Help for package ctxR

Type:

Package

Title:

Utilities for Interacting with the 'CTX' APIs

Version:

1.1.2

Description:

Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis. 'ctxR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') https://comptox.epa.gov/dashboard/ and other resources found at the EPA Computational Toxicology and Exposure Online Resources https://www.epa.gov/comptox-tools.

License:

GPL (≥ 3)

Imports:

cli, data.table, httr, jsonlite, purrr, rlang, stringr, tidyr, tibble, urltools

Encoding:

UTF-8

LazyData:

true

RoxygenNote:

7.3.2

Suggests:

countcolors, devtools, DT, ggplot2, gridExtra, htmlTable, httptest, kableExtra, knitr, prettydoc, rmarkdown, rmdformats, testthat (≥ 3.0.0), XML

URL:

https://github.com/USEPA/ctxR, https://usepa.github.io/ctxR/

BugReports:

https://github.com/USEPA/ctxR/issues

VignetteBuilder:

knitr

Config/testthat/edition:

Depends:

R (≥ 2.10)

NeedsCompilation:

Packaged:

2025-04-07 12:55:47 UTC; MFeshuk

Author:

Paul Kruse

[aut], Caroline Ring

[aut], Madison Feshuk

[cre], Carter Thunes [ctb], Jason Brown [ctb]

Maintainer:

Madison Feshuk <feshuk.madison@epa.gov>

Repository:

CRAN

Date/Publication:

2025-04-07 13:30:02 UTC

Bioactivity API Server url

Description

A section of url used in Bioactivity API Endpoints

Usage

bioactivity_api_server

Format

An object of class character of length 1.

Check API key

Description

Check API key

Usage

check_api_key(API_key = NULL, verbose = FALSE)

Arguments

API_key

User input API key during function call.

verbose

A logical indicating if some “progress report” should be given.

Value

Either the API key (input during function call or loaded) or NULL (neither input during function call nor loaded).

Check existence by DTXSID

Description

Check existence by DTXSID

Usage

check_existence_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating whether some "progress report" should be given.

Value

A data.table with information on whether the input DTXSID is valid, and where to find more information on the chemical when the DTXSID is valid.

Examples


# DTXSID for bpa
bpa <- check_existence_by_dtxsid('DTXSID7020182')
# False DTXSID
false_res <- check_existence_by_Dtxsid('DTXSID7020182f')

Check existence by DTXSID batch

Description

Check existence by DTXSID batch

Usage

check_existence_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSIDs

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request.

Server

The root address of the API endpoint

verbose

A logical indicating whether some "progress report" should be given.

Value

A data.table of information detailing valid and invalid DTXSIDs.

Examples


dtxsids <- c('DTXSID7020182F', 'DTXSID7020182', 'DTXSID0020232F')
existence <- check_existence_by_dtxsid_batch(DTXSID = dtxsids)

Chemical API Server url

Description

A section of url used in Chemical API Endpoints

Usage

chemical_api_server

Format

An object of class character of length 1.

Chemical contains

Description

Chemical contains

Usage

chemical_contains(
  word = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE,
  top = NULL
)

Arguments

word

A character string of a chemical name or portion of a chemical name

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

top

The number of results to return if there are multiple results available

Value

A data.frame of chemicals and related values matching the query parameters

Author(s)

Paul Kruse, Kristin Issacs

Examples


# Pull chemicals that contain substring
substring_chemicals <- chemical_contains(word = 'TXSID702018')

Chemical contains batch search

Description

Chemical contains batch search

Usage

chemical_contains_batch(
  word_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE,
  top = NULL
)

Arguments

word_list

A list of character strings of chemical names or portion of chemical names

API_key

User-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

top

The number of results to return if there are multiple results available

Value

A named list of data.frames of chemicals and related values matching the query parameters. The data.frames under the 'valid' entry contain chemical information for successful requests while the data.frames under the 'invalid' entry contain data.frames with chemical name suggestions based on the input search values.

Author(s)

Paul Kruse, Kristin Issacs

Examples


# Pull chemicals that contain substrings
substring_chemicals <- chemical_contains_batch(word_list = c('TXDIS702018',
                                                             'DTXSID70201'))

Chemical equal

Description

Chemical equal

Usage

chemical_equal(
  word = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

word

A character string of a chemical name or portion of a chemical name

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of chemicals and related values matching the query parameters

Author(s)

Paul Kruse, Kristin Issacs

Examples


# Pull chemicals with matching DTXSID
bpa_dtxsid <- chemical_equal(word = 'DTXSID7020182')

Chemical equal batch search

Description

Chemical equal batch search

Usage

chemical_equal_batch(
  word_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

word_list

A list of character strings of chemical names or portion of chemical names, DTXSIDs, CASRNs, InChIKeys.

API_key

User-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.tables of chemicals and related values matching the query parameters. The list contains two entries, 'valid' and 'invalid'; 'valid', contains a data.table of the results of the the searched chemical that were found in the databases; 'invalid' contains a data.table with 'suggestions' for each searched valued that did not return a chemical.

Author(s)

Paul Kruse, Kristin Issacs

Examples


# Pull chemicals that match input strings
bpa <- chemical_equal_batch(word_list = c('DTXSID7020182', 'DTXCID30182'))

Chemical starts with

Description

Chemical starts with

Usage

chemical_starts_with(
  word = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE,
  top = NULL
)

Arguments

word

A character string of a chemical name or portion of a chemical name

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

top

The number of results to return if there are multiple results available

Value

A data.frame of chemicals and related values matching the query parameters

Author(s)

Paul Kruse, Kristin Issacs

Examples


# Pull chemicals that start with a fragment DTXSID
dtxsid_fragment <- chemical_starts_with(word = 'DTXSID702018')

Chemical starts with batch search

Description

Chemical starts with batch search

Usage

chemical_starts_with_batch(
  word_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE,
  top = NULL
)

Arguments

word_list

A list of character strings of chemical names or portion of chemical names

API_key

User-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

top

The number of results to return if there are multiple results available

Value

Author(s)

Paul Kruse, Kristin Issacs

Examples


# Pull chemicals that start with given substrings
bpa_substrings <- chemical_starts_with_batch(word_list = c('DTXSID702018',
                                                           'DTXCID3018'))

Create chemical details data.table helper function

Description

Create chemical details data.table helper function

Usage

create_data.table_chemical_details(index = -1)

Arguments

index

Determine which format should be used.

Value

An empty data.table with columns matching the expected format of the get_chemical_details API call.

Hazard data.table helper function

Description

Hazard data.table helper function

Usage

create_hazard_data.table()

Value

A data.table used in various functions that wrap the hazard API endpoints.

Examples


hazard_dt <- create_hazard_data.table()

ctxR Options

Description

ctxR stores options as a named list in R's global options, i.e. getOption('ctxR'). It currently stores two such options, one for CCTE credentialing and one to suppress private API information in the URLs printed to the screen when web queries are placed. For both of those, see register_ctx_api_key().

Usage

set_ctxR_option(...)

has_ctxR_options()

has_ctxR_option(option)

Arguments

...

a named listing of options to set

option

a specific option to query, e.g. display_api_key

Value

set_ctxR_option() does not have a return value but has the side effect of setting options used by other functions.
has_ctxR_option() returns a Boolean.
has_ctxR_options() returns a Boolean.

Examples


# Set ctxR options
set_ctxR_option('display_api_key' = FALSE)


# Check if there are options registered to 'ctxR'
has_ctxR_options()


# Check if a specific option is registered for 'ctxR'
has_ctxR_option('display_api_key')

Exposure API Server url

Description

A section of url used in Exposure API Endpoints

Usage

exposure_api_server

Format

An object of class character of length 1.

Retrieve all assays

Description

Retrieve all assays

Usage

get_all_assays(
  API_key = NULL,
  Server = bioactivity_api_server,
  verbose = FALSE
)

Arguments

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing all the assays and associated information

Examples


# Retrieve all assays
assays <- get_all_assays()

Get all list types

Description

Get all list types

Usage

get_all_list_types(
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

API_key

The user-specific API key.

Server

The root address for the API endpoint.

verbose

A logical indicating if some "progress report" should be given.

Value

A character list of types of lists.

Examples


get_all_list_types()

Get all public chemical lists

Description

Get all public chemical lists

Usage

get_all_public_chemical_lists(
  Projection = "",
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

Projection

Optional parameter controlling return type. It takes values chemicallistall' and 'chemicallistname' with the former as the default value.

API_key

The user-specific api key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing information on all public chemical lists available from the CTX chemical api.

Examples


# Pull all chemical lists
all_lists <- get_all_public_chemical_lists()

Retrieve annotations for AEID

Description

Retrieve annotations for AEID

Usage

get_annotation_by_aeid(
  AEID = NULL,
  API_key = NULL,
  Server = bioactivity_api_server,
  verbose = FALSE
)

Arguments

AEID

The assay endpoint identifier AEID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing the annotated assays corresponding to the input AEID parameter

Examples


# Retrieve annotation for an assay
annotation <- get_annotation_by_aeid(AEID = 159)

Retrieve annotations for AEID batch

Description

Retrieve annotations for AEID batch

Usage

get_annotation_by_aeid_batch(
  AEID = NULL,
  API_key = NULL,
  Server = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

AEID

A list of AEID identifiers

API_key

The user-specific API key

Server

The root address for the API endpoint

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing annotation information for the assays with AEID matching the input parameter.

Examples


# Get annotations for multiple aeids
aeid_annotations <- get_annotation_by_aeid_batch(AEID = c(159, 160))

Retrieve bioactivity data from DTXSID, AEID, SPID, or m4id

Description

Retrieve bioactivity data from DTXSID, AEID, SPID, or m4id

Usage

get_bioactivity_details(
  DTXSID = NULL,
  AEID = NULL,
  SPID = NULL,
  m4id = NULL,
  API_key = NULL,
  Server = bioactivity_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

AEID

The assay endpoint identifier AEID

SPID

The ChemSpider chemical input

m4id

The chemical identifier m4id

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing bioactivity information for the chemical or assay endpoint with identifier matching the input parameter.

Examples


# Pull BPA bioactivity details
bpa <- get_bioactivity_details(DTXSID = 'DTXSID7020182')
# Pull assay bioactivity details
assay <- get_bioactivity_details(AEID = 159)

Retrieve bioactivity data from DTXSID or AEID batch

Description

Retrieve bioactivity data from DTXSID or AEID batch

Usage

get_bioactivity_details_batch(
  DTXSID = NULL,
  AEID = NULL,
  SPID = NULL,
  m4id = NULL,
  API_key = NULL,
  Server = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXSID

A list of chemical identifier DTXSIDs.

AEID

A list of assay endpoint identifiers AEIDs.

SPID

A list of ChemSpider chemical inputs

m4id

A list of chemical identifier m4ids

API_key

The user-specific API key.

Server

The root address for the API endpoint

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing bioactivity information for the chemicals with DTXSID or assays with AEID matching the input parameter.

Examples


# Pull bioactivity details for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
batch_bioactivity <- get_bioactivity_details_batch(DTXSID = dtxsid)
# Pull bioactivity details for multiple assays
batch_bioactivity <- get_bioactivity_details_batch(AEID = c(159, 160))

Bioactivity API Endpoint status

Description

Bioactivity API Endpoint status

Usage

get_bioactivity_endpoint_status()

Value

Status of Bioactivity API Endpoints

Examples


status <- get_bioactivity_endpoint_status()
print(status)

Retrieve bioactivity summary for AEID

Description

Retrieve bioactivity summary for AEID

Usage

get_bioactivity_summary(
  AEID = NULL,
  API_key = NULL,
  Server = bioactivity_api_server,
  verbose = FALSE
)

Arguments

AEID

The assay endpoint indentifier AEID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing summary information corresponding to the input AEID

Examples


# Pull an assay bioactivity summary
aeid_1386 <- get_bioactivity_summary(AEID = 1386)

Retrieve bioactivity summary data from AEID batch

Description

Retrieve bioactivity summary data from AEID batch

Usage

get_bioactivity_summary_batch(
  AEID = NULL,
  API_key = NULL,
  Server = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

AEID

A list of AEID identifiers

API_key

The user-specific API key.

Server

The root address for the API endpoint

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing bioactivity summary information for the assays with AEID matching the input parameter.

Examples


# Get bioactivity summary for multiple aeids
aeids <- get_bioactivity_summary_batch(AEID = c(159, 160))

Get cancer hazard

Description

Get cancer hazard

Usage

get_cancer_hazard(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of cancer hazard data related to the input DTXSID.

Examples


# Pull cancer hazard data for BPA
bpa_cancer <- get_cancer_hazard(DTXSID = 'DTXSID7020182')

Get cancer hazard batch

Description

Get cancer hazard batch

Usage

get_cancer_hazard_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSIDs

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between requests

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing cancer hazard and related data for each input DTXSID.

Examples


# Pull cancer hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_cancer_hazard <- get_cancer_hazard_batch(DTXSID = dtxsid)

Retrieve chemical information

Description

Retrieve chemical information

Usage

get_chem_info(
  DTXSID = NULL,
  type = "",
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

type

This specifies whether to only grab predicted or experimental results. If not specified, it will grab all details. The allowable input values are "predicted" or "experimental".

API_key

The user-specific API Key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing chemical information for the chemical with DTXSID matching the input parameter.

Examples


# Pull chemical information for BPA
bpa <- get_chem_info(DTXSID = 'DTXSID7020182')

Retrieve chemical information in batch search

Description

Retrieve chemical information in batch search

Usage

get_chem_info_batch(
  DTXSID = NULL,
  type = "",
  API_key = NULL,
  rate_limit = 0L,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

A vector of chemical identifier DTXSIDs

type

A vector of type used in get_chem_info(). This specifies whether to only grab predicted or experimental results. If not specified, it will grab all details. The allowable input values are "", predicted", or "experimental".

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing chemical information for the chemicals with DTXSID matching the input parameter.

Examples


# Pull chemical info for multiple chemicals
chem_info <- get_chem_info_batch(DTXSID = c('DTXSID7020182',
                                            'DTXSID2021315'))

Get chemicals by property and its value range

Description

Get chemicals by property and its value range

Usage

get_chemical_by_property_range(
  start = NULL,
  end = NULL,
  property = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

start

A numeric value, the beginning of the range

end

A numeric value, the end of the range

property

A string, the property in question

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing chemical information for chemicals matching the search criteria.

Examples


# Pull chemicals with a given property in a set range
density <- get_chemical_by_property_range(start = 1.311, end = 1.313,
                                          property = 'Density')

Retrieve chemicals by property and value range in batch search

Description

Retrieve chemicals by property and value range in batch search

Usage

get_chemical_by_property_range_batch(
  start_list = NULL,
  end_list = NULL,
  property_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

start_list

Numeric values, the beginning of the range

end_list

Numeric values, the end of the range

property_list

Strings, the properties being queried

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing chemical information for the chemicals matching the search criteria.

Examples


# Pull chemicals by property ranges
prop_ranges <- get_chemical_by_property_range_batch(start_list = c(1.311,
                                                                   211.99),
                                                    end_list = c(1.313,
                                                                     212.01),
                                                    property_list = c('Density',
                                                                      'Boiling Point'))

Retrieve chemical details from DTXSID of DTXCID

Description

Retrieve chemical details from DTXSID of DTXCID

Usage

get_chemical_details(
  DTXSID = NULL,
  DTXCID = NULL,
  Projection = "chemicaldetailstandard",
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

DTXCID

The chemical identifier DTXCID

Projection

The format and chemical detail data returned. Allowed values are 'chemicaldetailall', 'chemicaldetailstandard', 'chemicalidentifier', 'chemicalstructure', 'ntatoolkit', 'ccdchemicaldetails'. If left empty or there is a mismatch, the default format will be 'chemicaldetailstandard'.

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing chemical information for the chemical with DTXSID matching the input parameter.

Examples


# Pull chemical details for BPA
bpa <- get_chemical_details(DTXSID = 'DTXSID7020182')

Retrieve chemical details from DTXSID of DTXCID in batch search

Description

Retrieve chemical details from DTXSID of DTXCID in batch search

Usage

get_chemical_details_batch(
  DTXSID = NULL,
  DTXCID = NULL,
  Projection = "chemicaldetailstandard",
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

DTXCID

The chemical identifier DTXCID

Projection

The format and chemical detail data returned. Allowed values are 'chemicaldetailall', 'chemicaldetailstandard', chemicalidentifier', 'chemicalstructure', 'ntatoolkit', ccdchemicaldetails'. If left empty or there is a mismatch, the default format will be 'chemicaldetailstandard'.

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table (DTXSID) or a named list of data.tables (DTXCID) containing chemical information for the chemicals with DTXSID or DTXCID matching the input parameter.

Examples


# Pull chemical details for multiple chemicals by dtxsid
dtxsids <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_details <- get_chemical_details_batch(DTXSID = dtxsid)
# Pull chemical details for multiple chemicals by dtxcid
dtxcids <- c('DTXCID30182', 'DTXCID001315')
dtxcid_details <- get_chemical_details_batch(DTXCID = dtxcids)

Chemical API Endpoint status

Description

Chemical API Endpoint status

Usage

get_chemical_endpoint_status()

Value

Status of Chemical API Endpoints

Examples


status <- get_chemical_endpoint_status()
print(status)

Get image file by DTXSID or DTXCID

Description

Get image file by DTXSID or DTXCID

Usage

get_chemical_image(
  DTXSID = NULL,
  DTXCID = NULL,
  gsid = NULL,
  SMILES = NULL,
  format = "",
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

DTXCID

Chemical identifier DTXCID

gsid

DSSTox Generic Substance Identifier

SMILES

Chemical identifier SMILES

format

The image type, either "png" or "svg". If left blank, will default to "png".

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A Large array of three dimensions representing an image. For displaying this, one may use png::writePNG() or countcolors::plotArrayAsImage() among many such functions.

Examples


# Pull chemical image for BPA by dtxsid
bpa_image_matrix <- get_chemical_image(DTXSID = 'DTXSID7020182')
if (requireNamespace("countcolors", quietly = TRUE)){
  countcolors::plotArrayAsImage(bpa_image_matrix)
}
# Pull chemical image for BPA by dtxcid
bpa_image_matrix <- get_chemical_image(DTXCID = 'DTXCID30182')
if (requireNamespace("countcolors", quietly = TRUE)){
  countcolors::plotArrayAsImage(bpa_image_matrix)
}

Get image file by DTXSID or DTXCID batch

Description

Get image file by DTXSID or DTXCID batch

Usage

get_chemical_image_batch(
  DTXSID = NULL,
  DTXCID = NULL,
  SMILES = NULL,
  format = "",
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXSID

A list of chemical identifier DTXSIDs.

DTXCID

A list of chemical identifier DTXCIDs.

SMILES

A list of chemical identifier SMILES.

format

The image type, either "png" or "svg". If left blank, will default to "png".

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of Large arrays of three dimensions representing an image. For displaying an image, one may use png::writePNG() or countcolors::plotArrayAsImage() among many such functions.

Examples


# Pull images for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
images <- get_chemical_image_batch(DTXSID = dtxsid)
if (requireNamespace("countcolors", quietly = TRUE)){
  countcolors::plotArrayAsImage(images[[1]])
  countcolors::plotArrayAsImage(images[[2]])
}

Get chemical lists by type

Description

Get chemical lists by type

Usage

get_chemical_lists_by_type(
  type = NULL,
  Projection = "",
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

type

The type of list. This is a case sensitive parameter and returns lists only for values of "federal", "international", "state", and "other".

Projection

Optional parameter controlling return type. It takes values 'chemicallistall' and 'chemicallistname' with the former as the default value.

API_key

The user-specified API key.

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing information about lists that meet the search criteria.

Examples


# Pull chemical lists by type
federal <- get_chemical_lists_by_type(type = 'Federal')

Get chemical lists by type batch search

Description

Get chemical lists by type batch search

Usage

get_chemical_lists_by_type_batch(
  type_list = NULL,
  Projection = "",
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

type_list

A list of list types. This is a case sensitive parameter and returns lists only for values of "federal", "international", "state", and "other".

Projection

Optional parameter controlling return type. It takes values 'chemicallistall' and 'chemicallistname' with the former as the default value.

API_key

The user-specified API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing information about lists that meet the search criteria.

Examples


# Pull chemical lists by type
federal_state <- get_chemical_lists_by_type_batch(type_list = c('federal',
                                                                'state'))

Get mol file by DTXSID or DTXCID

Description

Get mol file by DTXSID or DTXCID

Usage

get_chemical_mol(
  DTXSID = NULL,
  DTXCID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

DTXCID

Chemical identifier DTXCID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A character string giving a mol file representation

Examples


# Pull mol file for BPA by dtxsid
bpa_mol <- get_chemical_mol(DTXSID = 'DTXSID7020182')
# Pull mol file for BPA by dtxcid
bpa_mol <- get_chemical_mol(DTXCID = 'DTXCID30182')

Get mol file by DTXSID or DTXCID batch

Description

Get mol file by DTXSID or DTXCID batch

Usage

get_chemical_mol_batch(
  DTXSID = NULL,
  DTXCID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXSID

A list of the chemical identifier DTXSIDs.

DTXCID

A list of the chemical identifier DTXCIDs.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of character strings giving a mol file representations of the given input chemicals.

Examples


# Pull mol files for multiple chemicals by DTXSID
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
mol_files <- get_chemical_mol_batch(DTXSID = dtxsid)
# Pull mol files for multiple chemicals by DTXCID
dtxcid <- c('DTXCID30182', 'DTXCID001315')
mol_files <- get_chemical_mol_batch(DTXCID = dtxcid)

Get mrv file by DTXSID or DTXCID

Description

Get mrv file by DTXSID or DTXCID

Usage

get_chemical_mrv(
  DTXSID = NULL,
  DTXCID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

DTXCID

The chemical identifier DTXCID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

XML file format for representing a mrv file.

Examples


# Pull mrv file for BPA by dtxsid
bpa_mrv <- get_chemical_mrv(DTXSID = 'DTXSID7020182')
# Pull mrv file for BPA by dtxcid
bpa_mrv <- getchemical_mrv(DTXCID = 'DTXCID30182')

Ger mrv file by DTXSID or DTXCID batch

Description

Ger mrv file by DTXSID or DTXCID batch

Usage

get_chemical_mrv_batch(
  DTXSID = NULL,
  DTXCID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXSID

A list of the chemical identifier DTXSIDs.

DTXCID

A list of the chemical identifier DTXCIDs.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of XML file format for representing a mrv file for each chemicals.

Examples


# Pull mrv files for multiple chemicals by DTXSID
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
mrv_files <- get_chemical_mrv_batch(DTXSID = dtxsid)
# Pull mrv files for multiple chemicals by DTXCID
dtxcid <- c('DTXCID30182', 'DTXCID001315')
mrv_files <- get_chemical_mrv_batch(DTXCID = dtxcid)

Get chemical synonym

Description

Get chemical synonym

Usage

get_chemical_synonym(
  DTXSID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of synonym information for the input DTXSID

Examples


# Pull synonyms for BPA
bpa_synonym <- get_chemical_synonym(DTXSID = 'DTXSID7020182')

Get chemical synonym batch

Description

Get chemical synonym batch

Usage

get_chemical_synonym_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXSID

A list of chemical identifier DTXSIDs

API_key

The user-specific API key.

rate_limit

The number of seconds to wait between requests.

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of lists containing synonym information for each input DTXSID.

Examples


# Pull synonyms for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
batch_synonyms <- get_chemical_synonym_batch(DTXSID = dtxsid)

Get chemicals in a given chemical list

Description

Get chemicals in a given chemical list

Usage

get_chemicals_in_list(
  list_name = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

list_name

The name of the list of chemicals

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of the chemical list

Examples


# Retrieve chemicals contained in chemical list 'CCL4'
ccl4_chemicals <- get_chemicals_in_list(list_name = 'CCL4')

Get chemicals in a given chemical list batch

Description

Get chemicals in a given chemical list batch

Usage

get_chemicals_in_list_batch(
  list_names = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

list_names

A list of names of chemical lists.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames each containing chemicals in the corresponding chemical lists.

Examples


# Pull chemicals in lists for multiple lists
chemicals_in_lists <- get_chemicals_in_list_batch(list_names = c('CCL4', 'NATADB'))

Get chemicals in a list specified by contained characters

Description

Get chemicals in a list specified by contained characters

Usage

get_chemicals_in_list_contain(
  list_name = NULL,
  word = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

list_name

The name of the list to search

word

The contained characters to match chemicals in the given list

API_key

The user-specific api key

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A list of DTXSIDs matching the list and search word criteria

Examples


bis_biosolids_2021 <- get_chemicals_in_list_contain(list_name = 'BIOSOLIDS2021',
                                                    word = 'Bis')

Get chemicals in a list specified by characters contained batch search

Description

Get chemicals in a list specified by characters contained batch search

Usage

get_chemicals_in_list_contain_batch(
  list_names = NULL,
  words = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

list_names

The names of the lists to search.

words

The search words, one for each list.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request.

verbose

A logical indicating if some "progress report" should be given.

Value

A named list of lists, with names corresponding to search terms and lists corresponding to DTXSIDs associated to the search terms

Examples


# Search `CCL4` for chemicals containing with 'Bis' and `BIOSOLIDS2021` for
# chemicals containing with 'Zyle'.
bis_and_zyle <- get_chemicals_in_list_contain_batch(list_names = c('CCL4',
                                                              'BIOSOLIDS2021'),
                                                 words = c('Bis', 'Zyle'))

Get chemicals in a list specified by exact characters

Description

Get chemicals in a list specified by exact characters

Usage

get_chemicals_in_list_exact(
  list_name = NULL,
  word = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

list_name

The name of the list to search

word

The exact characters to match chemicals in the given list

API_key

The user-specific api key

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A list of DTXSIDs matching the list and search word criteria

Examples


bis_biosolids_2021 <- get_chemicals_in_list_exact(list_name = 'BIOSOLIDS2021',
                                                  word = 'Bisphenol A')

Get chemicals in a list specified by exact characters batch search

Description

Get chemicals in a list specified by exact characters batch search

Usage

get_chemicals_in_list_exact_batch(
  list_names = NULL,
  words = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

list_names

The names of the lists to search.

words

The search words, one for each list.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request.

verbose

A logical indicating if some "progress report" should be given.

Value

A named list of lists, with names corresponding to search terms and lists corresponding to DTXSIDs associated to the search terms

Examples


# Search `CCL4` for chemicals exactly matching with 'Bisphenol A' and
# `BIOSOLIDS2021` for chemicals exactly matching with 'Bisphenol A'.
bisphenol_a <- get_chemicals_in_list_exact_batch(list_names = c('CCL4',
                                                              'BIOSOLIDS2021'),
                                                 words = rep('Bisphenol A', 2))

Get chemicals in a list specified by starting characters

Description

Get chemicals in a list specified by starting characters

Usage

get_chemicals_in_list_start(
  list_name = NULL,
  word = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

list_name

The name of the list to search

word

The starting characters to match chemicals in the given list

API_key

The user-specific api key

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A list of DTXSIDs matching the list and search word criteria

Examples


bis_biosolids_2021 <- get_chemicals_in_list_start(list_name = 'BIOSOLIDS2021',
                                                  word = 'Bi')

Get chemicals in a list specified by starting characters batch search

Description

Get chemicals in a list specified by starting characters batch search

Usage

get_chemicals_in_list_start_batch(
  list_names = NULL,
  words = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

list_names

The names of the lists to search.

words

The search words, one for each list.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request.

verbose

A logical indicating if some "progress report" should be given.

Value

A named list of lists, with names corresponding to search terms and lists corresponding to DTXSIDs associated to the search terms

Examples


# Search `CCL4` for chemicals starting with 'Bis' and `BIOSOLIDS2021` for
# chemicals starting with 'Tri'.
bis_and_tri <- get_chemicals_in_list_start_batch(list_names = c('CCL4',
                                                              'BIOSOLIDS2021'),
                                                 words = c('Bis', 'Tri'))

Get demographic exposure prediction data

Description

Get demographic exposure prediction data

Usage

get_demographic_exposure_prediction(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A data.table of demographic exposure prediction data.

Examples


# Pull general exposure prediction data for BPA
bpa <- get_demographic_exposure_prediction(DTXSID = 'DTXSID7020182')

Retrieve demographic exposure predictions for chemicals via batch

Description

Retrieve demographic exposure predictions for chemicals via batch

Usage

get_demographic_exposure_prediction_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames, each containing demographic exposure prediction data for each input DTXSID.

Examples


# Pull demographic exposure prediction data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
exp_demo <- get_demographic_exposure_prediction_batch(DTXSID = dtxsid)

Get ecotox hazard data by DTXSID

Description

Get ecotox hazard data by DTXSID

Usage

get_ecotox_hazard_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing chemical (ecotox) hazard data

Examples


# Pull ecotox hazard data for BPA
bpa_ecotox <- get_ecotox_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')

Get ecotox hazard data by DTXSID batch

Description

Get ecotox hazard data by DTXSID batch

Usage

get_ecotox_hazard_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

A list of chemical identifier DTXSIDs.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing chemical ecotox hazard data.

Examples


# Pull ecotox hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_ecotox_hazard <- get_ecotox_hazard_by_dtxsid_batch(DTXSID = dtxsid)

Exposure API Endpoint status

Description

Exposure API Endpoint status

Usage

get_exposure_endpoint_status()

Value

Status of Exposure API Endpoints

Examples


status <- get_exposure_endpoint_status()
print(status)

Retrieve exposure related functional use data

Description

Retrieve exposure related functional use data

Usage

get_exposure_functional_use(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of functional use data.

Examples


# Pull functional use data for BPA
bpa <- get_exposure_functional_use(DTXSID = 'DTXSID7020182')

Retrieve exposure related functional use data batch

Description

Retrieve exposure related functional use data batch

Usage

get_exposure_functional_use_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames, each containing exposure functional use data for each input DTXSID.

Examples


# Pull exposure functional use data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_func_use <- get_exposure_functional_use_batch(DTXSID = dtxsid)

Retrieve functional use categories

Description

Retrieve functional use categories

Usage

get_exposure_functional_use_category(
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of functional use categories.

Examples


# Pull functional use category data for BPA
functional_use_categories <- get_exposure_functional_use_category()

Retrieve probability of exposure for functional use category

Description

Retrieve probability of exposure for functional use category

Usage

get_exposure_functional_use_probability(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame with probabilities corresponding to various routes of exposure related to functional use.

Examples


# Pull functional use probability data for BPA
bpa <- get_exposure_functional_use_probability(DTXSID = 'DTXSID7020182')

Retrieve exposure functional use probability data batch

Description

Retrieve exposure functional use probability data batch

Usage

get_exposure_functional_use_probability_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table, with each row containing exposure functional use probability data for each input DTXSID. NA values are filled in for categories that have probability of 0

Examples


# Pull exposure functional use probability data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_func_use_prob <- get_exposure_functional_use_batch(DTXSID = dtxsid)

Retrieve list presence tags

Description

Retrieve list presence tags

Usage

get_exposure_list_presence_tags(
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame with all the list presence tags and associated data.

Examples


# Pull list presence tags
tags <- get_exposure_list_presence_tags()

Retrieve document data and list presence tags for a chemical

Description

Retrieve document data and list presence tags for a chemical

Usage

get_exposure_list_presence_tags_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of document information and list presence tags

Examples


# Pull list presence tags for BPA
bpa <- get_exposure_list_presence_tags(DTXSID = 'DTXSID7020182')

Retrieve document data and list presence tags for chemicals batch

Description

Retrieve document data and list presence tags for chemicals batch

Usage

get_exposure_list_presence_tags_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames, each containing exposure list presence tags use data for each input DTXSID.

Examples


# Pull exposure functional use data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
exp_list_tags <- get_exposure_list_presence_tags_by_dtxsid_batch(DTXSID = dtxsid)

Retrieve product data for exposure purposes

Description

Retrieve product data for exposure purposes

Usage

get_exposure_product_data(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame with product information relating to exposure to the given chemical

Examples


# Pull exposure product data for BPA
bpa <- get_exposure_product_data(DTXSID = 'DTXSID7020182')

Retrieve product data for exposure purposes batch

Description

Retrieve product data for exposure purposes batch

Usage

get_exposure_product_data_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames, each containing exposure product data for each input DTXSID.

Examples


# Pull exposure functional use data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_product_data <- get_exposure_product_data_batch(DTXSID = dtxsid)

Retrieve product use categories related to exposure

Description

Retrieve product use categories related to exposure

Usage

get_exposure_product_data_puc(
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame consisting of all the product use categories

Examples


# Pull product data use categories for BPA
puc_categories <- get_exposure_product_data_puc()

Get fate by DTXSID

Description

Get fate by DTXSID

Usage

get_fate_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing chemical information for the chemical with DTXSID matching the input parameter.

Examples


# Pull chemical fate data for BPA
bpa <- get_fate_by_dtxsid(DTXSID = 'DTXSID7020182')

Retrieve chemical fate data in batch search

Description

Retrieve chemical fate data in batch search

Usage

get_fate_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

A vector of chemicals identifier DTXSIDs

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing chemical fate information for the chemicals with DTXSID matching the input parameter.

Examples


# Pull chemical fate by dtxsids
chemical_fates <- get_fate_by_dtxsid_batch(DTXSID = c('DTXSID7020182',
                                                      'DTXSID2021315'))

Get general exposure prediction data

Description

Get general exposure prediction data

Usage

get_general_exposure_prediction(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A data.table of general exposure prediction data or NULL if data is missing.

Examples


# Pull general exposure prediction data for BPA
bpa <- get_general_exposure_prediction(DTXSID = 'DTXSID7020182')

Retrieve general exposure predictions for chemicals via batch

Description

Retrieve general exposure predictions for chemicals via batch

Usage

get_general_exposure_prediction_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

Chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames, each containing general exposure prediction data for each input DTXSID.

Examples


# Pull general exposure prediction data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
exp_pred <- get_general_exposure_prediction_batch(DTXSID = dtxsid)

Get genetox details

Description

Get genetox details

Usage

get_genetox_details(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of genetox detail data related to the input DTXSID.

Examples


# Pull genetox details for BPA
bpa_genetox_details <- get_genetox_details(DTXSID = 'DTXSID7020182')

Get genetox details batch

Description

Get genetox details batch

Usage

get_genetox_details_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSIDs

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between requests

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table of genetox detail data for each input DTXSID.

Examples


# Pull genetox details data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_genetox_details_hazard <- get_genetox_details_batch(DTXSID = dtxsid)

Get genetox summary

Description

Get genetox summary

Usage

get_genetox_summary(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame of genetox summary data related to the input DTXSID.

Examples


# Pull genetox summary for BPA
bpa_genetox_summary <- get_genetox_summary(DTXSID = 'DTXSID7020182')

Get genetox summary batch

Description

Get genetox summary batch

Usage

get_genetox_summary_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSIDs

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between requests

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table of genetox summary data for each input DTXSID.

Examples


# Pull genetox summary data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_genetox_summary_hazard <- get_genetox_summary_batch(DTXSID = dtxsid)

Get hazard data by DTXSID

Description

Get hazard data by DTXSID

Usage

get_hazard_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing chemical (human and eco) hazard data

Examples


# Pull hazard data for BPA
bpa <- get_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')

Get hazard data by DTXSID batch

Description

Get hazard data by DTXSID batch

Usage

get_hazard_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

A list of chemical identifier DTXSIDs

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing chemical (human and eco) hazard data for each input chemical.

Examples


# Pull hazard data for multiple chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
batch_hazard <- get_hazard_by_dtxsid_batch(DTXSID = dtxsid)

Hazard API Endpoint status

Description

Hazard API Endpoint status

Usage

get_hazard_endpoint_status()

Value

Status of Hazard API Endpoints

Examples


status <- get_hazard_endpoint_status()
print(status)

Get httk data

Description

Get httk data

Usage

get_httk_data(
  DTXSID = NULL,
  API_key = NULL,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A data.table of httk data for the given input chemical.

Examples


# Pull httk data for BPA
bpa_httk <- get_httk_data(DTXSID = 'DTXSID7020182')

Retrieve httk data via batch search

Description

Retrieve httk data via batch search

Usage

get_httk_data_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = exposure_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some "progress report" should be given.

Value

A named list of httk data corresponding to the input chemicals

Examples


# Retrieve information for BPA and Caffeine
dtxsids <- c('DTXSID7020182', 'DTXSID0020232')
httk_data <- get_httk_data_batch(DTXSID = dtxsids)

Get human hazard data by DTXSID

Description

Get human hazard data by DTXSID

Usage

get_human_hazard_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing chemical human hazard data

Examples


# Pull human hazard data for BPA
bpa_human <- get_human_hazard_by_dtxsid(DTXSID = 'DTXSID7020182')

Get human hazard data by DTXSID batch

Description

Get human hazard data by DTXSID batch

Usage

get_human_hazard_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

A list of chemical identifier DTXSIDs.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.table containing chemical human hazard data.

Examples


# Pull human hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_human_hazard <- get_human_hazard_by_dtxsid_batch(DTXSID = dtxsid)

Get InChI

Description

Get InChI

Usage

get_inchi(
  name = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

name

Chemical name

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A string giving the associated inchi string.

Examples


bpa_inchi <- get_inchi(name = "Bisphenol A")

Get InChIKey

Description

Get InChIKey

Usage

get_inchikey(
  name = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

name

Chemical name

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A string giving the associated InChIKey.

Examples


bpa_inchikey <- get_inchikey(name = "Bisphenol A")

Get chemical lists containing given chemical

Description

Get chemical lists containing given chemical

Usage

get_lists_containing_chemical(
  DTXSID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A list of names of chemical lists that contain the given chemical

Examples


# Pull chemical lists containing BPA
bpa_lists <- get_lists_containing_chemical(DTXSID = 'DTXSID7020182')

Get chemical lists containing given chemical batch

Description

Get chemical lists containing given chemical batch

Usage

get_lists_containing_chemical_batch(
  chemical_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

chemical_list

A list of the chemical identifier DTXSIDs.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of chemical lists that contain the given chemicals.

Examples


# Pull lists containing chemicals for multiple chemicals
lists <- get_lists_containing_chemical_batch(chemical_list = c('DTXSID7020182',
                                                               'DTXSID2021315'))

Get msready by DTXCID

Description

Get msready by DTXCID

Usage

get_msready_by_dtxcid(
  DTXCID = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

DTXCID

The chemical identifier DTXCID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A character list of DTXSIDs with DTXCIDs matching the search criteria

Examples


# Pull chemicals with matching DTXCID
dtxcid_msready <- get_msready_by_dtxcid(DTXSID = 'DTXCID30182')

Get msready by DTXCID batch search

Description

Get msready by DTXCID batch search

Usage

get_msready_by_dtxcid_batch(
  DTXCID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

DTXCID

A list of chemical identifier DTXCIDs

API_key

A user-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of character lists of DTXSIDs with DTXCIDs matching the search criteria

Examples


# Pull msready chemicals matching specific DTXCID
dtxcid_msready <- get_msready_by_dtxcid_batch(DTXCID = c('DTXCID30182',
                                                         'DTXCID001315'))

Get msready by formula

Description

Get msready by formula

Usage

get_msready_by_formula(
  formula = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

formula

A string denoting the input chemical formula

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A character list of DTXSIDs with chemical formulas matching the search criteria

Examples


# Pull chemicals that match input formula
mass_formula <- get_msready_by_formula(formula = 'C16H24N2O5S')

Get msready by formula batch search

Description

Get msready by formula batch search

Usage

get_msready_by_formula_batch(
  formula_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

formula_list

A list of strings denoting the input chemicals formulas

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of character lists of DTXSIDs with chemical formulas matching the search criteria

Examples


# Pull msready data for several chemical formulas
msready_data <- get_msready_by_formula_batch(formula_list = c('C16H24N2O5S',
                                                              'C15H16O2'))

Get msready by mass

Description

Get msready by mass

Usage

get_msready_by_mass(
  start = NULL,
  end = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

start

The starting value for mass range

end

The ending value for mass range

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A list of DTXSIDs with msready mass falling within the given range.

Examples


# Pull chemicals with msready mass in given range
mass_range <- get_msready_by_mass(start = 200.9, end = 200.95)

Get ms ready by mass batch search

Description

Get ms ready by mass batch search

Usage

get_msready_by_mass_batch(
  start_list = NULL,
  end_list = NULL,
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

start_list

A numeric list of starting values for mass range

end_list

A numeric list of ending values for mass range

API_key

The user-specific API key

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of character lists with DTXSIDs with msready masses falling within the given ranges.

Examples


# Pull msready chemicals by mass ranges
msready_data <- get_msready_by_mass_batch(start_list = c(200.9, 200.95),
                                          end_list = c(200.95, 201.00))

Get msready by mass and error offset

Description

Get msready by mass and error offset

Usage

get_msready_by_mass_with_error_batch(
  masses = NULL,
  error = NULL,
  API_key = NULL,
  rate_limit = 0,
  verbose = FALSE
)

Arguments

masses

A numeric list of masses.

error

The mass offset value.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some "progress report" should be given.

Value

A list (of lists) of DTXSIDs, with a list returned for each input mass value.

Examples


#Pull chemicals by msready mass and error offset
msready_data <- get_msready_by_mass_with_error_batch(masses = c(226, 228),
                                                     error = 4)

Get chemical list by name

Description

Get chemical list by name

Usage

get_public_chemical_list_by_name(
  list_name = NULL,
  Projection = "",
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

list_name

The name of the list of chemicals

Projection

Optional parameter controlling return type. It takes values chemicallistall' and 'chemicallistname' with the former as the default value.

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing information about the chemical list. Note, this is not the chemical list itself. To access the chemicals in the list, use get_chemicals_in_list.

Examples


# Pull chemical list by list name
ccl4 <- get_public_chemical_list_by_name(list_name = 'CCL4')

Get chemical list by name batch

Description

Get chemical list by name batch

Usage

get_public_chemical_list_by_name_batch(
  name_list = NULL,
  Projection = "",
  API_key = NULL,
  rate_limit = 0L,
  verbose = FALSE
)

Arguments

name_list

A list of chemical list names.

Projection

Optional parameter controlling return type. It takes values 'chemicallistall' and 'chemicallistname' with the former as the default value.

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing information about the chemical lists. Note, these are not the chemical lists themselves. To access the chemicals in a given list, use get_chemicals_in_list.

Examples


# Pull chemical list information by list names
list_info <- get_public_chemical_list_by_name_batch(name_list = c('CCL4',
                                                                  'NATADB'))

Get skin and eye hazard

Description

Get skin and eye hazard

Usage

get_skin_eye_hazard(
  DTXSID = NULL,
  API_key = NULL,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSID

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A data.frame containing skin and eye hazard data.

Examples


# Pull skin and eye hazard data for BPA
bpa_skin_eye <- get_skin_eye_hazard_batch(DTXSID = 'DTXSID7020182')

Get skin and eye hazard batch

Description

Get skin and eye hazard batch

Usage

get_skin_eye_hazard_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = hazard_api_server,
  verbose = FALSE
)

Arguments

DTXSID

The chemical identifier DTXSIDs

API_key

The user-specific API key.

rate_limit

Number of seconds to wait between each request

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A named list of data.frames containing skin and eye hazard data for each input DTXSID.

Examples


# Pull skin eye hazard data for multiples chemicals
dtxsid <- c('DTXSID7020182', 'DTXSID2021315')
dtxsid_skin_eye_hazard <- get_skin_eye_hazard_batch(DTXSID = dtxsid)

Get Smiles

Description

Get Smiles

Usage

get_smiles(
  name = NULL,
  API_key = NULL,
  Server = chemical_api_server,
  verbose = FALSE
)

Arguments

name

Chemical name

API_key

The user-specific API key

Server

The root address for the API endpoint

verbose

A logical indicating if some “progress report” should be given.

Value

A string giving a SMILES string for the input chemical.

Examples


bpa_smiles <- get_smiles(name = "Bisphenol A")

Hazard API Server url

Description

A section of url used in Hazard API Endpoints

Usage

hazard_api_server

Format

An object of class character of length 1.

Prepare url helper function

Description

Prepare url helper function

Usage

prepare_word(word)

Arguments

word

A character string

Value

A character string that is ready for use in http request

Register CTX API Key for ctxR

Description

This page contains documentation tools related to enabling CTX API services in R.

Usage

showing_key()

ctxR_show_api_key()

ctxR_hide_api_key()

register_ctx_api_key(key, write = FALSE)

## S3 method for class 'ctx_credentials'
print(...)

ctx_key()

has_ctx_key()

Arguments

key

an API key

write

if TRUE, stores the secrets provided in the .Renviron file

...

a dumped formal argument to the generic print method

Details

To obtain an API key and enable services, go to https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis. This documentation shows you how to obtain an API key to allow access to the CTX APIs.

To tell ctxR about your API key, use register_ctx_api_key(), e.g. register_ctx_api_key(key = 'grbwigbwoginrowgbwibgdibdvinrginiwgo') (that's a fake key). This will set your API key for the current session, but if you restart R, you'll need to do it again. You can set it permanently by setting write = TRUEm see the examples. If you set it permanently it will be stored in a local file, and that will be accessed by ctxR persistently across sessions.

Users should be aware that the API key, a string of garbled characters/numbers/symbols, is a PRIVATE key - it uniquely identifies and authenticates you to CTX's services. If anyone gets your API key, they can use it to masquerade as you to CTX. To mitigate against users inadvertently sharing their keys, by default ctxR never displays a user's key in messages displayed to the console.

Users should be aware that ctxR has no mechanism with which to safeguard the private key once registered with R. That is to say, once you register your API key, any R function will have access to it. As a consequence, ctxR will not know if another function, potentially from a compromised package, accesses the key and uploads it to a third party. For this reason, when using ctxR we recommend a heightened sense of security and self-awareness: only use trusted packages, do not save the API keys in script files, etc.

Value

showing_key returns a Boolean.
ctxR_show_api_key() has no return value but has the side effect of changing the display settings of the API key.
ctxR_hide_api_key() has no return value but has the side effect of changing the display settings of the API key.
register_ctx_api_key() has no return value but has the side effect of storing the API key.
print.ctx_credentials() has no return value and is an S3 method for printing the ctx_credentials class.
ctx_key() returns a string, either the stored API key or NA_character_.
has_ctx_key() returns a Boolean.

Examples


# Check if API key is showing
showing_key()


# Toggle API key to display
ctxR_show_api_key()


# Toggle API key to be hidden
ctxR_hide_api_key()


# Register key for this session
register_ctx_api_key(key = 'YOUR API KEY')
# Register key over sessions
register_ctx_api_key(key = 'YOUR API KEY', write = TRUE)


# Print function for ctx_credentials class
print.ctx_credentials()


# Display ctx API key
ctx_key()


# Check whether API key is registered
has_ctx_key()