README.md

In benscarlson/anno:

Setup

Build package

devtools::document(); devtools::build()

Install package

R CMD INSTALL ~/projects/anno_0.1.0.tar.gz

See inst/scripts/setup.sh for commands to put anno scripts on your path

Example use

datName=mydat

cd analysis

dat=data/mydat.csv
gcsimport=gs://mol-playground/benc/ingest_ee/$datName
gcsanno=gs://mol-playground/benc/annotated/$datName
asset=users/benscarlson/annotate/tracks/$datName

annoprep $dat
annoimport -d $dat -g $gcsimport -a $asset
#annotate in playground: annotate/annotate_by_static_or_ts.js
annoprocess -d $dat -g $gcsanno
annocleanup -d $dat -i $gcsimport -g $gcsanno

workflow

• Each command accepts the same data set name as input (e.g. mydat.csv). However, the commands parse this name and often build different input/output file names.
• annoimport

annoprep

• adds anno_id to the dataset
• subsets fields to just those that should be uploaded to gee
• saves file as _forgee.csv (can now import csv to gee)

annoimport

• uploads file to gcs
• imports from gcs to gee

annoprocess

• downloads files to ./raw folder
• calls processGEEraw.r to merge raw files, convert units, join back to *_anno.csv file

Other notes

• Uploaded dataset should have anno_id that is a unique index for each feature
• Annotated environmental value should have column name env_val

benscarlson/anno documentation built on Nov. 26, 2020, 10:17 p.m.