Package 'wqbench'

Description

Internal to allow for testing

Usage

combine_bc_species(bc_species, db_species)

Arguments

Value

A data frame

Examples

## Not run: 
data <- combine_bc_species(bc_species, db_species)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_bc_wqg(bc_wqg, db_chemicals)

Arguments

Value

A data frame

Examples

## Not run: 
data <- combine_bc_wqg(bc_wqg, db_chemicals)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_conc_conversions(concentration_std, db_concentration_unit_codes)

Arguments

Value

A data frame

Examples

## Not run: 
data <- combine_conc_conversions(
  concentration_std, db_concentration_unit_codes
)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_concentration_endpoints(endpoint_concentration_pick, db_endpoint_code)

Arguments

Value

A data frame

Examples

## Not run: 
data <- combine_concentration_endpoints(
  endpoint_concentration_pick, db_endpoint_code
)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_duration_conversions(duration_std, db_duration_unit_codes)

Arguments

Value

A data frame

Examples

## Not run: 
duration_unit_codes_std <- combine_duration_conversions(
  duration_std, db_duration_unit_codes
)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_lifestage(lifestage_codes, db_lifestage_codes)

Arguments

Value

A data frame

Examples

## Not run: 
lifestage_groups <- combine_lifestage(lifestage_codes, db_lifestage_codes)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_media(db_media_type)

Arguments

Value

A data frame

Examples

## Not run: 
media_type <- combine_media(db_media_type)

## End(Not run)

Description

Internal to allow for testing

Usage

combine_trophic_group(trophic_groups, db_species)

Arguments

Value

A data frame

Examples

## Not run: 
species_trophic_group <- combine_trophic_group(trophic_groups, db_species)

## End(Not run)

Description

Internal to wqb_join_data() to allow for testing.

Usage

join_data(
  db_results,
  db_tests,
  db_endpoint_codes,
  db_species,
  db_lifestage_codes,
  db_chemicals,
  db_duration_unit_codes,
  db_concentration_unit_codes,
  db_references,
  db_effect_codes,
  db_media_type_codes,
  db_meta_data_download
)

Arguments

Value

Invisible data frame

Examples

## Not run: 
data <- wqb_join_data(
  db_results, db_tests, db_endpoint_codes, db_species, db_lifestage_codes,
  db_chemicals, db_duration_unit_codes, db_concentration_unit_codes,
  db_references, db_effect_codes, db_media_type_codes, db_meta_data_download
)

## End(Not run)

Description

Internal to allow for testing

Usage

read_bc_species(bc_species_file_path, db_species)

Arguments

Value

A data frame

Examples

## Not run: 
data <- read_bc_species(bc_species_file_path, db_species)

## End(Not run)

Description

Internal to allow for testing

Usage

read_bc_wqg(db_chemicals)

Arguments

Value

A data frame

Examples

## Not run: 
chemicals_bc_wqg <- read_bc_wqg(db_chemicals)

## End(Not run)

Description

Internal to allow for testing

Usage

read_conc_conversions(concentration_std_file_path, db_concentration_unit_codes)

Arguments

Value

A data frame

Examples

## Not run: 
concentration_unit_codes_std <- read_conc_conversions(
  concentration_std_file_path, db_concentration_unit_codes
)

## End(Not run)

Description

Internal to allow for testing

Usage

read_concentration_endpoints(conc_endpoints_file_path, db_endpoint_code)

Arguments

Value

A data frame

Examples

## Not run: 
endpoint_concentration <- read_concentration_endpoints(
  conc_endpoints_file_path, db_endpoint_code
)

## End(Not run)

Description

Internal to allow for testing

Usage

read_duration_conversions(duration_std_file_path, db_duration_unit_codes)

Arguments

Value

A data frame

Examples

## Not run: 
duration_unit_codes_std <- read_duration_conversions(
  duration_std_file_path, db_duration_unit_codes
)

## End(Not run)

Description

Internal to allow for testing

Usage

read_lifestage(lifestage_file_path, db_lifestage_codes)

Arguments

Value

A data frame

Examples

## Not run: 
lifestage_groups <- read_lifestage(lifestage_file_path, db_lifestage_codes)

## End(Not run)

Description

Internal to allow for testing

Usage

read_trophic_group(trophic_groups_file_path, db_species)

Arguments

Value

A data frame

Examples

## Not run: 
species_trophic_group <- read_trophic_group(trophic_groups_file_path, db_species)

## End(Not run)

Description

Template for Adding your own Data

Usage

template

Format

A data.frame with columns:

name

Row description.

latin_name

The latin name of the test species.

endpoint

Toxicity endpoint.

effect

The effect that was being tested.

lifestage

The lifestage the species was during the test.

effect_conc_mg.L

Contaminant concentration that corresponds to the endpoint.

effect_conc_std_mg.L

The effect concentration standardized to include the acute to chronic ratio to extrapolate acute and/or effect concentrations to chronic and/or no-effect concentrations in mg/L.

trophic_group

Trophic group of species.

ecological_group

Identification of salmonids and planktonic invertebrates. If neither of these, listed as “other”.

species_present_in_bc

Species is present in British Columbia if entry = TRUE

Description

Read in a list of British Columbia species and add a column to the species table in the database to indicate if the species is present in British Columbia.

Usage

wqb_add_bc_species(database, quiet = FALSE)

Arguments

Details

The BC species data is contained in a csv file in the extdata folder of the package. This file can be edited by adding new species or removing species. Do not add new columns, rename columns or rename the file. The file must only contain a single column named latin_name.

The latin_name column must consist of the genus and species separated by a space. The latin_name column in the bc-species.csv file is matched to the latin_name column in the species table of the database. A new column species_present_in_bc is added to the species table that codes each species as TRUE if it matches a value in the bc-species.csv or FALSE if there is no match.

Value

Invisible data frame

Examples

## Not run: 
bc_species <- wqb_add_bc_species(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

bc_species <- wqb_add_bc_species(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Read in the British Columbia water quality guidelines (wqg) and add a column to the chemicals tables in the database to indicate if the chemical is present in the British Columbia water quality guidelines.

Usage

wqb_add_bc_wqg(database, quiet = FALSE)

Arguments

Details

The wqg data is stored in the BC Data Catalogue.

The CAS_number column in the bc wqg data is matched to the cas_number column in the chemicals table of the database. A new column present_in_bc_wqg is added to the chemicals table that codes each chemical as TRUE if the chemical is present in wqg or FALSE if the chemical is not present in wqg.

Value

Invisible data frame

Examples

## Not run: 
chem_bc_wqg <- wqb_add_bc_wqg(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

chem_bc_wqg <- wqb_add_bc_wqg(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Read in the concentration-conversion file and code units that can be converted and which ones will be removed. Three columns will be added to the concentration_unit_codes table in the database, indicate which units are being kept, the conversion factor, and the units it is being converted to. Currently units are converted to mg/L or equivalent.

Usage

wqb_add_conc_conversions(database, quiet = FALSE)

Arguments

Details

The list of units to be converted are contained in a csv file in the extdata folder of the package. The csv file can be edited by adding or removing rows. To add new rows get the code and description values from the concentration_unit_codes table in the database and paste them into the csv file.

Do not add new columns, rename columns or rename the file. The file must only contain the columns: code, description, conc_conversion_flag, conc_conversion_value_multiplier and conc_conversion_unit.

The conc_conversion_flag column indicates which units are being converted and which are being removed because they can not be converted or are not in the aquatic portion of the data.The conc_conversion_value_multiplier column contains the value need to convert the unit into the unit listed in the conc_conversion_unit column.

The code values in the concentration-conversion file are matched to the code values in the concentration_unit_codes table in the database.

Value

Invisible data frame

Examples

## Not run: 
concentration_unit_code_standardization <- wqb_add_conc_conversions(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

concentration_unit_code_standardization <- wqb_add_conc_conversions(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Read in the concentration endpoints that have been selected to keep in the final data set. Add a column to the endpoint_codes table in the database to mark the corresponding endpoints.

Usage

wqb_add_concentration_endpoints(database, quiet = FALSE)

Arguments

Details

The list of concentration endpoints is contained in a csv file in the extdata folder of the package. The csv file can be edited by adding or removing rows. To add new rows get the code and description values from the endpoint_codes table in the database and paste them into the csv file.

Do not add new columns, rename columns or rename the file. The file must only contain the code and description column.

The code values in the endpoint-concentration file are matched to the code values in the endpoint_code table in the database. A new column concentration_flag is added to the endpoint_code table that codes each endpoint as TRUE if the endpoint is present in endpoint-concentration.csv file.

Value

Invisible data frame

Examples

## Not run: 
wqb_add_concentration_endpoints(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

wqb_add_concentration_endpoints(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Read in the duration-conversion file and code unit values that can be converted and which ones will be removed. Two columns will be added to the duration_unit_codes table in the database to indicate which units are being kept and the conversion factor. Currently duration units are converted to hours.

Usage

wqb_add_duration_conversions(database, quiet = FALSE)

Arguments

Details

The list of units to be converted are contained in a csv file in the extdata folder of the package. The csv file can be edited by adding or removing rows. To add new rows get the code and description values from the duration_unit_codes table in the database and paste them into the csv file.

Do not add new columns, rename columns or rename the file. The file must only contain the columns: code, description, duration_units_to_keep and duration_value_multiplier_to_hours.

The code values in the duration-conversion file are matched to the code values in the duration_unit_codes table in the database.

The duration_units_to_keep column indicates which units are being converted and which are being removed because they can not be converted or are not in the aquatic portion of the data. The duration_value_multiplier_to_hours column contains the value need to convert the unit into hours.

Value

Invisible data frame

Examples

## Not run: 
duration_unit_code_standardization <- wqb_add_duration_conversions(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

duration_unit_code_standardization <- wqb_add_duration_conversions(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Read in the life stage simple groups and add a column in the lifestage_code table in the database to mark the corresponding values.

Usage

wqb_add_lifestage(database, quiet = FALSE)

Arguments

Details

Only life stages related to fish or amphibians have been coded. The purpose of the coding is to be able to simplify the many life stages into three categories: els (early life stage), juveniles and adults. Not all life stages have been coded into these three groups.

The life stage data is contained in a csv file in the extdata folder of the package. The csv file can be edited by adding or removing rows. To add new rows get the code and description values from the lifestage_code table in the dataset and paste them into the csv file and then add the value to the simple_lifestage column.

Do not add new columns, rename columns or rename the file. The file must only contain the code, description_lifestage and simple_lifestage column.

The code values in the lifestage-codes.csv file are matched to the code values in the lifestage_code table in the database. Any codes that match are coded in a new column called simple_lifestage.

Value

Invisible data frame

Examples

## Not run: 
lifestage_codes <- wqb_add_lifestage(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

lifestage_codes <- wqb_add_lifestage(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Code the media type information into three categories: salt water, fresh water and not reported.

Usage

wqb_add_media(database, quiet = FALSE)

Arguments

Details

Read in the media_type_codes table from the database and code the 24 groups into three categories: salt water, fresh water or not reported. The new categories are added to a column in the table called media_type_group.

Value

Invisible data frame

Examples

## Not run: 
media_info <- wqb_add_media(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

media_info <- wqb_add_media(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Read in the trophic and ecological groups and and add a column to the species table in the database that lists the groups for each species.

Usage

wqb_add_trophic_group(database, quiet = FALSE)

Arguments

Details

The trophic group data is contained in a csv file in the extdata folder of the package. This file can be edited by adding or removing groups and classes. Do not add new columns, rename columns or rename the file.

The trophic groups file must contain the columns: class, order, trophic_group, and ecological_group. The class and order columns are matched to the class and tax_order columns in the species table of the database and then adds the trophic_group and ecological_group columns to the species table.

Value

Invisible data frame

Examples

## Not run: 
trophic_group <- wqb_add_trophic_group(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

trophic_group <- wqb_add_trophic_group(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Determines the species variation factor, ecological assessment factor and B.C. species factor.

Usage

wqb_af(data)

Arguments

Details

This is a wrapper function that calls wqb_af_bc_species(), wqb_af_ecological() and wqb_af_variation().

Value

A data frame

Examples

## Not run: 
data <- wqb_af(data)

## End(Not run)

Description

Determines an assessment factor based on the number of BC species present.

Usage

wqb_af_bc_species(data)

Arguments

Details

Check the resource document for how the assessment factor was calculated.

Value

A data frame

Examples

## Not run: 
data <- wqb_af_bc_species(data)

## End(Not run)

Description

Determines the assessment factor based on the presence of certain ecological groups.

Usage

wqb_af_ecological(data)

Arguments

Details

Check the resource document for how the assessment factor was calculated.

Value

A data frame

Examples

## Not run: 
data <- wqb_af_ecological(data)

## End(Not run)

Description

Determine the assessment factor based on the number of trophic groups and species.

Usage

wqb_af_variation(data)

Arguments

Details

Check the resource document for how the assessment factor was calculated.

Value

A data frame

Examples

## Not run: 
data <- wqb_af_variation(data)

## End(Not run)

Description

Aggregate data to select the most sensitive value for each species. The priority of effect level depends on the benchmark method that will be used.

Usage

wqb_aggregate(data)

Arguments

Details

Check the resource document for the rules used to aggregate the data down to a single value per species. This is Step 5.

Value

A data frame

Examples

## Not run: 
data <- wqb_aggregate(data)

## End(Not run)

Description

Determine if a species sensitivity distribution (SSD) or deterministic method will be used to determine the aquatic life water quality benchmark value for the data. A column called method will be added to the data indicating which method will be used.

Usage

wqb_benchmark_method(data)

Arguments

Details

Check the resource document for the rules used to determine which benchmark method will be used. This is Step 4.

Value

A data frame

Examples

## Not run: 
data <- wqb_benchmark_method(data)
data <- wqb_benchmark_method(aggregated_data)

## End(Not run)

Description

Checks the uploaded data for the basic requirements to ensure the data matches the downloaded Ecotox data.

Usage

wqb_check_add_data(data, template)

Arguments

Details

The values for the endpoint, trophic_group, and ecological_group columns are checked against the data tables used to build the database. To update the allowed values the corresponding csv file needs to be updated.

Value

A data frame

Examples

## Not run: 
data <- wqb_check_add_data(data, template)

## End(Not run)

Description

Classify each test as either acute or chronic in the duration_class column.

Usage

wqb_classify_duration(data, quiet = FALSE)

Arguments

Details

Check the resource document for the rules used to determine the classification for each trophic group. This is Step 2.

Value

A data frame

Examples

## Not run: 
classified_data <- wqb_classify_duration(compiled_data)

## End(Not run)

Description

Join database tables together and start filtering and cleaning data.

Usage

wqb_clean_data(data, quiet = FALSE)

Arguments

Details

Check the resource document more details on the data added, filter conditions and cleaning steps. This is part of Step 1.

Value

Invisible data frame

Examples

## Not run: 
data <- wqb_clean_data(data)

## End(Not run)

Description

This function downloads the data, creates and adds all the data to the database, compiles, standardizes, and classifies the data. The output of this function is fed into the app.

Usage

wqb_create_data_set(
  file_path = "~/Ecotoxicology/ecotox",
  version = 1,
  folder_path = "~/Ecotoxicology/ecotox_db/",
  quiet = FALSE,
  ask = TRUE,
  save_rds = TRUE
)

Arguments

Value

A data frame

Examples

## Not run: 
wqb_create_data_set(
  file_path = "~/Ecotoxicology/ecotox",
  version = 1,
  folder_path = "~/Ecotoxicology/ecotox_db/"
)

## End(Not run)

Description

Create a SQLite database from the US EPA ECOTOX downloaded files.

Usage

wqb_create_epa_ecotox(folder_path = ".", data_path, quiet = FALSE, ask = TRUE)

Arguments

Details

This functions reads in the text files in the folder and writes them to the database.

This function will overwrite a database if already present.

Value

Invisible string of the file path of the database.

Examples

## Not run: 
wqb_create_epa_ecotox(data_path = "ecotox_ascii_12_15_2022")

## End(Not run)

Description

Download the ECOTOX data files from their FTP website. The default is to download the most recent version of the data.

Usage

wqb_download_epa_ecotox(
  file_path = ".",
  version = 1,
  ask = TRUE,
  quiet = FALSE
)

Arguments

Details

You have the option of downloading older version of the data but only up to the four most recent version. The most recent version is set as 1 and the oldest version is version 4.

The downloaded folder will contain various files that are needed to build the database.

You must have a working internet connection to run this function successfully.

Value

Invisible string of the file path the downloaded files were saved.

References

US EPA ECOTOX website: https://cfpub.epa.gov/ecotox/

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

Examples

## Not run: 
wqb_download_epa_ecotox()

wqb_download_epa_ecotox("data_download")

# pull previous version of the database
wqb_download_epa_ecotox("data_download", version = 2)

## End(Not run)

Description

Filter to a Single Chemical

Usage

wqb_filter_chemical(data, cas_num)

Arguments

Value

A data frame

Examples

## Not run: 
data <- wqb_filter_chemical(data, "129909906")
data <- wqb_filter_chemical(data, "1000984359")

## End(Not run)

Description

Determine the critical toxicity value for the species. The function will apply the method listed in the method column.

Usage

wqb_generate_ctv(data, dists = ssdtools::ssd_dists_bcanz())

Arguments

Details

The ctv_est_mg.L is the estimate of the critical toxicity value for the species. The ctv_lcl_mg.L is the lower confidence limit. The ctv_ucl_mg.L is the upper confidence limit.

The Deterministic method will always produce missing values in the ctv_lcl_mg.L and ctv_ucl_mg.L columns.

Value

A data frame

Examples

## Not run: 
ctv <- wqb_generate_ctv(data)

## End(Not run)

Description

Join database tables together and start filtering and cleaning data.

Usage

wqb_join_data(database, quiet = FALSE)

Arguments

Details

Check the resource document more details on the data added, filter conditions and cleaning steps. This is part of Step 1.

Value

Invisible data frame

Examples

## Not run: 
data_compiled <- wqb_join_data(
  database = "ecotox_ascii_09_15_2022.sqlite"
)

data_compiled <- wqb_join_data(
  database = "ecotox_db/ecotox_ascii_09_15_2022.sqlite"
)

## End(Not run)

Description

Use the deterministic method to generate the critical toxicity value for the data set.

Usage

wqb_method_det(data)

Arguments

Details

Check the resource document for more details . This is Step 1.

Value

A data frame

Examples

## Not run: 
bench_iodine <- wqb_method_det(data)

## End(Not run)

Description

Use a species sensitivity distribution to calculate the critical toxicity value for the data set. The critical toxicity value is the hazardous concentration for 5% of species (HC5) when the SSD method is used.

Usage

wqb_method_ssd(data, fit, nboot = 1000)

Arguments

Details

A wrapper on the ssdtools package function ssdtools::ssd_hc_bcanz() that only returns the HC5 concentration.

Value

A data frame

Examples

## Not run: 
hc5 <- wqb_method_ssd(data, fit)

## End(Not run)

Description

Plot the standardized data to see the concentrations per species for each endpoint.

Usage

wqb_plot(data)

Arguments

Examples

## Not run: 
wqb_plot(data)

## End(Not run)

Description

Plot deterministic results to see the standardized data, critical toxicity value and aquatic life benchmark.

Usage

wqb_plot_det(data)

Arguments

Examples

## Not run: 
wqb_plot_det(data)

## End(Not run)

Description

Plot results to see the species sensitivity distribution. The dashed line shows the HC5 value.

Usage

wqb_plot_ssd(data, fit)

Arguments

Details

This is a wrapper on ssdtools::predict() and ssdtools::ssd_plot().

Examples

## Not run: 
wqb_plot_ssd(data, fit)

## End(Not run)

Description

Wrapper to ssdtools::ssd_fit_bcanz(). The sp_aggre_conc_mg.L values are the concentrations used.

Usage

wqb_ssd_fit(data, dists = ssdtools::ssd_dists_bcanz())

Arguments

Value

A data frame

Examples

## Not run: 
fit <- wqb_ssd_fit(data)

## End(Not run)

Description

Wrapper to the ssdtools::ssd_hc_bcanz() function and selects only the row which is 5%.

Usage

wqb_ssd_hc5(fit, nboot = 1000)

Arguments

Details

The number of bootstrap samples is set to 1000 so the estimates are quick to generate. Check out ssdtools::ssd_hc_bcanz() for more details.

Value

A data frame

Examples

## Not run: 
hc5 <- wqb_ssd_hc5(fit)

## End(Not run)

Description

Determine and apply factor needed to standardize the endpoints.

Usage

wqb_standardize_effect(data, quiet = FALSE)

Arguments

Details

Check the resource document for details the rules used to determine standardized the endpoints. This is Step 3.

Value

A data frame

Examples

## Not run: 
standardized_effect_data <- wqb_standardize_effect(data)
standardized_effect_data <- wqb_standardize_effect(classified_data)

## End(Not run)

Description

Create summary table of the species variation factor, ecological assessment factor and B.C. species factor.

Usage

wqb_summary_af(data)

Arguments

Value

A data frame

Examples

## Not run: 
summary_af <- wqb_summary_af(data)

## End(Not run)

Description

Summary Table of Assessment Factors Information

Usage

wqb_summary_trophic_groups(data)

Arguments

Value

A data frame

Examples

## Not run: 
summary_af <- wqb_summary_trophic_groups(data)

## End(Not run)

Description

Summary Table of Number of Species per Trophic Group

Usage

wqb_summary_trophic_species(data)

Arguments

Value

A data frame.

Examples

## Not run: 
summary_trophic <- wqb_summary_trophic_species(data)

## End(Not run)