )

} # }