README

Cloning and updating the repo

# do this to get the repo, first time only
git clone https://www.github.com/fawda123/oss2017_synthesis.git

# do this every time before you make changes
git pull

# do this after you make changes
git add -A
git commit -m "informative message"
git pull
git push

View info online

Data aggregation: https://fawda123.github.io/oss2017_synthesis/tbrest

Final presentation: https://fawda123.github.io/oss2017_synthesis/presentations/final_pres

Extra slides: https://fawda123.github.io/oss2017_synthesis/presentations/final_pres_supp

Shiny: http://tbeptech.org:3939/content/5/, http://tbeptech.org:3939/content/6/

Jiggly plot: https://fawda123.github.io/oss2017_synthesis/presentations/final_pres-figure/bayes_network.html

Repository info

Folders:

• data RData files, load with data(filename)
• data-raw - put raw and intermediate data files here, e.g., .xlsx., .txt., .csv
• Diagrams - workflow diagrams
• Model - BN model files
• presentations presentation files
• R - R scripts

RData files (these should be text files?) in data, normalized:

• allchg.RData All chlorophyll data with habitat, water treatment, and salinity levels, discretized and continuous chl
• bmpdat.RData restoration projects for water treatment
• bmpstat.RData locations of restoration projects for water treatment
• chlbar.RData final data of chlorophyll splits for BN
• chlchg.RData All chl data with habitat, water treatment bef/aft projects, discretized and continuous
• chlchgout.RData All chl data with habitat, water treatment bef/aft projects, discretized and continuous, intermediate step
• habdat.RData restoration projects for habitat
• habstat.RData locations of restoration projects for habitat
• restdat.RData restoration projects combined
• reststat.RData location of restoration projects combined
• salchg.RData All salinity data with habitat, water treatment bef/aft projects, discretized and continuous
• salchgout.RData All salinity data with habitat, water treatment bef/aft projects, discretized and continuous, intermediate step
• wqdat.RData TB water quality data by site, date, var, val
• wqstat.RData TB water quality stations as lat/lon