Levi Waldron
Levi Waldron
I'm not sure if the warning in the subject is itself a problem, but I can't seem to run your example. I have a new installation of Anaconda with Python3...
I thought it'd be nice to do some introductions here, to connect GitHub IDs to names and faces during the meetings. I'm Levi, I'm an assistant professor of Biostatistics at...
Having `BiocManager::install()` return the "pkgs" argument is not especially useful. Could it instead return success/error codes? Otherwise, how can you tell in a script whether the requested packages were installed...
Unless I've missed something, you have to use an alternative like `devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())` to install a local package normally or in Dockerfiles, taking us away from...
`qqnormsim()` is great! But looking at the [html version of Exercise 3](http://htmlpreview.github.io/?https://github.com/andrewpbray/oiLabs-base-R/blob/master/normal_distribution/normal_distribution.html) doesn't make it clear how to define the function. Perhaps either include a `source()` command or put it...
bodysite for HMP_2012 anerior_nares samples should be "nose" or "external nares", not "nasal cavity"
The anterior nares subsite is not part of the nasal cavity. `nose` and `external nares` are both parent terms in the Uberon Anatomy Ontology ([link](https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_2001427&lang=en&viewMode=PreferredRoots&siblings=false)). I would vote for `nose`...
We need maps between terms in the [template](https://github.com/waldronlab/curatedMetagenomicDataCuration/blob/master/inst/extdata/template.csv) and formal ontologies. Preferred ontologies for: * body_site & body_subsite -> Uberon Ontology * disease & disease_subsite -> Experimental Factor Ontology *...
Create a formal data dictionary as a table with the following columns: 1. variable name 2. definition of variable (from template.csv "description") 3. variable value 4. definition of variable value...
metadata table is loaded by #38, then output would look like https://github.com/waldronlab/curatedMetagenomicDataCuration/blob/master/inst/extdata/Updated%20template.csv
not using travis anymore