Fix build-warnings and other issues #44
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…dom mats from each); will eventually replace with @levisc8's code to get more balanced subsamples
…s.data.frame and head to prevent build warnings, and strip out species/study/matrix counts within asCompadreDB()
…erwise), remove version time-stamp, and remove post-merge tests (these can be added to package tests)
…onversion of legacy dbs (direct to convertLegacyDB), simplify code with helper fns, and change functionality to return mean mats for ALL populations (even if from only a single matrix)
…rnings, and move subset methods to separate file and doc
…e sapply to vapply, and remove auto-conversion of legacy dbs (direct to convertLegacyDB)
…asCompadreDB (strip out species/study/matrix counts from version)
…kage, and remove dontrun{} tags
…l of automatic asCompadreDB conversion
…ples, and change appveyor and travis links in README to branch devel
…essors) and CompadreDB-Methods (other methods)
…R (doc CompadreDB-Subsetting)
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Fantastic work there @patrickbarks! |
This was referenced Nov 27, 2018
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Fixes all the build warnings. Apart from those updates, I've made some additional changes:
Removed coercion to CompadreDB class from all fns except
convertLegacyDBandfetchDBFunctions now fail if db not CompadreDB class, and direct users to
convertLegacyDB. The conversion is fairly time-consuming, so I think it's preferable to encourage users to incorporate a single conversion into their workflow, rather than potentially many somewhat-hidden conversions within other functions.Removed
subsetDBand updated dependent fns accordinglyWe now have methods for
[andsubset, which that I think are preferable.Cut version time-stamp updates from
[andmergeDBsThey don't improve reproducibility, and there are other ways that users could modify a db without getting a time-stamp, so getting time-stamps only during select operations is potentially confusing.
Updated and restructured CompadreDB documentation
Documented slot names and all method params, and split CompadreDB code and documentation into three files: CompadreDB.R (class and accessors), CompadreDB-Subsetting.R (
[andsubsetmethods and examples), and CompadreDB-Methods.R (other methods such ashead,names,as.data.frame,merge, etc.). Not sure this is the best way to organize, but there are so many methods that I think they should be split somehow, to make the documentation easier to follow.Other changes:
cleanDB(closes Add check_singular_U flag to cleanDB #30)fetchDBfn to fetch db from web or local file (closes Add fetchDB function? #31)asCompadreDBconversion (closes Cut species/study/matrix counts from db@version #42)