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]

wqbench_0.2.0.tar.gz
wqbench_0.2.0.zip(r-4.5)wqbench_0.2.0.zip(r-4.4)wqbench_0.2.0.zip(r-4.3)
wqbench_0.2.0.tgz(r-4.4-any)wqbench_0.2.0.tgz(r-4.3-any)
wqbench_0.2.0.tar.gz(r-4.5-noble)wqbench_0.2.0.tar.gz(r-4.4-noble)
wqbench_0.2.0.tgz(r-4.4-emscripten)wqbench_0.2.0.tgz(r-4.3-emscripten)
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'))

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

Datasets:

template - Template for Adding your own Data

On CRAN:

31 exports 3.30 score 127 dependencies 7 scripts

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

Target	Result	Date
Doc / Vignettes	OK	Sep 17 2024
R-4.5-win	ERROR	Sep 17 2024
R-4.5-linux	ERROR	Sep 17 2024
R-4.4-win	ERROR	Sep 17 2024
R-4.4-mac	ERROR	Sep 17 2024
R-4.3-win	ERROR	Sep 17 2024
R-4.3-mac	ERROR	Sep 17 2024

Exports:wqb_add_bc_species wqb_add_bc_wqg wqb_add_conc_conversions wqb_add_concentration_endpoints wqb_add_duration_conversions wqb_add_lifestage wqb_add_media wqb_add_trophic_group wqb_af wqb_af_bc_species wqb_af_ecological wqb_af_variation wqb_aggregate wqb_benchmark_method wqb_check_add_data wqb_classify_duration wqb_create_data_set wqb_create_epa_ecotox wqb_download_epa_ecotox wqb_filter_chemical wqb_generate_ctv wqb_method_det wqb_method_ssd wqb_plot wqb_plot_det wqb_plot_ssd wqb_ssd_fit wqb_standardize_effect wqb_summary_af wqb_summary_trophic_groups wqb_summary_trophic_species

Dependencies:abind askpass base64enc bcdata bit bit64 blob bslib cachem cellranger chk chktemplate class classInt cli clipr codetools colorspace cpp11 crayon crosstalk crul curl DBI dbplyr digest dplyr e1071 evaluate fansi farver fastmap fontawesome fs furrr future generics ggplot2 globals glue goftest gtable highr hms htmltools htmlwidgets httpcode httr isoband jquerylib jsonlite KernSmooth knitr labeling lattice lazyeval leaflet leaflet.extras leaflet.providers lifecycle listenv magrittr MASS Matrix memoise mgcv mime munsell nlme openssl parallelly pillar pkgconfig plogr plyr png prettyunits progress proxy purrr R6 rappdirs raster rbibutils RColorBrewer Rcpp RcppEigen Rdpack readr readxl rematch rlang rmarkdown RSQLite rvest s2 sass scales selectr sf sp ssddata ssdtools stringi stringr sys terra tibble tidyr tidyselect tinytex TMB triebeard tzdb units universals urltools utf8 vctrs VGAM viridisLite vroom withr wk xfun xml2 yaml

Developer Instructions

Rendered fromDeveloper-instructions.Rmdusingknitr::rmarkdownon Sep 17 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Combine BC Species and DB Species	combine_bc_species
Combine BC Water Quality Guidelines with DB Chemicals	combine_bc_wqg
Combine Concentration Unit Conversation Values with DB Concentration Unit	combine_conc_conversions
Combine the Concentration Endpoints list to db endpoints	combine_concentration_endpoints
Combine Duration Unit Conversation Values and DB duration unit	combine_duration_conversions
Combine Life Stage Groups and db life stage	combine_lifestage
Combine Media Type Coding	combine_media
Combine Trophic Groups and DB species	combine_trophic_group
Join Data	join_data
Read in BC Species CSV	read_bc_species
Read BC Water Quality Guidelines	read_bc_wqg
Read Concentration Unit Conversation Values	read_conc_conversions
Read the Concentration Endpoints	read_concentration_endpoints
Read Duration Unit Conversation	read_duration_conversions
Read Life Stage Groups	read_lifestage
Read Trophic Groups and DB species	read_trophic_group
Template for Adding your own Data	template
Add BC Species	wqb_add_bc_species
Add BC Water Quality Guidelines	wqb_add_bc_wqg
Add Concentration Unit Conversation Values	wqb_add_conc_conversions
Add the Concentration Endpoints	wqb_add_concentration_endpoints
Add Duration Unit Conversation Values	wqb_add_duration_conversions
Add Life Stage Groups	wqb_add_lifestage
Add Media Type Coding of Salt or Fresh Water	wqb_add_media
Add Trophic Groups to Database	wqb_add_trophic_group
Determine the Assessment Factors	wqb_af
Determine the BC Species Assessment Factor	wqb_af_bc_species
Determine the Ecological Assessment Factors	wqb_af_ecological
Determine the Species Variation Assessment Factor	wqb_af_variation
Aggregate Data for each Species	wqb_aggregate
Determine Benchmark Method	wqb_benchmark_method
Check the Uploaded Data	wqb_check_add_data
Classify Duration	wqb_classify_duration
Compile Data	wqb_clean_data
Create the Data Set for the App	wqb_create_data_set
Create the ECOTOX Database	wqb_create_epa_ecotox
Download ECOTOX Data Files	wqb_download_epa_ecotox
Filter to a Single Chemical	wqb_filter_chemical
Generate Critical Toxicity Value	wqb_generate_ctv
Join Data	wqb_join_data
Deterministic Method to Generate Critical Toxicity Value for the Chemical	wqb_method_det
SSD Method to Calculate Critical Toxicity Value for the Chemical	wqb_method_ssd
Plot Data	wqb_plot
Plot the Deterministic Method Results	wqb_plot_det
Plot Species Sensitivity Distribution	wqb_plot_ssd
Fit BCANZ Distributions	wqb_ssd_fit
Run SSD to get Hazard Concentrations	wqb_ssd_hc5
Standardize type of Effect	wqb_standardize_effect
Summary Table of the Assessment Factor Values	wqb_summary_af
Summary Table of Assessment Factors Information	wqb_summary_trophic_groups
Summary Table of Number of Species per Trophic Group	wqb_summary_trophic_species