Closed schifferl closed 2 years ago
From @lwaldron on December 8, 2017 21:30
I think the canonical location for variable documentation is in the "Description" column of https://github.com/waldronlab/curatedMetagenomicDataCuration/blob/master/inst/extdata/template.csv. If you would add this @edoardopasolli (and check the adequacy of the rest of the descriptions), then we'll convert this issue to one for @schifferl to parse this file to create automatic codebooks in the vignette and in the combined_metadata
help page.
study_condition
is always one word, and is the label for this participant for the purposes of the analysis this study was designed around. In case-control studies, the controls are labeled "control". In studies without a contrast, all participants are labeled "control". The main comparison group is labeled according to what that condition or exposure is.
disease
can be a semicolon-delimited array of diseases associated with the participant, even if they are not under study. "none" if no disease is known for the participant.
annotate the design of each an array of study designs, consistently with bugsigdb.org:
I think the main action item here is for @QuanWan89 to include a study design
field in the study table in the new metadata database, with the following values. That can be started in Quan's project management (although I don't have access to that):
From @edoardopasolli on December 7, 2017 19:50
An external user may have some difficulties in understanding how we defined the "study_condition" and "disease" fields. Should we clarify this aspect better somewhere?
Copied from original issue: waldronlab/curatedMetagenomicData#118