tsufz / recotox Goto Github PK
View Code? Open in Web Editor NEWREcoTox is a semi-automated, interactive R workflow to process US EPA ECOTOX Knowledgebase entire database ASCII files
License: Other
REcoTox is a semi-automated, interactive R workflow to process US EPA ECOTOX Knowledgebase entire database ASCII files
License: Other
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
So far, we include limit tests. But, some users might do not want to integrate limit tests.
Some issue with obs_duration_mean
observed. A type adjustment might help.
A default species list with pre-selected species per ecotox_group
is appreciated to avoid repetitive work.
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) {
#}
The readme is not correct, it is not necessary to download whole repo, but install from Github should be mentioned
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.
Wrong date
So far, NA is used. This is confusing and should be changed to 0
The folder initialisation is confusing, Check and refine messages.
The chemical list output could only contain data with missing information to make editing easier
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