| 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
 [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()