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REcoTox is a semi-automated, interactive R workflow to process US EPA ECOTOX Knowledgebase entire database ASCII files

License: Other

R 7.76% TeX 0.43% HTML 91.81%
hazard-assessment ecotoxicology toxic-unit data-aggregation data-retrieval ecotoxicology-knowlegdebase enviromental-chemistry

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recotox's Issues

Unit group selection

The unit group selection is static (only water concentrations allowed), mapped to the term "dosing group". Could be more flexible by providing a regular expression input. A helper function to extract units, considering all other parameters might be meaningful.

Update Readme

The readme is not correct, it is not necessary to download whole repo, but install from Github should be mentioned

Integrate with ECOTOXr

Hi Tobias,

Just came across your package. It seems that you are working on processes that I intended to implement in the ECOTOXr package. That package downloads the ASCII tables from ECOTOX and builds a local SQLite database, which can then be queried. It only removes the most prominent errors in the ASCII files (required for building the database) but it does not do any further processing of the data. This was something I had planned for the future, but is something you have apparently been working on. Do you think it would be opportune to merge the packages, or should we continue developing as separate packages?

Cheers,

Pepijn

Include endpoint filter is not working

if(unique(endpoints$include_endpoint) == 0) {
stop("[EcoToxR]: There are only 0 in the endpoint selection filter. Check the species selection list and re-run the workflow.")
}

#if(unique(endpoints$include_endpoint)[[1]] == 0) {

stop("[EcoToxR]: There are only 0 in the endpoint selection filter. Check the species selection list and re-run the

workflow.")

#}

Fix field type

Some issue with obs_duration_mean observed. A type adjustment might help.

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