{ECOTOXr} Harness information from the US EPA ECOTOXicology Knowledgebase R build status version cranlogs

Overview

ECOTOXr logo {ECOTOXr} can be used to explore and analyse data from the US EPA ECOTOX database. More specifically you can:

Why use {ECOTOXr}?

The {ECOTOXr} package allows you to search and extract data from the ECOTOXicological Knowledgebase and import it directly into R. This will allow you to formalize and document the search- and extract-procedures in R code. This makes it easier to share and reproduce such procedures and its results. Moreover, you can directly apply any statistical analysis offered in R.

Installation

Get CRAN version

install.packages("ECOTOXr")

Get development version on github

devtools::install_github('pepijn-devries/ECOTOXr')

Usage

Preparing the database

Although {ECOTOXr} has experimental features to search the on-line database. The package will reach its full potential when you build a copy of the database on your local machine.

Download and build a local copy of the latest ASCII export of the US EPA ECOTOX database

download_ecotox_data()

Searching the local database for species and substances

Obviously, searching the local database is only possible after the download and build is ready (see previous section).

Search the local database for tests of water flea Daphnia magna exposed to benzene

search_ecotox(
  list(
    latin_name    = list(terms = "Daphnia magna", method = "exact"),
    chemical_name = list(terms = "benzene",       method = "exact")
  )
)

Three ways of querying the local database

Let’s have a look at 3 different approaches for retrieving a specific record from the local database, using the unique identifier result_id. The first option is to use the build in search_ecotox function. It uses simple R syntax and allows you to search and collect any field from any table in the database. Furthermore, all requested output fields are automatically joined to the result without the end-user needing to know anything about the database structure.

Using the prefab function search_ecotox packaged by {ECOTOXr}

search_ecotox(
  list(
    result_id = list(terms = "401386", method = "exact")
  ),
  as_data_frame = F
)
#> 'dose_responses.response_site' was renamed 'dose_link_response_site'
#> 'chemicals.cas_number' was renamed 'test_cas'
#> 'chemicals.chemical_name' was renamed 'test_chemical'
#> 'dose_responses.dose_resp_id' was renamed 'dose_link_dose_resp_id'
#> # A tibble: 1 x 98
#>   test_cas test_grade test_gra~1 test_~2 test_~3 test_~4 test_~5 test_~6 test_~7
#> *    <int> <chr>      <chr>      <chr>   <chr>   <chr>   <chr>   <chr>   <chr>  
#> 1    71432 NR         ""         ""      NR      <NA>    NR      <NA>    NR     
#> # ... with 89 more variables: test_purity_comments <chr>,
#> #   organism_lifestage <chr>, organism_age_mean_op <chr>,
#> #   organism_age_mean <chr>, organism_age_min_op <chr>, organism_age_min <chr>,
#> #   organism_age_max_op <chr>, organism_age_max <chr>,
#> #   exposure_duration_mean_op <chr>, exposure_duration_mean <chr>,
#> #   exposure_duration_min_op <chr>, exposure_duration_min <chr>,
#> #   exposure_duration_max_op <chr>, exposure_duration_max <chr>, ...

If you like to use {dplyr} verbs, you are in luck. SQLite database can be approached using {dplyr} verbs. This approach will only return information from the results table. The end-user will have to join other information (like test species and test substance) manually. This does require knowledge of the database structure.

Using {dplyr} verbs

con <- dbConnectEcotox()
dplyr::tbl(con, "results") %>%
  dplyr::filter(result_id == "401386") %>%
  dplyr::collect()
#> # A tibble: 1 x 137
#>   result_id test_id sample_siz~1 sampl~2 sampl~3 sampl~4 sampl~5 sampl~6 sampl~7
#>       <int>   <int> <chr>        <chr>   <chr>   <chr>   <chr>   <chr>   <chr>  
#> 1    401386 1020021 ""           NC      ""      NC      ""      NC      NC     
#> # ... with 128 more variables: sample_size_comments <chr>,
#> #   obs_duration_mean_op <chr>, obs_duration_mean <chr>,
#> #   obs_duration_min_op <chr>, obs_duration_min <chr>,
#> #   obs_duration_max_op <chr>, obs_duration_max <chr>, obs_duration_unit <chr>,
#> #   obs_duration_comments <chr>, endpoint <chr>, endpoint_comments <chr>,
#> #   trend <chr>, effect <chr>, effect_comments <chr>, measurement <chr>,
#> #   measurement_comments <chr>, response_site <chr>, ...

If you prefer working using SQL directly, that is fine too. The {RSQLite} package allows you to get queries using SQL statements. The result is identical to that of the previous approach. Here too the end-user needs knowledge of the database structure in order to join additional data.

Using SQL syntax

dbGetQuery(con, "SELECT * FROM results WHERE result_id='401386'") %>%
  dplyr::as_tibble()
#> # A tibble: 1 x 137
#>   result_id test_id sample_siz~1 sampl~2 sampl~3 sampl~4 sampl~5 sampl~6 sampl~7
#>       <int>   <int> <chr>        <chr>   <chr>   <chr>   <chr>   <chr>   <chr>  
#> 1    401386 1020021 ""           NC      ""      NC      ""      NC      NC     
#> # ... with 128 more variables: sample_size_comments <chr>,
#> #   obs_duration_mean_op <chr>, obs_duration_mean <chr>,
#> #   obs_duration_min_op <chr>, obs_duration_min <chr>,
#> #   obs_duration_max_op <chr>, obs_duration_max <chr>, obs_duration_unit <chr>,
#> #   obs_duration_comments <chr>, endpoint <chr>, endpoint_comments <chr>,
#> #   trend <chr>, effect <chr>, effect_comments <chr>, measurement <chr>,
#> #   measurement_comments <chr>, response_site <chr>, ...

Disclaimers

It is the end-users own responsibility to check the quality of collected data, using the original referenced source in order to evaluate its fitness for use, see also: https://cfpub.epa.gov/ecotox/help.cfm#info-limitations.

Note that the package maintainer is not affiliated with the US EPA, this package is therefore not official US EPA software.

Resources