Version: 0.0.2
Date: 2022-08-08
Title: Ecotoxicological Information from the Standartox Database
Maintainer: Andreas Scharmüller <andschar@protonmail.com>
Description: The http://standartox.uni-landau.de database offers cleaned, harmonized and aggregated ecotoxicological test data, which can be used for assessing effects and risks of chemical concentrations found in the environment.
Depends: R (≥ 3.5.0)
Imports: stats, httr (≥ 1.4.1), jsonlite (≥ 1.6.1), fst (≥ 0.9.4), data.table (≥ 1.13.0)
License: MIT + file LICENSE
URL: https://github.com/andschar/standartox
BugReports: https://github.com/andschar/standartox/issues
RoxygenNote: 7.1.2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-08-06 19:56:38 UTC; scharmueller
Author: Andreas Scharmüller ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2022-08-08 11:00:02 UTC

Retrieve data catalog

Description

Retrieve a data catalog for all variables (and their values) that can be retrieved with stx_query()

Usage

stx_catalog(vers = NULL)

Arguments

vers

integer; Choose the version of the EPA Ecotox on which Standartox is based on. NULL (default) accesses the most recent version

Value

Returns a list of data.frames containing information on data base variables

Author(s)

Andreas Scharmueller andschar@protonmail.com

Examples


# might fail if API is not available
stx_catalog()

Retrieve chemical data

Description

Retrieve data on all chemicals in Standartox.

Usage

stx_chem()

Value

Returns a data.table containing informaiton on chemicals in Standartox.

Author(s)

Andreas Scharmueller andschar@protonmail.com

Examples


# might fail if API is not available
stx_chem()

Retrieve Standartox toxicity values

Description

Retrieve toxicity values from the Standartox data base http://standartox.uni-landau.de/.

Usage

stx_query(
  cas = NULL,
  concentration_unit = NULL,
  concentration_type = NULL,
  duration = NULL,
  endpoint = c("XX50", "NOEX", "LOEX"),
  effect = NULL,
  exposure = NULL,
  chemical_role = NULL,
  chemical_class = NULL,
  taxa = NULL,
  ecotox_grp = NULL,
  trophic_lvl = NULL,
  habitat = NULL,
  region = NULL,
  vers = NULL,
  ...
)

Arguments

cas

character, integer; Limit data base query to specific CAS numbers, multiple entries possible (e.g. 1071-83-6, 1071836), NULL (default).

concentration_unit

character; Limit data base query to specific concentration units (e.g. ug/l - default).

concentration_type

character; Limit data base query to specific concentration types, can be one of NULL (default), 'active ingredient', 'formulation', 'total', 'not reported', 'unionized', 'dissolved', 'labile'. See https://cfpub.epa.gov/ecotox/pdf/codeappendix.pdf p.4.

duration

integer vector of length two; Limit data base query to specific test durations (hours) (e.g. c(24, 48)). NULL (default).

endpoint

character; Choose endypoint type, must be one of 'XX50' (default), 'NOEX', 'LOEX'.

effect

character; Limit data base query to specific effect groups, multiple entries possible (e.g. 'Mortality', 'Intoxication', 'Growth'). See https://cfpub.epa.gov/ecotox/pdf/codeappendix.pdf p.95. NULL (default).

exposure

character; Choose exposure type, (e.g. aquatic, environmental, diet). NULL (default).

chemical_role

character; Limit data base query to specific chemical roles (e.g. insecticide), multiple entries possible. NULL (default).

chemical_class

character; Limit data base query to specific chemical classes (e.g. neonicotinoid), multiple entries possible. NULL (default).

taxa

character; Limit data base query to specific taxa, multiple entries possible. NULL (default).

ecotox_grp

character; Convenience grouping of organisms in ecotoxicology, must be one of NULL (default), 'invertebrate', 'fish', 'plant_land', 'macrophyte', 'algae'.

trophic_lvl

character; Trophic level of organism, must be one of NULL (default), 'autotroph', 'heterotroph'.

habitat

character; Limit data base query to specific organism habitats, can be one of NULL (default) 'marine', 'brackish', 'freshwater', 'terrestrial'.

region

character; Limit data base query to organisms occurring in specific regions, can be one of NULL (default) 'africa', 'america_north', 'america_south', 'asia', 'europe', 'oceania'.

vers

integer; Choose the version of the EPA Ecotox on which Standartox is based on. NULL (default) accesses the most recent version.

...

currently not used

Value

Returns a list of three data.tables (filtered data base query results, aggregated data base query results, meta information)

Author(s)

Andreas Scharmueller andschar@protonmail.com

Examples


# might fail if API is not available
stx_query('1071-83-6')
stx_query(cas = '1071-83-6',
          duration = c(48, 120),
          concentration_unit = 'ug/l')
stx_query(cas = '1071-83-6',
          duration = c(48, 120),
          concentration_unit = 'ug/l',
          endpoint = 'XX50')

Retrieve taxa data

Description

Retrieve data on all taxa in Standartox.

Usage

stx_taxa()

Value

Returns a data.table containing informaiton on taxa in Standartox.

Author(s)

Andreas Scharmueller andschar@protonmail.com

Examples


# might fail if API is not available
stx_taxa()