Package: wqbench 0.2.0

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], Province of British Columbia [cph]

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wqbench.pdf |wqbench.html✨
wqbench/json (API)
NEWS

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

Peer review:

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

Datasets:
  • template - Template for Adding your own Data

On CRAN:

3.78 score 1 packages 5 scripts 31 exports 126 dependencies

Last updated 8 months agofrom:b2a5e02e20. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winERRORNov 16 2024
R-4.5-linuxERRORNov 16 2024
R-4.4-winERRORNov 16 2024
R-4.4-macERRORNov 16 2024
R-4.3-winERRORNov 16 2024
R-4.3-macERRORNov 16 2024

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:abindaskpassbase64encbcdatabitbit64blobbslibcachemcellrangerchkchktemplateclassclassIntclicliprcodetoolscolorspacecpp11crayoncrosstalkcrulcurlDBIdbplyrdigestdplyre1071evaluatefansifarverfastmapfontawesomefsfurrrfuturegenericsggplot2globalsgluegoftestgtablehighrhmshtmltoolshtmlwidgetshttpcodehttrisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevalleafletleaflet.extrasleaflet.providerslifecyclelistenvmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslparallellypillarpkgconfigplogrplyrpngprettyunitsprogressproxypurrrR6rappdirsrasterrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlrematchrlangrmarkdownRSQLitervests2sassscalesselectrsfspssddatassdtoolsstringistringrsysterratibbletidyrtidyselecttinytexTMBtriebeardtzdbunitsuniversalsurltoolsutf8vctrsviridisLitevroomwithrwkxfunxml2yaml

Developer Instructions

Rendered fromDeveloper-instructions.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-03-25
Started: 2024-03-25

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