wqbench
October 31, 2024 · View on GitHub
This package contains the functions and tools to generate aquatic life water quality benchmarks.
Installation
# install.packages("devtools")
devtools::install_github("bcgov/wqbench")
Workflow
library(wqbench)
Create Data Set for Shiny App
The wqb_create_data_set() function will download the US EPA
ECOTOX1 database, create a local .sqlite database, add other
data sources and filter conditions, clean and process the data, classify
the duration, standardize the effect and output the completed data set
needed for the shinywqbench app. The function will create an RDS file of
the data set as well. It takes a few minutes to download and create the
data set.
The default argument for:
file_pathwill save the raw text files at"~/Ecotoxicology/ecotox".folder_pathwill save the .sqlite database and RDS file is at"~/Ecotoxicology/ecotox_db/".versionwill download the most recent version of the data set available on the website.
data_set <- wqb_create_data_set()
The data set can be read in after it has been created.
data_set <- readRDS("~/Ecotoxicology/ecotox_db/ecotox_ascii_09_12_2024.rds")
Generate Benchmark
set.seed(101)
Deterministic Example
data <- wqb_filter_chemical(wqbenchdata::aquatic_data, "100016")
data <- wqb_benchmark_method(data)
data_agg <- wqb_aggregate(data)
data_agg <- wqb_af(data_agg)
ctv <- wqb_generate_ctv(data_agg)
ctv
## # A tibble: 1 × 3
## ctv_est_mg.L ctv_lcl_mg.L ctv_ucl_mg.L
## <dbl> <dbl> <dbl>
## 1 2.5 NA NA
To calculate the benchmark for the chemical, divide the critical toxicity value (ctv) by the assessment factors.
benchmark <- ctv / (data_agg$af_bc_species * data_agg$af_salmon * data_agg$af_planktonic * data_agg$af_variation)
benchmark
## ctv_est_mg.L ctv_lcl_mg.L ctv_ucl_mg.L
## 1 0.04166667 NA NA
Deterministic method only generates an estimate, the lcl and ucl columns will always be blank .
# Plot data set
wqb_plot(data)
# Plot the results
wqb_plot_det(data_agg)
SSD Example
data <- wqb_filter_chemical(wqbenchdata::aquatic_data, "1071836")
data <- wqb_benchmark_method(data)
data_agg <- wqb_aggregate(data)
data_agg <- wqb_af(data_agg)
ctv <- wqb_generate_ctv(data_agg)
ctv
## # A tibble: 1 × 3
## ctv_est_mg.L ctv_lcl_mg.L ctv_ucl_mg.L
## <dbl> <dbl> <dbl>
## 1 0.00981 0.00105 0.0543
To calculate the benchmark for the chemical, divide the critical toxicity value (ctv) by the assessment factors.
benchmark <- ctv / (data_agg$af_bc_species * data_agg$af_salmon * data_agg$af_planktonic * data_agg$af_variation)
benchmark
## ctv_est_mg.L ctv_lcl_mg.L ctv_ucl_mg.L
## 1 0.009808029 0.001050889 0.05426475
SSD method can generate a lower and upper confidence interval.
# Plot data set
wqb_plot(data)
# Plot the results
fit <- wqb_ssd_fit(data_agg)
wqb_plot_ssd(data_agg, fit)
Summary Tables
wqb_summary_trophic_species(data_agg)
``$
## # \text{A} \text{tibble}: 5 \times 2
## $Trophic Group` `Number of Species`
## <fct> <int>
## 1 Algae 6
## 2 Amphibian 4
## 3 Fish 11
## 4 Invertebrate 12
## 5 Plant 8
``` r
wqb_summary_trophic_groups(data_agg)
## # A tibble: 4 × 2
## Consideration Result
## <chr> <chr>
## 1 Trophic group(s) Algae, Amphibian, Fish, Invertebrate, Plant
## 2 Salmonid(s) Oncorhynchus kisutch, Oncorhynchus mykiss, Oncorhynch…
## 3 Planktonic Invertebrate Artemia franciscana
## 4 B.C. species Cyprinus carpio, Lemna minor, Myriophyllum aquaticum,…
wqb_summary_af(data_agg)
``$
## # \text{A} \text{tibble}: 3 \times 3
## \text{Consideration} $Assessment Factor` Description
## <chr> <int> <chr>
## 1 Species variation factor 1 Accounts for uncertainty due…
## 2 Ecological assessment factor 1 Accounts for uncertainty whe…
## 3 B.C. species 1 Accounts for uncertainty of …
## Developer Instructions
See the [Developer
Instructions](https://bcgov.github.io/wqbench/articles/Developer-instructions.html)
on the package website for instructions on updating the reference data
for the database and updating the “Add Data” template
See the [README in the shinywqbench
repository](https://github.com/bcgov/shinywqbench?tab=readme-ov-file#shinywqbench)
for instructions for updating and deploying the [shiny
app](https://bcgov-env.shinyapps.io/shinywqbench/).
## Getting Help or Reporting an Issue
To report issues, bugs or enhancements, please file an
[issue](https://github.com/bcgov/wqbench/issues). Check out the
[support](https://github.com/bcgov/wqbench/blob/main/.github/SUPPORT.md)
for more info.
## Code of Conduct
Please note that the shinywqbench project is released with a
[Contributor Code of
Conduct](https://github.com/bcgov/wqbench/CODE_OF_CONDUCT.md). By
contributing to this project, you agree to abide by its terms.
## License
The code is released under the Apache License 2.0
> Copyright 2023 Province of British Columbia
>
> Licensed under the Apache License, Version 2.0 (the “License”); you
> may not use this file except in compliance with the License. You may
> obtain a copy of the License at
>
> <https://www.apache.org/licenses/LICENSE-2.0>
>
> Unless required by applicable law or agreed to in writing, software
> distributed under the License is distributed on an “AS IS” BASIS,
> WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
> implied. See the License for the specific language governing
> permissions and limitations under the License.
## Reference
1. Olker, J. H., Elonen, C. M., Pilli, A., Anderson, A., Kinziger, B.,
Erickson, S., Skopinski, M., Pomplun, A., LaLone, C. A., Russom, C.
L., & Hoff, D. (2022). The ECOTOXicology Knowledgebase: A Curated
Database of Ecologically Relevant Toxicity Tests to Support
Environmental Research and Risk Assessment. Environmental Toxicology
and Chemistry, 41(6):1520-1539. <https://doi.org/10.1002/etc.5324>