Title: Species Sensitivity Distribution Data
Version: 1.0.0
Description: Reference data sets of species sensitivities to compare the results of fitting species sensitivity distributions using software such as 'ssdtools' and 'Burrlioz'. It consists of 17 primary data sets from four different Australian and Canadian organizations as well as five datasets from anonymous sources. It also includes a data set of the results of fitting various distributions using different software.
License: Apache License (== 2.0)
Depends: R (≥ 3.5)
Imports: chk, dplyr, Rdpack, utils
Suggests: covr, testthat (≥ 3.0.0)
RdMacros: Rdpack
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
NeedsCompilation: no
Packaged: 2021-11-04 02:39:29 UTC; rfisher
Author: Rebecca Fisher [aut, cre], Joe Thorley ORCID iD [aut], Carl Schwarz [ctb], David Fox [ctb]
Maintainer: Rebecca Fisher <R.Fisher@aims.gov.au>
Repository: CRAN
Date/Publication: 2021-11-05 08:10:02 UTC

ssddata: Species Sensitivity Distribution Data

Description

Reference data sets of species sensitivities to compare the results of fitting species sensitivity distributions using software such as 'ssdtools' and 'Burrlioz'. It consists of 17 primary data sets from four different Australian and Canadian organizations as well as five datasets from anonymous sources. It also includes a data set of the results of fitting various distributions using different software.

Author(s)

Maintainer: Rebecca Fisher R.Fisher@aims.gov.au

Authors:

Other contributors:

Species Sensitivity Data for aluminium_marine

Description

Species Sensitivity Data provided by the Australian Institute of Marine Science for aluminium in marine water.

Usage

aims_aluminium_marine

Format

An object of class tbl_df (inherits from tbl, data.frame) with 20 rows and 9 columns.

Details

These data were sourced from: van Dam JW, Trenfield MA, Streten C, Harford AJ, Parry D, van Dam RA (2018). “Water quality guideline values for aluminium, gallium and molybdenum in marine environments.” Environmental Science and Pollution Research, 25(26), 26592–26602. ISSN 16147499, https://link.springer.com/article/10.1007/s11356-018-2702-y.

The columns are as follows:

Common

The species common name (chr).

Conc

The chemical concentration in micrograms per Litre (dbl).

Domain

Tropical, temperate or other filter (chr).

Life_stage

Life stage of the test organism (chr).

Phylum

The Phylum name (chr).

Source

The endpoint primary data source (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Examples


print(aims_aluminium_marine, n=Inf)

Species Sensitivity Data provided by AIMS

Description

Species Sensitivity Data provided by the Australian Institute of Marine Science.

Usage

aims_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 40 rows and 11 columns.

Details

Additional information may be available from the primary source for each chemical:

aluminium_marine

van Dam JW, Trenfield MA, Streten C, Harford AJ, Parry D, van Dam RA (2018). “Water quality guideline values for aluminium, gallium and molybdenum in marine environments.” Environmental Science and Pollution Research, 25(26), 26592–26602. ISSN 16147499, https://link.springer.com/article/10.1007/s11356-018-2702-y.

gallium_marine

van Dam JW, Trenfield MA, Streten C, Harford AJ, Parry D, van Dam RA (2018). “Water quality guideline values for aluminium, gallium and molybdenum in marine environments.” Environmental Science and Pollution Research, 25(26), 26592–26602. ISSN 16147499, https://link.springer.com/article/10.1007/s11356-018-2702-y.

molybdenum_marine

van Dam JW, Trenfield MA, Streten C, Harford AJ, Parry D, van Dam RA (2018). “Water quality guideline values for aluminium, gallium and molybdenum in marine environments.” Environmental Science and Pollution Research, 25(26), 26592–26602. ISSN 16147499, https://link.springer.com/article/10.1007/s11356-018-2702-y.

The columns are as follows, noting that all information may not be available for all chemicals:

Chemical

The chemical name (chr).

Common

The species common name (chr).

Conc

The chemical concentration in micrograms per Litre (dbl).

Domain

Tropical, temperate or other filter (chr).

Life_stage

Life stage of the test organism (chr).

Medium

The medium - fresh or marine water (chr).

Phylum

The Phylum name (chr).

Source

The endpoint primary data source (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Examples


head(aims_data)

Species Sensitivity Data for gallium_marine

Description

Species Sensitivity Data provided by the Australian Institute of Marine Science for gallium in marine water.

Usage

aims_gallium_marine

Format

An object of class tbl_df (inherits from tbl, data.frame) with 6 rows and 9 columns.

Details

These data were sourced from: van Dam JW, Trenfield MA, Streten C, Harford AJ, Parry D, van Dam RA (2018). “Water quality guideline values for aluminium, gallium and molybdenum in marine environments.” Environmental Science and Pollution Research, 25(26), 26592–26602. ISSN 16147499, https://link.springer.com/article/10.1007/s11356-018-2702-y.

The columns are as follows:

Common

The species common name (chr).

Conc

The chemical concentration in micrograms per Litre (dbl).

Domain

Tropical, temperate or other filter (chr).

Life_stage

Life stage of the test organism (chr).

Phylum

The Phylum name (chr).

Source

The endpoint primary data source (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Examples


print(aims_gallium_marine, n=Inf)

Species Sensitivity Data for molybdenum_marine

Description

Species Sensitivity Data provided by the Australian Institute of Marine Science for molybdenum in marine water.

Usage

aims_molybdenum_marine

Format

An object of class tbl_df (inherits from tbl, data.frame) with 14 rows and 9 columns.

Details

These data were sourced from: van Dam JW, Trenfield MA, Streten C, Harford AJ, Parry D, van Dam RA (2018). “Water quality guideline values for aluminium, gallium and molybdenum in marine environments.” Environmental Science and Pollution Research, 25(26), 26592–26602. ISSN 16147499, https://link.springer.com/article/10.1007/s11356-018-2702-y.

The columns are as follows:

Common

The species common name (chr).

Conc

The chemical concentration in micrograms per Litre (dbl).

Domain

Tropical, temperate or other filter (chr).

Life_stage

Life stage of the test organism (chr).

Phylum

The Phylum name (chr).

Source

The endpoint primary data source (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Examples


print(aims_molybdenum_marine, n=Inf)

Anonymous Species Sensitivity Data anon_a

Description

Species Sensitivity Data from anonymous sources.

Usage

anon_a

Format

An object of class tbl_df (inherits from tbl, data.frame) with 18 rows and 2 columns.

Details

This example data were sourced from:

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

The columns are as follows:

Chemical

The chemical name (chr).

Conc

The chemical concentration (dbl).

Examples


print(anon_a, n=Inf)

Anonymous Species Sensitivity Data anon_b

Description

Species Sensitivity Data from anonymous sources.

Usage

anon_b

Format

An object of class tbl_df (inherits from tbl, data.frame) with 10 rows and 2 columns.

Details

This example data were sourced from:

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

The columns are as follows:

Chemical

The chemical name (chr).

Conc

The chemical concentration (dbl).

Examples


print(anon_b, n=Inf)

Anonymous Species Sensitivity Data anon_c

Description

Species Sensitivity Data from anonymous sources.

Usage

anon_c

Format

An object of class tbl_df (inherits from tbl, data.frame) with 16 rows and 2 columns.

Details

This example data were sourced from:

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

The columns are as follows:

Chemical

The chemical name (chr).

Conc

The chemical concentration (dbl).

Examples


print(anon_c, n=Inf)

Anonymous Species Sensitivity Data anon_d

Description

Species Sensitivity Data from anonymous sources.

Usage

anon_d

Format

An object of class tbl_df (inherits from tbl, data.frame) with 12 rows and 2 columns.

Details

This example data were sourced from:

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

The columns are as follows:

Chemical

The chemical name (chr).

Conc

The chemical concentration (dbl).

Examples


print(anon_d, n=Inf)

Anonymous Species Sensitivity Data

Description

Species Sensitivity Data from Anonymous sources

Usage

anon_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 73 rows and 2 columns.

Details

Additional information on each of the chemicals may be available from their primary source, at:

a

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

c

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

d

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

b

DAWE (2021). “Unpublished data, anonymous/confidential information supplied by Department of Agriculture Water and the Environment, Australia.” April 20.

e

Fox DR, van Dam RA, Fisher R, Batley GE, Tillmanns AR, Thorley J, Schwarz CJ, Spry DJ, McTavish K (2021). “Recent developments in Species Sensitivity Distribution Modeling.” Environmental Toxicology and Chemistry, 40(2), 293–308. doi: 10.1002/etc.4925, https://setac.onlinelibrary.wiley.com/doi/abs/10.1002/etc.4925.

Chemical

The chemical (chr), in this case an anonymous unique identifier.

Conc

The chemical concentration (dbl).

Examples


head(anon_data)

Anonymous Species Sensitivity Data anon_e

Description

Species Sensitivity Data from anonymous sources.

Usage

anon_e

Format

An object of class tbl_df (inherits from tbl, data.frame) with 17 rows and 2 columns.

Details

This example data were sourced from:

Fox DR, van Dam RA, Fisher R, Batley GE, Tillmanns AR, Thorley J, Schwarz CJ, Spry DJ, McTavish K (2021). “Recent developments in Species Sensitivity Distribution Modeling.” Environmental Toxicology and Chemistry, 40(2), 293–308. doi: 10.1002/etc.4925, https://setac.onlinelibrary.wiley.com/doi/abs/10.1002/etc.4925.

The columns are as follows:

Chemical

The chemical name (chr).

Conc

The chemical concentration (dbl).

Examples


print(anon_e, n=Inf)

ANZG Species Sensitivity Data

Description

ANZG Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia.

Usage

anzg_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 21 rows and 12 columns.

Details

These data are licensed under CC BY 4.0 (summary of terms provided here: https://creativecommons.org/licenses/by/4.0/).

Additional information is available from the Water Quality website at https://www.waterquality.gov.au/.

Additional information may be available from the primary source for each chemical:

metolachlor_fresh

ANZG (2020). “Toxicant default guideline values for aquatic ecosystem protection: Metolachlor in freshwater.” Australian and New Zealand Governments and Australian State and Territory Governments, Canberra, Australia. https://www.waterquality.gov.au/anz-guidelines/guideline-values/default/water-quality-toxicants/toxicants/metolachlor-fresh-2020.

The columns are as follows, noting that some information may not be available for all chemicals:

Chemical

The chemical name (chr).

Conc

The chemical concentration in micrograms per Litre (dbl).

Duration

The duration of the test in days (dbl).

Genus

The Genus name (chr).

Group

The taxonomic group (chr).

Life_stage

Life stage of the test organism (chr).

Medium

The medium - fresh or marine water (chr).

Notes

Other notes (chr).

Phylum

The Phylum name (chr).

Species

The species binomial name (chr).

Test_endpoint

The test endpoint measure (chr).

Toxicity_measure

The toxicity measure used (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

Examples


head(anzg_data)

Species Sensitivity Data for metolachlor_fresh

Description

ANZG Species Sensitivity Data provided by the Department of Agriculture Water and the Environment, Australia for metolachlor in fresh water.

Usage

anzg_metolachlor_fresh

Format

An object of class tbl_df (inherits from tbl, data.frame) with 21 rows and 10 columns.

Details

These data are licensed under CC BY 4.0 (summary of terms provided here: https://creativecommons.org/licenses/by/4.0/) Additional information is available from the Water Quality website at https://www.waterquality.gov.au/

Please cite these data as: ANZG (2020). “Toxicant default guideline values for aquatic ecosystem protection: Metolachlor in freshwater.” Australian and New Zealand Governments and Australian State and Territory Governments, Canberra, Australia. https://www.waterquality.gov.au/anz-guidelines/guideline-values/default/water-quality-toxicants/toxicants/metolachlor-fresh-2020.

The columns are as follows:

Conc

The chemical concentration in micrograms per Litre (dbl).

Duration

The duration of the test in days (dbl).

Genus

The Genus name (chr).

Group

The taxonomic group (chr).

Life_stage

Life stage of the test organism (chr).

Notes

Other notes (chr).

Phylum

The Phylum name (chr).

Species

The species binomial name (chr).

Test_endpoint

The test endpoint measure (chr).

Toxicity_measure

The toxicity measure used (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

Examples


print(anzg_metolachlor_fresh, n=Inf)

CCME Species Sensitivity Data for ccme_boron

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for boron.

Usage

ccme_boron

Format

An object of class tbl_df (inherits from tbl, data.frame) with 28 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/16.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_boron, n=Inf)

CCME Species Sensitivity Data for ccme_cadmium

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for cadmium.

Usage

ccme_cadmium

Format

An object of class tbl_df (inherits from tbl, data.frame) with 36 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/20.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_cadmium, n=Inf)

CCME Species Sensitivity Data for ccme_chloride

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for chloride.

Usage

ccme_chloride

Format

An object of class tbl_df (inherits from tbl, data.frame) with 28 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/28.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_chloride, n=Inf)

CCME Species Sensitivity Data

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment. The taxonomic groups are Amphibian, Fish, Invertebrate and Plant. Plants includes freshwater algae.

Usage

ccme_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 144 rows and 5 columns.

Details

Additional information on each of the chemicals is available from the CCME website.

boron

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/16.

cadmium

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/20.

chloride

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/28.

endosulfan

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/93.

glyphosate

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/102.

uranium

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/225.

silver

(2021). “CCME.” May 06, https://ccme.ca/en/chemical/198.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


head(ccme_data)

CCME Species Sensitivity Data for ccme_endosulfan

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for endosulfan.

Usage

ccme_endosulfan

Format

An object of class tbl_df (inherits from tbl, data.frame) with 12 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/93.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_endosulfan, n=Inf)

CCME Species Sensitivity Data for ccme_glyphosate

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for glyphosate.

Usage

ccme_glyphosate

Format

An object of class tbl_df (inherits from tbl, data.frame) with 18 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/102.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_glyphosate, n=Inf)

CCME Species Sensitivity Data for ccme_silver

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for silver.

Usage

ccme_silver

Format

An object of class tbl_df (inherits from tbl, data.frame) with 9 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/198.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_silver, n=Inf)

CCME Species Sensitivity Data for ccme_uranium

Description

Species Sensitivity Data from the Canadian Council of Ministers of the Environment for uranium.

Usage

ccme_uranium

Format

An object of class tbl_df (inherits from tbl, data.frame) with 13 rows and 5 columns.

Details

Additional information is available from (2021). “CCME.” May 06, https://ccme.ca/en/chemical/225.

The columns are as follows:

Chemical

The chemical (chr).

Species

The species binomial name (chr).

Conc

The chemical concentration (dbl).

Group

The taxonomic group (fct).

Units

The units of Conc (chr).

Examples


print(ccme_uranium, n=Inf)

Species Sensitivity Data for chlorine_marine

Description

Species Sensitivity Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia for chlorine in marine water.

Usage

csiro_chlorine_marine

Format

An object of class tbl_df (inherits from tbl, data.frame) with 30 rows and 2 columns.

Details

These data were sourced from: Batley GE, Simpson SL (2020). “Short-Term Guideline Values for Chlorine in Marine Waters.” Environmental Toxicology and Chemistry. ISSN 15528618, https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.4661.

The columns are as follows:

Conc

The chemical concentration (dbl).

Group

Taxonomic grouping information (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

All concentration data are ug/L unless otherwise stated.

Examples


print(csiro_chlorine_marine, n=Inf)

Species Sensitivity Data for cobalt_marine

Description

Species Sensitivity Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia for cobalt in marine water.

Usage

csiro_cobalt_marine

Format

An object of class tbl_df (inherits from tbl, data.frame) with 14 rows and 7 columns.

Details

These data were sourced from: Batley G (2021). “Unpublished data, anonymous/confidential information.” March 23.

The columns are as follows:

Conc

The chemical concentration (dbl).

Duration

Test duration (chr).

Group

Taxonomic grouping information (chr).

Life_stage

Life stage of the test organism (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

All concentration data are ug/L unless otherwise stated.

Examples


print(csiro_cobalt_marine, n=Inf)

Species Sensitivity Data provided by CSIRO

Description

Species Sensitivity Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia.

Usage

csiro_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 91 rows and 11 columns.

Details

Additional information may be available from the primary source for each chemical:

chlorine_marine

Batley GE, Simpson SL (2020). “Short-Term Guideline Values for Chlorine in Marine Waters.” Environmental Toxicology and Chemistry. ISSN 15528618, https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.4661.

nickel_fresh

Stauber J, Golding L, Peters A, Merrington G, Adams M, Binet M, Batley G, Gissi F, Mcknight K, Garman E, Middleton E, Gadd J, Schlekat C (2021). “Environmental Toxicology Application of Bioavailability Models to Derive Chronic Guideline Values for Nickel in Freshwaters of Australia and New Zealand.” Environmental Toxicology and Chemistry, 40(1), 100–112. doi: 10.1002/etc.4885, https://setac.onlinelibrary.wiley.com/doi/abs/10.1002/etc.4885.

cobalt_marine

Batley G (2021). “Unpublished data, anonymous/confidential information.” March 23.

lead_marine

Batley G (2021). “Unpublished data, anonymous/confidential information.” March 23.

The columns are as follows, noting that not all information are available for all chemicals:

Chemical

The chemical name (chr).

Conc

The chemical concentration (dbl).

Domain

Tropical, temperate or other filter (chr).

Duration

Test duration (chr).

Group

Taxonomic grouping information (chr).

Life_stage

Life stage of the test organism (chr).

Medium

The medium - fresh or marine water (chr).

Notes

Other notes (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

All concentration data are ug/L unless otherwise stated.

Examples


head(csiro_data)

Species Sensitivity Data for lead_marine

Description

Species Sensitivity Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia for lead in marine water.

Usage

csiro_lead_marine

Format

An object of class tbl_df (inherits from tbl, data.frame) with 16 rows and 7 columns.

Details

These data were sourced from: Batley G (2021). “Unpublished data, anonymous/confidential information.” March 23.

The columns are as follows:

Conc

The chemical concentration (dbl).

Duration

Test duration (chr).

Group

Taxonomic grouping information (chr).

Life_stage

Life stage of the test organism (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Toxicity_measure

Type of toxicity measure used (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

All concentration data are ug/L unless otherwise stated.

Examples


print(csiro_lead_marine, n=Inf)

Species Sensitivity Data for nickel_fresh

Description

Species Sensitivity Data provided by the Commonwealth Scientific and Industrial Research Organisation of Australia for nickel in fresh water.

Usage

csiro_nickel_fresh

Format

An object of class tbl_df (inherits from tbl, data.frame) with 31 rows and 6 columns.

Details

These data were sourced from: Stauber J, Golding L, Peters A, Merrington G, Adams M, Binet M, Batley G, Gissi F, Mcknight K, Garman E, Middleton E, Gadd J, Schlekat C (2021). “Environmental Toxicology Application of Bioavailability Models to Derive Chronic Guideline Values for Nickel in Freshwaters of Australia and New Zealand.” Environmental Toxicology and Chemistry, 40(1), 100–112. doi: 10.1002/etc.4885, https://setac.onlinelibrary.wiley.com/doi/abs/10.1002/etc.4885.

The columns are as follows:

Conc

The chemical concentration (dbl).

Domain

Tropical, temperate or other filter (chr).

Group

Taxonomic grouping information (chr).

Notes

Other notes (chr).

Species

The species names name (chr).

Test_endpoint

Endpoint statistic, EC10, NEC etc (chr).

Where toxicity measure is not a chronic NEC, EC10 or NOEC value, concentration has been converted using the appropriate default ratio, as follows: 10 from acute EC50/LC50 to chronic EC10; 5 from chronic EC50 to EC10; 2.5 from LOEC to EC10. Please see the primary reference material for more information.

All concentration data are ug/L unless otherwise stated.

Examples


print(csiro_nickel_fresh, n=Inf)

Get SSD dataset

Description

Retrieves a specific SSD dataset, filtering and groups by species and applies a geometric mean in the case of duplicate records.

Usage

get_ssddata(
  dataset_name,
  filter_val = NULL,
  use_gmmean = TRUE,
  spp_vec = c("Species", "Genus"),
  conc = "Conc"
)

Arguments

dataset_name

The name (chr) of the desired dataset in ssddata.

filter_val

A character string, indicating the filter to be applied (value) (colname) and which column it applies to, separated by "_". Must be in the form colname_value.

use_gmmean

Logical indicating if a geometric mean should be applied.

spp_vec

The group_by columns to use for grouping data and applying a geometric mean.

conc

The name of the concentration (x data) column.

Value

The data.frame for dataset_name with any applied groupings and summary.

Examples

get_ssddata("ccme_boron")

Extract package dataset

Description

Retrieves a dataset from a loaded package by name

Usage

getdata(...)

Arguments

...

Arguments passed utils::data

Value

An object of class data frame.

Calculate geometric mean

Description

Calculates the geometric mean of a numeric vector

Usage

gm_mean(x, na.rm = FALSE, zero.propagate = TRUE)

Arguments

x

A numeric vector

na.rm

A flag specifying whether to remove missing values.

zero.propagate

A flag specifying whether to propagate zero values.

Value

A number of the geometric mean.

Examples

gm_mean(c(3, 66, 22, 17))

Species Sensitivity Distribution Fit Data

Description

Species Sensitivity Distribution Fit Data

Usage

ssd_fits

Format

A tibble with 12 columns.

Dataset

The name of the dataset in the ssddata package (chr).

Filter

Any filtering applied to the data (chr).

Software

The name of the software (chr).

Version

The version of the software (chr).

Distribution

The name of the distribution (chr)

PC

The percent of the community protected (int).

Estimate

The estimated concentration (dbl).

SE

The standard error of the estimated concentration (dbl).

Lower

The lower 95% CI of the estimated concentration (dbl).

Upper

The upper 95% CI of the estimated concentration (dbl).

Source

The source of the fit (chr).

Notes

Additional information on the fitting process (chr).

Examples

head(ssd_fits)