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e2dfb2f
Renamed vignette files but made no changes to the contents of the files.
rachmaninoffpk Jan 13, 2025
169993c
Incremented version number to dev.
rachmaninoffpk Jan 13, 2025
fd2bb51
Added new heading for dev version.
rachmaninoffpk Jan 13, 2025
86bec63
Updated introduction, rearranged ordering of examples, updated headin…
rachmaninoffpk Jan 21, 2025
6bb06c4
Converted part of overview into list format and linked to relevant he…
rachmaninoffpk Jan 22, 2025
be51949
Merge pull request #45 from USEPA/44-update-exposure-vignette
rachmaninoffpk Jan 23, 2025
6cdcbd4
Changes made to exposure vignette need to be merged before renaming t…
rachmaninoffpk Jan 23, 2025
9d6f8ca
Merge pull request #43 from USEPA/42-rename-vignette-files-for-correc…
rachmaninoffpk Jan 23, 2025
1119a38
Added new projection value.
rachmaninoffpk Feb 10, 2025
f469b40
Added new projection value.
rachmaninoffpk Feb 10, 2025
d902857
Added functions for aggregate and single record MMDB data retrieval f…
rachmaninoffpk Feb 26, 2025
eeeeeca
Added batch versions of functions covering new MMDB endpoints.
rachmaninoffpk Feb 28, 2025
c28ee7e
Update chemical search resource documentation #52
bridirks Apr 8, 2025
fa8346c
Update chemical search resource documentation #52
bridirks Apr 8, 2025
f9530d1
Merge pull request #58 from USEPA/52-update-chemical-search-resource-…
bridirks Apr 8, 2025
46a2c45
Merge pull request #47 from USEPA/46-add-new-projection-values-to-che…
madison-feshuk Apr 8, 2025
d7469e8
chemical_equal_batch() throws error if a CASRN doesn't return any res…
bridirks Apr 9, 2025
60bda0b
Special character handling by chemical_contains/chemical_contains_bat…
bridirks Apr 9, 2025
f2b97e1
Merge pull request #59 from USEPA/53-chemical_equal_batch-throws-erro…
bridirks Apr 17, 2025
9591ceb
Merge pull request #60 from USEPA/56-special-character-handling-by-ch…
madison-feshuk Jun 12, 2025
1e6047b
Merge branch 'dev' into ctxr1.1.2-to-dev
madison-feshuk Jul 23, 2025
ed19a5c
update desc authors and README
madison-feshuk Jul 23, 2025
6775dbc
remove empty line in DESCRIPTION file
madison-feshuk Jul 23, 2025
ac37fef
add missing ) to DESCRIPTION file
madison-feshuk Jul 24, 2025
e052df3
update author info
madison-feshuk Jul 24, 2025
7fdf045
add missing ) to DESCRIPTION
madison-feshuk Jul 24, 2025
04324be
Merge pull request #64 from USEPA/ctxR1.1.2-to-dev
madison-feshuk Jul 24, 2025
fc354cd
Initial commit.
rachmaninoffpk Jul 24, 2025
5e98ae0
Added citation information.
rachmaninoffpk Jul 28, 2025
885a546
Merge pull request #66 from USEPA/65-add-citation-for-new-ctxr-paper
rachmaninoffpk Jul 28, 2025
b186ab9
Merge branch 'dev' into 49-add-functions-for-new-exposure-endpoints
rachmaninoffpk Sep 16, 2025
3effe51
Initial commit.
rachmaninoffpk Sep 16, 2025
01e7229
Fixed errors in two tests.
rachmaninoffpk Sep 16, 2025
c887e20
Added documentation to new functions. Fixed `Server` parameter and in…
rachmaninoffpk Sep 16, 2025
bf79865
Added function exports.
rachmaninoffpk Sep 16, 2025
f357e84
Initial commit.
rachmaninoffpk Sep 17, 2025
1967ab2
Added function exports for new CCD endpoints.
rachmaninoffpk Sep 17, 2025
40eae17
Added new functions for CCD endpoints.
rachmaninoffpk Sep 17, 2025
c6c82bc
Initial commit.
rachmaninoffpk Sep 17, 2025
f69d3d6
Fixed uppercase and lowercase related errors.
rachmaninoffpk Sep 17, 2025
cd9fcf4
Added batch versions of MMDB functions.
rachmaninoffpk Sep 17, 2025
8cef672
Added function exports for batch version of MMDB endpoints.
rachmaninoffpk Sep 17, 2025
b726902
Initial commit.
rachmaninoffpk Sep 17, 2025
0b1bf2c
Fixed incorrect parameter documentation.
rachmaninoffpk Sep 17, 2025
447d120
Added batch fucntions for CCD endpoints.
rachmaninoffpk Sep 17, 2025
05758f8
Added exports for batch functions for CCD endpoints.
rachmaninoffpk Sep 17, 2025
d844c9c
Added new root path abbreviation.
rachmaninoffpk Sep 18, 2025
7b996c6
Added examples for new endpoint functions. Fixed ctxR image placement.
rachmaninoffpk Sep 18, 2025
bb64f1f
Initial commit.
rachmaninoffpk Sep 18, 2025
eb552e2
Reran vignette to record new requests and responses.
rachmaninoffpk Sep 18, 2025
b63a011
Fixed error messages.
rachmaninoffpk Sep 18, 2025
8e6d264
Added tests for new exposure endpoint functions.
rachmaninoffpk Sep 18, 2025
822e8ac
Initial commit.
rachmaninoffpk Sep 18, 2025
8344673
Reran tests to capture updated responses and requests.
rachmaninoffpk Sep 18, 2025
d4a58ef
Reran requests and recordings for vignette and tests.
rachmaninoffpk Sep 18, 2025
6a6390d
Fixed one substitution causing issues and added a second substitution.
rachmaninoffpk Sep 18, 2025
09ef2a4
Fixed failing tests.
rachmaninoffpk Sep 18, 2025
2801bf2
Reran test requests and response recordings for fixed tests.
rachmaninoffpk Sep 18, 2025
70a721d
Documented new features and updates to Exposure functions and vignettes.
rachmaninoffpk Sep 19, 2025
ae29c9f
Updated PR reference.
rachmaninoffpk Sep 19, 2025
bed5a55
Reran tests to capture updated request and response recordings.
rachmaninoffpk Sep 24, 2025
57bf0fc
Reran vignette to capture updated request and response recordings.
rachmaninoffpk Sep 24, 2025
7232bb0
Reran vignette to capture updated request and response recordings.
rachmaninoffpk Sep 24, 2025
61626bc
Reran vignette to capture updated request and response recordings.
rachmaninoffpk Sep 24, 2025
06e29c1
Reran vignette to capture updated request and response recordings.
rachmaninoffpk Sep 24, 2025
b00a6f3
Updated root address to new location.
rachmaninoffpk Sep 24, 2025
4e27d6d
Updated vignettes to reflect adjusted functions.
rachmaninoffpk Sep 24, 2025
bd03e5e
Adjusted tests to reflect updated functions.
rachmaninoffpk Sep 24, 2025
a1008e9
Updated substitutions.
rachmaninoffpk Sep 24, 2025
e9115f8
Updated version.
rachmaninoffpk Sep 24, 2025
4cf9ce8
Updated version.
rachmaninoffpk Sep 24, 2025
3576266
Updated root address to new location.
rachmaninoffpk Sep 24, 2025
3625e0a
Added new substitution.
rachmaninoffpk Sep 24, 2025
2c00663
Reran tests to capture new request and response recordings.
rachmaninoffpk Sep 24, 2025
6bf8e28
Reram tests to capture new request and response recordings.
rachmaninoffpk Sep 24, 2025
86c26c2
Reran vignettes to capture new recordings.
rachmaninoffpk Sep 24, 2025
a4e00e6
Reran vignettes to capture new recordings.
rachmaninoffpk Sep 24, 2025
9c16f94
Removed old case study.
rachmaninoffpk Sep 25, 2025
df2bd46
Added library import.
rachmaninoffpk Sep 30, 2025
380e157
Added new functions and adjusted existing functions for backwards com…
rachmaninoffpk Sep 30, 2025
e328da2
Added new substitution.
rachmaninoffpk Sep 30, 2025
13b0d23
Reran tests to record new requests and responses.
rachmaninoffpk Sep 30, 2025
2a3ff77
Adjusted or removed tests based on new function behavior.
rachmaninoffpk Sep 30, 2025
32d1916
Added library import.
rachmaninoffpk Sep 30, 2025
d0c05bf
Deprecated functions affected by change in API schema.
rachmaninoffpk Sep 30, 2025
2e92409
Updated documentation of deprecated functions.
rachmaninoffpk Sep 30, 2025
0ba8f28
Updated tests of deprecated functions.
rachmaninoffpk Sep 30, 2025
d146bc4
Removed examples of deprecated functions.
rachmaninoffpk Sep 30, 2025
dc458f4
Reversed function deprecation.
rachmaninoffpk Oct 1, 2025
739288e
Reran test to record new requests and responses.
rachmaninoffpk Oct 1, 2025
d099b80
Updated example of function previously deprecated.
rachmaninoffpk Oct 1, 2025
f6a8f8b
Initial commit.
rachmaninoffpk Oct 1, 2025
6056564
Added function exports.
rachmaninoffpk Oct 1, 2025
2587bff
Added Roxygen code for exporting and documenting new functions.
rachmaninoffpk Oct 1, 2025
8cb74f5
Merge pull request #72 from USEPA/69-change-api-host-from-cloudgov-to…
rachmaninoffpk Oct 2, 2025
883f5c1
Merged dev to branch and resolved conflicts.
rachmaninoffpk Oct 2, 2025
be8cd05
Reran vignette to update recordings of requests and responses.
rachmaninoffpk Oct 2, 2025
2290d5b
update DESCRIPTION for fix warning message, remove extra title in vig…
madison-feshuk Oct 2, 2025
1b3a9eb
run revdep check and pkgdown
madison-feshuk Oct 2, 2025
31745af
Merge pull request #71 from USEPA/49-add-functions-for-new-exposure-e…
madison-feshuk Oct 2, 2025
5425822
Updated API host address.
rachmaninoffpk Oct 2, 2025
7e4fe4e
Deleted old recordings using old API host.
rachmaninoffpk Oct 2, 2025
d4db491
Merge branch 'dev' into 74-v113-release
rachmaninoffpk Oct 2, 2025
2234eed
reran test to record new requests and responses.
rachmaninoffpk Oct 3, 2025
ea3de65
update NEWS
madison-feshuk Oct 3, 2025
96f9dd4
regenerate docs, io pages, manual + update cran comments
madison-feshuk Oct 6, 2025
7038be0
Merge pull request #75 from USEPA/74-v113-release
madison-feshuk Oct 6, 2025
ef7106b
Commented out tests producing large recordings.
rachmaninoffpk Oct 6, 2025
65467e9
remove some tests to decrease package size
madison-feshuk Oct 6, 2025
b5d459b
Adjusted chunk options not to record requests that were too large.
rachmaninoffpk Oct 6, 2025
95f5a6f
Reran test to capture updated recordings.
rachmaninoffpk Oct 6, 2025
81c779c
Reran vignette to update recordings.
rachmaninoffpk Oct 6, 2025
edcbc9b
Merge branch '74-v113-release' of https://github.com/USEPA/ctxR into …
rachmaninoffpk Oct 6, 2025
a043d95
Merge pull request #76 from USEPA/74-v113-release
madison-feshuk Oct 6, 2025
e749d5c
Fixed links that were broken and adjusted exposition accordingly.
rachmaninoffpk Oct 6, 2025
cdafba1
Merge pull request #77 from USEPA/74-v113-release
madison-feshuk Oct 6, 2025
0a3a25b
fix ORCID comment in description, drop citations column with bad Pubm…
madison-feshuk Oct 8, 2025
6971d97
Merge pull request #78 from USEPA/74-v113-release
madison-feshuk Oct 8, 2025
382435a
update version #
madison-feshuk Oct 8, 2025
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29 changes: 11 additions & 18 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,22 +1,14 @@
Type: Package
Package: ctxR
Title: Utilities for Interacting with the 'CTX' APIs
Version: 1.1.2
Version: 1.1.3
Authors@R: c(
person("Paul", "Kruse", email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0001-5516-9717")),
person("Caroline", "Ring", email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0002-0463-1251")),
person("Madison", "Feshuk", role = "cre",
email = "[email protected]",
comment = c(ORCID = "0000-0002-1390-6405")),
person("Carter", "Thunes", role = "ctb",
email = "[email protected]"),
person("Jason", "Brown", role = "ctb",
email = "[email protected]")
)
person(given = "Paul", family = "Kruse", role = c("aut"), comment = c(ORCID = "0000-0001-5516-9717")),
person(given = "Caroline", family = "Ring", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-0463-1251")),
person(given = "Madison", family = "Feshuk", role = c("ctb","cre"), email = "[email protected]", comment = c(ORCID = "0000-0002-1390-6405")),
person(given = "Brianna",family = "Dirks", role = "ctb", comment = c(ORCID = "0009-0003-3691-1543")),
person(given = "Carter", family = "Thunes", role = "ctb"),
person(given = "Jason", family = "Brown", role = "ctb", comment = c(ORCID = "0009-0000-2294-641X")))
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>.
Expand All @@ -37,11 +29,12 @@ Imports:
stringr,
tidyr,
tibble,
urltools
urltools,
lifecycle
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
Suggests:
countcolors,
devtools,
Expand All @@ -62,4 +55,4 @@ BugReports: https://github.com/USEPA/ctxR/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
Depends:
R (>= 2.10)
R (>= 3.5)
27 changes: 27 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,10 @@ export(chemical_starts_with_batch)
export(ctxR_hide_api_key)
export(ctxR_show_api_key)
export(ctx_key)
export(get_aggregate_records_by_dtxsid)
export(get_aggregate_records_by_dtxsid_batch)
export(get_aggregate_records_by_medium)
export(get_aggregate_records_by_medium_batch)
export(get_all_assays)
export(get_all_list_types)
export(get_all_public_chemical_lists)
Expand All @@ -22,10 +26,17 @@ export(get_bioactivity_details_batch)
export(get_bioactivity_endpoint_status)
export(get_bioactivity_summary)
export(get_bioactivity_summary_batch)
export(get_biomonitoring_data)
export(get_biomonitoring_data_batch)
export(get_cancer_hazard)
export(get_cancer_hazard_batch)
export(get_chem_info)
export(get_chem_info_batch)
export(get_chem_props_exp)
export(get_chem_props_exp_batch)
export(get_chem_props_pred)
export(get_chem_props_pred_batch)
export(get_chem_props_summary)
export(get_chemical_by_property_range)
export(get_chemical_by_property_range_batch)
export(get_chemical_details)
Expand All @@ -41,6 +52,8 @@ export(get_chemical_mrv)
export(get_chemical_mrv_batch)
export(get_chemical_synonym)
export(get_chemical_synonym_batch)
export(get_chemical_weight_fraction)
export(get_chemical_weight_fraction_batch)
export(get_chemicals_in_list)
export(get_chemicals_in_list_batch)
export(get_chemicals_in_list_contain)
Expand Down Expand Up @@ -69,6 +82,8 @@ export(get_fate_by_dtxsid)
export(get_fate_by_dtxsid_batch)
export(get_general_exposure_prediction)
export(get_general_exposure_prediction_batch)
export(get_general_use_keywords)
export(get_general_use_keywords_batch)
export(get_genetox_details)
export(get_genetox_details_batch)
export(get_genetox_summary)
Expand All @@ -84,15 +99,26 @@ export(get_inchi)
export(get_inchikey)
export(get_lists_containing_chemical)
export(get_lists_containing_chemical_batch)
export(get_medium_categories)
export(get_msready_by_dtxcid)
export(get_msready_by_dtxcid_batch)
export(get_msready_by_formula)
export(get_msready_by_formula_batch)
export(get_msready_by_mass)
export(get_msready_by_mass_batch)
export(get_msready_by_mass_with_error_batch)
export(get_product_use_categories_batch)
export(get_product_use_category)
export(get_production_volume)
export(get_production_volume_batch)
export(get_public_chemical_list_by_name)
export(get_public_chemical_list_by_name_batch)
export(get_reported_functional_use)
export(get_reported_functional_use_batch)
export(get_single_sample_records_by_dtxsid)
export(get_single_sample_records_by_dtxsid_batch)
export(get_single_sample_records_by_medium)
export(get_single_sample_records_by_medium_batch)
export(get_skin_eye_hazard)
export(get_skin_eye_hazard_batch)
export(get_smiles)
Expand All @@ -102,3 +128,4 @@ export(has_ctx_key)
export(register_ctx_api_key)
export(set_ctxR_option)
export(showing_key)
import(data.table)
27 changes: 26 additions & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
@@ -1,17 +1,42 @@
# ctxR 1.1.3

## Major improvements and fixes

* Update api host from cloud.gov to local server throughout package (#70)

## New Features

* Added functions for the Exposure domain CCD endpoints `get_product_use_category()`,
`get_product_use_categories_batch()`, `get_production_volume()`,
`get_production_volume_batch()`, `get_biomonitoring_data()`, `get_biomonitoring_data_batch()`,
`get_general_use_keywords()`, `get_general_use_keywords_batch()`, `get_reported_functional_use()`,
`get_reported_functional_use_batch()`, `get_chemical_weight_fraction()`, and
`get_chemical_weight_fraction_batch()` (#71).

* Added functions for Exposure domain MMDB endpoints `get_medium_categories()`,
`get_single_sample_records_by_dtxsid()`, `get_single_sample_records_by_dtxsid_batch()`,
`get_single_sample_records_by_medium()`, `get_single_sample_records_by_medium_batch()`,
`get_aggregate_records_by_dtxsid()`, `get_aggregate_records_by_dtxsid_batch`(),
`get_aggregate_records_by_medium()`, `get_aggregate_records_by_medium_batch`() (#71).

* Added examples to `ctxR_04_Exposure.Rmd` vignette for new CCD and MMDB endpoint
functions (#71).

# ctxR 1.1.2

## Minor improvements and fixes

* Updated roles in `DESCRIPTION` file and Roxygen version (#57).


# ctxR 1.1.1

## Minor improvements and fixes

* Updated roles in `DESCRIPTION` file (#55).

# ctxR 1.1.0

# ctxR 1.1.0

## Minor improvements and fixes

Expand Down
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