Everything you need to know when you start using the ECOTOXr package.
The ECOTOXr provides the means to efficiently search, extract and analyse US EPA ECOTOX data, with a focus on reproducible results. Although the package creator/maintainer is confident in the quality of this software, it is the end users sole responsibility to assure the quality of his or her work while using this software. As per the provided license terms the package maintainer is not liable for any damage resulting from its usage. That being said, below we present some tips for generating reproducible results with this package.
Installing this package is only the first step to get things started. You need to perform the following steps in order to use the package to its full capacity.
First download a copy of the complete EPA database. This can be done by calling
This may not always work on all machines as R does not always accept the website SSL certificate from the EPA.
In those cases the zipped archive with the database files can be downloaded manually with a different (more
forgiving) browser. The files from the zip archive can be extracted to a location of choice. Alternatively,
the user could try to use
download_ecotox_data(ssl_verifypeer = 0L) when the download URL is trusted.
Next, an SQLite database needs to be build from the downloaded files. This will be done automatically when
download_ecotox_data in the previous step. When you have manually downloaded the files
you can call
build_ecotox_sqlite to build the database locally.
When the previous steps have been performed successfully, you can now search the database by calling
search_ecotox. You can also use
dbConnectEcotox to open a connection to the
database. You can query the database using this connection and any of the methods provided from the
DBI or RSQLite packages.
Each individual user is responsible for evaluating the reproducibility of his or her work. Although this package offers instruments to achieve reproducibility, it is not guaranteed. In order to increase the chances of generating reproducible results, one should adhere at least to the following rules:
Always use an official release from CRAN, and cite the version used in your analyses (
Different versions, may produce different end results (although we will strive for backward compatibility).
Make sure you are working with a clean (unaltered) version of the database. When in doubt, download and build
a fresh copy of the database (
download_ecotox_data). Also cite the (release) version of the downloaded
cite_ecotox), and the system operating system in which the local database was build
get_ecotox_info). Or, just make sure that you never modify the database (e.g., write data to it, delete
data from it, etc.)
In order to avoid platform dependencies it is advised to only include non-accented alpha-numerical characters in search terms. See also search_ecotox and build_ecotox_sqlite.
When trying to reproduce database extractions from earlier database releases, filter out additions after that specific release. This can be done by adding output fields 'tests.modified_date', 'tests.created_date' and 'tests.published_date' to your search and compare those with the release date of the database you are trying to reproduce results from.
This package doesn't come bundled with a copy of the database which needs to be downloaded the first time the package is used. Why is this? There are several reasons:
The database is maintained and updated by the US EPA. This process is and should be outside the sphere of influence of the package maintainer.
Packages on CRAN are not allowed to contain large amounts of data. Publication on CRAN is key to control the quality of this package and therefore outweighs the convenience of having the data bundled with the package.
The user has full control over the release version of the database that is being used.
Although this is possible, there are several reasons why we opted for creating a local copy:
The user would be restricted to the search options provided on the website (ECOTOX).
The online database doesn't come with an API that would allow for convenient interface.
The user is not limited by an internet connection and its bandwidth.
Not all database fields can be retrieved from the online interface.
Pepijn de Vries
Official US EPA ECOTOX website: https://cfpub.epa.gov/ecotox/
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