Package: wqbench 0.4.0

Angeline Tillmanns

wqbench: Calculate Aquatic Life Benchmarks

Download recent versions of the US EPA ECOTOX database. Clean, standardize and classify data so values are comparable. Use a SSD or deterministic method to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.

Authors:Ayla Pearson [aut], Angeline Tillmanns [aut, cre], Joe Thorley [ctb], Andy Teucher [ctb], Province of British Columbia [cph]

wqbench_0.4.0.tar.gz
wqbench_0.4.0.zip(r-4.7)wqbench_0.4.0.zip(r-4.6)wqbench_0.4.0.zip(r-4.5)
wqbench_0.4.0.tgz(r-4.6-any)wqbench_0.4.0.tgz(r-4.5-any)
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wqbench_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wqbench/json (API)

# Install 'wqbench' in R:
install.packages('wqbench', repos = c('https://poissonconsulting.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bcgov/wqbench/issues

Pkgdown/docs site:https://bcgov.github.io

Datasets:
  • template - Template for Adding your own Data

On CRAN:

Conda:

4.38 score 1 packages 7 scripts 31 exports 125 dependencies

Last updated from:62c79a8797. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR216
source / vignettesOK267
linux-release-x86_64ERROR216
macos-release-arm64ERROR115
macos-oldrel-arm64ERROR174
windows-develERROR158
windows-releaseERROR159
windows-oldrelERROR175
wasm-releaseOK181

Exports:wqb_add_bc_specieswqb_add_bc_wqgwqb_add_conc_conversionswqb_add_concentration_endpointswqb_add_duration_conversionswqb_add_lifestagewqb_add_mediawqb_add_trophic_groupwqb_afwqb_af_bc_specieswqb_af_ecologicalwqb_af_variationwqb_aggregatewqb_benchmark_methodwqb_check_add_datawqb_classify_durationwqb_create_data_setwqb_create_epa_ecotoxwqb_download_epa_ecotoxwqb_filter_chemicalwqb_generate_ctvwqb_method_detwqb_method_ssdwqb_plotwqb_plot_detwqb_plot_ssdwqb_ssd_fitwqb_standardize_effectwqb_summary_afwqb_summary_trophic_groupswqb_summary_trophic_species

Dependencies:askpassbase64encbcdatabitbit64blobbslibcachemcellrangerchkchktemplateclassclassIntclicliprcodetoolscommonmarkcpp11crayoncrosstalkcrulcurlDBIdbplyrdigestdplyre1071evaluatefarverfastmapfontawesomefsfurrrfuturegenericsggplot2ggtextglobalsgluegoftestgridtextgtablehighrhmshtmltoolshtmlwidgetshttpcodehttrisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclelistenvlitedownmagrittrmarkdownMASSMatrixmemoisemimeopensslparallellypillarpkgconfigpngprettyunitsprogressproxypurrrR6rappdirsrasterrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlrematchrlangrmarkdownRSQLitervests2S7sassscalesselectrsfspssddatassdtoolsstringistringrsysterratibbletidyrtidyselecttinytexTMBtriebeardtzdbunitsuniversalsurltoolsutf8vctrsVGAMviridisLitevroomwithrwkxfunxml2yaml

Developer Instructions
Updating Reference Data for the Database | Process | Reference File Review Process | Concentration Conversion | Duration Conversion | Trophic Groups | Life Stage Codes | BC Species | Concentration Endpoints
Rendered fromDeveloper-instructions.Rmdusingknitr::rmarkdown

Last update: 2025-03-10
Started: 2024-04-12

Update the Add Data Templates
Updating the Add Data Template | Associated Reference Data | To update the template | Push and install the pacakge
Rendered fromupdate-add-data-template.Rmdusingknitr::rmarkdown

Last update: 2024-10-31
Started: 2024-10-31

Readme and manuals

Help Manual

Help pageTopics
Combine BC Species and DB Speciescombine_bc_species
Combine BC Water Quality Guidelines with DB Chemicalscombine_bc_wqg
Combine Concentration Unit Conversation Values with DB Concentration Unitcombine_conc_conversions
Combine the Concentration Endpoints list to db endpointscombine_concentration_endpoints
Combine Duration Unit Conversation Values and DB duration unitcombine_duration_conversions
Combine Life Stage Groups and db life stagecombine_lifestage
Combine Media Type Codingcombine_media
Combine Trophic Groups and DB speciescombine_trophic_group
Join Datajoin_data
Read in BC Species CSVread_bc_species
Read BC Water Quality Guidelinesread_bc_wqg
Read Concentration Unit Conversation Valuesread_conc_conversions
Read the Concentration Endpointsread_concentration_endpoints
Read Duration Unit Conversationread_duration_conversions
Read Life Stage Groupsread_lifestage
Read Trophic Groups and DB speciesread_trophic_group
Template for Adding your own Datatemplate
Add BC Specieswqb_add_bc_species
Add BC Water Quality Guidelineswqb_add_bc_wqg
Add Concentration Unit Conversation Valueswqb_add_conc_conversions
Add the Concentration Endpointswqb_add_concentration_endpoints
Add Duration Unit Conversation Valueswqb_add_duration_conversions
Add Life Stage Groupswqb_add_lifestage
Add Media Type Coding of Salt or Fresh Waterwqb_add_media
Add Trophic Groups to Databasewqb_add_trophic_group
Determine the Assessment Factorswqb_af
Determine the BC Species Assessment Factorwqb_af_bc_species
Determine the Ecological Assessment Factorswqb_af_ecological
Determine the Species Variation Assessment Factorwqb_af_variation
Aggregate Data for each Specieswqb_aggregate
Determine Benchmark Methodwqb_benchmark_method
Check the Uploaded Datawqb_check_add_data
Classify Durationwqb_classify_duration
Compile Datawqb_clean_data
Create the Data Set for the Appwqb_create_data_set
Create the ECOTOX Databasewqb_create_epa_ecotox
Download ECOTOX Data Fileswqb_download_epa_ecotox
Filter to a Single Chemicalwqb_filter_chemical
Generate Critical Toxicity Valuewqb_generate_ctv
Join Datawqb_join_data
Deterministic Method to Generate Critical Toxicity Value for the Chemicalwqb_method_det
SSD Method to Calculate Critical Toxicity Value for the Chemicalwqb_method_ssd
Plot Datawqb_plot
Plot the Deterministic Method Resultswqb_plot_det
Plot Species Sensitivity Distributionwqb_plot_ssd
Fit BCANZ Distributionswqb_ssd_fit
Run SSD to get Hazard Concentrationswqb_ssd_hc5
Standardize type of Effectwqb_standardize_effect
Summary Table of the Assessment Factor Valueswqb_summary_af
Summary Table of Assessment Factors Informationwqb_summary_trophic_groups
Summary Table of Number of Species per Trophic Groupwqb_summary_trophic_species