Package 'ctxR'

Description

A section of url used in Bioactivity API Endpoints

Usage

bioactivity_api_server

Format

An object of class character of length 1.

Description

Check API key

Usage

check_api_key(API_key = NULL, verbose = FALSE)

Arguments

Value

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

Description

Check existence by DTXSID

Usage

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

Arguments

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')

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

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)

Description

A section of url used in Chemical API Endpoints

Usage

chemical_api_server

Format

An object of class character of length 1.

Description

Chemical contains

Usage

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

Arguments

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')

Description

Chemical contains batch search

Usage

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

Arguments

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'))

Description

Chemical equal

Usage

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

Arguments

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')

Description

Chemical equal batch search

Usage

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

Arguments

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'))

Description

Chemical starts with

Usage

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

Arguments

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')

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

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

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

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.

See Also

register_ctx_api_key()

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')

Description

A section of url used in Exposure API Endpoints

Usage

exposure_api_server

Format

An object of class character of length 1.

Description

Get aggregate records by DTXSID

Usage

get_aggregate_records_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame of aggregate record data by DTXSID.

Examples

#Pull aggregate records for BPA by DTXSID
bpa_agg_records <- get_aggregate_records_by_dtxsid(DTXSID = 'DTXSID7020182')

Description

Get Aggregate Records by DTXSID via batch

Usage

get_aggregate_records_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames containing aggregate records data for each input DTXSID.

Examples

# Retrieve aggregate records data for BPA and Caffeine
get_aggregate_records_by_dtxsid_batch(DTXSID = c('DTXSID0020232',
  'DTXSID7020182'))

Description

Get aggregate records by medium

Usage

get_aggregate_records_by_medium(
  Medium = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  pageNumber = 1,
  verbose = FALSE
)

Arguments

Value

A list of search parameters and data of aggregate record data by medium.

Examples

#Pull aggregate records for BPA by medium
bpa_agg_records <- get_aggregate_records_by_medium(Medium = 'surface water')

Description

Get Aggregate Records by medium via batch

Usage

get_aggregate_records_by_medium_batch(
  Medium = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames containing aggregate records data for each input medium.

Examples

# Retrieve aggregate records data for 'surface water' and 'soil'
  get_aggregate_records_by_medium_batch(Medium = c('surface water', 'soil'))

Description

Retrieve all assays

Usage

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

Arguments

Value

A data.frame containing all the assays and associated information

Examples

# Retrieve all assays
assays <- get_all_assays()

Description

Get all list types

Usage

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

Arguments

Value

A character list of types of lists.

Examples

get_all_list_types()

Description

Get all public chemical lists

Usage

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

Arguments

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()

Description

Retrieve annotations for AEID

Usage

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

Arguments

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)

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

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))

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

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)

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

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))

Description

Bioactivity API Endpoint status

Usage

get_bioactivity_endpoint_status()

Value

Status of Bioactivity API Endpoints

Examples

status <- get_bioactivity_endpoint_status()
print(status)

Description

Retrieve bioactivity summary for AEID

Usage

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

Arguments

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)

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

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))

Description

Get Biomonitoring data

Usage

get_biomonitoring_data(
  DTXSID = NULL,
  API_key = NULL,
  Projection = "",
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame containing general use keywords.

Examples

# Get biomonitoring data for Caffeine
get_biomonitoring_data('DTXSID0020232')

Description

Get biomonitoring data via batch

Usage

get_biomonitoring_data_batch(
  DTXSID = NULL,
  API_key = NULL,
  Projection = "",
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames of biomonitoring data corresponding to the input DTXSIDs.

Examples

# Retrieve biomonitoring data for BPA and Caffeine
get_biomonitoring_data_batch(DTXSID = c('DTXSID7020182', 'DTXSID0020232'))

Description

Get cancer hazard

Usage

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

Arguments

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')

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

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)

Description

Retrieve chemical information

Usage

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

Arguments

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')

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

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'))

Description

Get experimental physical-chemical property data

Usage

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

Arguments

Value

A data.frame of experimental physchem property data

Examples

# Get experimental physchem properties for BPA
bpa_exp_props <- get_chem_props_exp(DTXSID = 'DTXSID7020182')

Description

Get experimental physical-chemical property data via batch

Usage

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

Arguments

Value

A data.table of experimental physchem property data

Examples

# Get experimental physchem properties for BPA and Caffeine
chem_props_exp <- get_chem_props_exp(DTXSID = c('DTXSID7020182',
                                                'DTXSID0020232'))

Description

Get predicted physical-chemical property data

Usage

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

Arguments

Value

A data.frame of predicted physchem property data

Examples

# Get predicted physchem properties for BPA
bpa_pred_props <- get_chem_props_pred(DTXSID = 'DTXSID7020182')

Description

Get predicted physical-chemical property data via batch

Usage

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

Arguments

Value

A data.table of predicted physchem property data

Examples

# Get predicted physchem properties for BPA and Caffeine
chem_props_pred <- get_chem_props_pred(DTXSID = c('DTXSID7020182',
                                                  'DTXSID0020232'))

Description

Get Summary information on chemical properties

Usage

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

Arguments

Value

A data.frame of summary data for chemical properties.

Examples

# Get summary data for BPA
bpa_props_summary <- get_chem_props_summary(DTXSID = 'DTXSID7020182')

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

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')

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

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'))

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

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')

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

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)

Description

Chemical API Endpoint status

Usage

get_chemical_endpoint_status()

Value

Status of Chemical API Endpoints

Examples

status <- get_chemical_endpoint_status()
print(status)

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

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)
}

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

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]])
}

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

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')

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

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'))

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

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')

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

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)

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

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')

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

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)

Description

Get chemical synonym

Usage

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

Arguments

Value

A named list of synonym information for the input DTXSID

Examples

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

Description

Get chemical synonym batch

Usage

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

Arguments

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)

Description

Get Chemical Weight Fractions

Usage

get_chemical_weight_fraction(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame containing chemical weight fraction data.

Examples

# Get chemical weight fraction data for Caffeine
get_chemical_weight_fraction('DTXSID0020232')

Description

Get chemical weight fraction via batch

Usage

get_chemical_weight_fraction_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames of hemical weight fraction data corresponding to the input DTXSIDs.

Examples

# Retrieve chemical weight fraction data for BPA and Caffeine
get_chemical_weight_fraction_batch(DTXSID = c('DTXSID7020182',
                                              'DTXSID0020232'))

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

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')

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

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'))

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

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')

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

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'))

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

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')

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

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))

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

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')

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

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'))

Description

Get demographic exposure prediction data

Usage

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

Arguments

Value

A data.table of demographic exposure prediction data.

Examples

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

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

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)

Description

Exposure API Endpoint status

Usage

get_exposure_endpoint_status()

Value

Status of Exposure API Endpoints

Examples

status <- get_exposure_endpoint_status()
print(status)

Description

Retrieve exposure related functional use data

Usage

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

Arguments

Value

A data.frame of functional use data.

Examples

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

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

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)

Description

Retrieve functional use categories

Usage

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

Arguments

Value

A data.frame of functional use categories.

Examples

# Pull functional use category data for BPA
functional_use_categories <- get_exposure_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

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')

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

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)

Description

Retrieve list presence tags

Usage

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

Arguments

Value

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

Examples

# Pull list presence tags
tags <- get_exposure_list_presence_tags()

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

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')

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

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)

Description

Retrieve product data for exposure purposes

Usage

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

Arguments

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')

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

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)

Description

Retrieve product use categories related to exposure

Usage

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

Arguments

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()

Description

Get fate by DTXSID

Usage

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

Arguments

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')

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

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'))

Description

Get general exposure prediction data

Usage

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

Arguments

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')

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

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)

Description

Get General Use Keywords

Usage

get_general_use_keywords(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame containing general use keywords.

Examples

# Get general use keywords for Caffeine
get_general_use_keywords('DTXSID0020232')

Description

Get general use keywords via batch

Usage

get_general_use_keywords_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames of general use keywords corresponding to the input DTXSIDs.

Examples

# Retrieve general use keywords for BPA and Caffeine
get_general_use_keywords_batch(DTXSID = c('DTXSID7020182', 'DTXSID0020232'))

Description

Get genetox details

Usage

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

Arguments

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')

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

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)

Description

Get genetox summary

Usage

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

Arguments

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')

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

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)

Description

The function was deprecated due to updates and restructing of the CTX APIs.

Usage

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

Arguments

Value

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

Examples

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

Description

The function was deprecated due to updates and restructing of the CTX APIs.

Usage

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

Arguments

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)

Description

Hazard API Endpoint status

Usage

get_hazard_endpoint_status()

Value

Status of Hazard API Endpoints

Examples

status <- get_hazard_endpoint_status()
print(status)

Description

Get httk data

Usage

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

Arguments

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')

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

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)

Description

Get InChI

Usage

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

Arguments

Value

A string giving the associated inchi string.

Examples

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

Description

Get InChIKey

Usage

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

Arguments

Value

A string giving the associated InChIKey.

Examples

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

Description

Get chemical lists containing given chemical

Usage

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

Arguments

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')

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

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'))

Description

Retrieve MMDB medium categories

Usage

get_medium_categories(
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame of harmonized medium categories from MMDB and relevant descriptions.

Examples

# Retrieve medium categories and descriptions
get_medium_categories()

Description

Get msready by DTXCID

Usage

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

Arguments

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')

Description

Get msready by DTXCID batch search

Usage

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

Arguments

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'))

Description

Get msready by formula

Usage

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

Arguments

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')

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

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'))

Description

Get msready by mass

Usage

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

Arguments

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)

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

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))

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

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)

Description

Get Product Use categories via batch

Usage

get_product_use_categories_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames of product use categories data corresponding to the input DTXSIDs.

Examples

# Retrieve product use categories for BPA and Caffeine
get_product_use_categories_batch(DTXSID = c('DTXSID7020182',
                                            'DTXSID0020232'))

Description

Get Product Use Categories

Usage

get_product_use_category(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame containing product use categories.

Examples

# Get product use categories for Caffeine
get_product_use_category('DTXSID0020232')

Description

Get Production Volume

Usage

get_production_volume(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame containing production volume data.

Examples

# Get production volume data for Caffeine
get_production_volume('DTXSID0020232')

Description

Get Production Volume data via batch

Usage

get_production_volume_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames of production volume data corresponding to the input DTXSIDs.

Examples

# Retrieve production volume data for BPA and Caffeine
get_production_volume_batch(DTXSID = c('DTXSID7020182', 'DTXSID0020232'))

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

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.

See Also

get_chemicals_in_list

Examples

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

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

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.

See Also

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'))

Description

Get Reported Functional Use

Usage

get_reported_functional_use(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame containing reported functional use data.

Examples

# Get reported functional use data for Caffeine
get_reported_functional_use('DTXSID0020232')

Description

Get reported functional use via batch

Usage

get_reported_functional_use_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames of reported functional use corresponding to the input DTXSIDs.

Examples

# Retrieve reported functional use for BPA and Caffeine
get_reported_functional_use_batch(DTXSID = c('DTXSID7020182',
                                             'DTXSID0020232'))

Description

Get single sample records by DTXSID

Usage

get_single_sample_records_by_dtxsid(
  DTXSID = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A data.frame of single sample record data by DTXSID.

Examples

#Pull single sample records for BPA by DTXSID
bpa_sample_records <- get_single_sample_records_by_dtxsid(DTXSID = 'DTXSID7020182')

Description

Get Single Sample Records by DTXSID via batch

Usage

get_single_sample_records_by_dtxsid_batch(
  DTXSID = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames containing single sample records data for each input DTXSID.

Examples

# Retrieve single sample records data for BPA and Caffeine
get_single_sample_records_by_dtxsid_batch(DTXSID = c('DTXSID0020232',
  'DTXSID7020182'))

Description

Get single sample records by medium

Usage

get_single_sample_records_by_medium(
  Medium = NULL,
  API_key = NULL,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  pageNumber = 1,
  verbose = FALSE
)

Arguments

Value

A list of search parameters and data of single sample record data by medium.

Examples

#Pull single records for BPA by medium
bpa_sample_records <- get_single_sample_records_by_medium(Medium = 'surface water')

Description

Get Single Sample Records by medium via batch

Usage

get_single_sample_records_by_medium_batch(
  Medium = NULL,
  API_key = NULL,
  rate_limit = 0L,
  Server = "https://comptox.epa.gov/ctx-api/exposure",
  verbose = FALSE
)

Arguments

Value

A list of data.frames containing single sample records data for each input medium.

Examples

# Retrieve single sample records data for 'surface water' and 'soil'
get_single_sample_records_by_medium_batch(Medium = c('surface water', 'soil'))

Description

Get skin and eye hazard

Usage

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

Arguments

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')

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

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)

Description

Get Smiles

Usage

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

Arguments

Value

A string giving a SMILES string for the input chemical.

Examples

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

Description

A section of url used in Hazard API Endpoints

Usage

hazard_api_server

Format

An object of class character of length 1.

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

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.