phase out plyr / reshape2 in favor of data.table

[dylanbeaudette]

Keeping track of changes / testing related to data.table replacement of plyr / reshape functionality. Each change should be checked and a new test added if there isn't sufficient coverage. Handy bash script:

grep 'join(' * | awk '{print "  - [ ] `"$1"`"}' | tr -d ':.R' | sort | uniq

plyr

join

• sampleasterStackByMU

ddply

• FFD
• componentadjmatrix

ldply

• PLSS2LL
• sampleasterStackByMU
• samplingStability

dlply

• componentadjmatrix
• site_photos_kmlkml_placemarks

reshape2

reshape2::dcast → data.table::dcast

• componentadjmatrix
• geomorphBySoilSeries-SSUGO
• multinominal2logical
• vizAnnualClimate

Note that value argument becomes value.var.

melt → data.table::melt

• diagnosticPropertyPlot
• vizFlatsPosition
• vizGeomorphicComponent
• vizHillslopePosition
• vizMountainPosition
• vizTerracePosition

Caveats

• It appears that data.table::melt will not preserve factor type / levels unless asked to do so explicitly via value.factor argument. A reasonable solution is to set it after the reshape operation when appropriate.
• id.vars should not contain duplicated column names
• melt.data.table expects that all measure.vars are of the same type (e.g. all numeric) otherwise warning issued