twb2:

# twb2_collection_load.R
# John Bannister
# 
# pull twb2 surface roughness collection data from Formation ArcGIS online 
# server, clean and output to csv.
load_all()
load_all("../Rowens")
library(dplyr)
library(jsonlite)

tok <- "RbSEUvle03bm-eoYxec48kiOXWSWNB1Es51A1NK1wIlVMdfTiC8admd27PGrOUdT"
df1 <- query_AGOL("OwensLake_TwB2", 
                  "Owens_TwB2_Surface_FieldCollection_Active", 0, tok)
df1 <- flatten(df1$features)
colnames(df1) <- gsub("attributes.", "", colnames(df1))
colnames(df1) <- gsub("geometry.", "", colnames(df1))
colnames(df1) <- tolower(colnames(df1))
colnames(df1) <- gsub("_", ".", colnames(df1))
df1 <- select(df1, date=date.time, site.id, 
              observer=monitoring.initials,
              rs=ridge.spacing, fd=furrom.depth, irs=interrow.spacing, 
              rh=ridge.height, f1.pnt5to3, f1.gt3, f2.pnt5to3, f2.gt3, 
              f3.pnt5to3, f3.gt3, x, y, notes)
df1$date <- convert_ESRI_date(df1$date)
df1$site.id <- toupper(df1$site.id)
df1$site.id <- gsub("-", "", df1$site.id)
df1$site.id <- gsub(" ", "", df1$site.id)
df1$site.id <- gsub("_", "", df1$site.id)
for (i in 8:13){
  df1[ , i] <- clod_percents(df1[ , i])
}
for (i in 1:nrow(df1)){
df1$mean.clod.prnct[i] <- mean(c(df1$f1.pnt5to3[i] + df1$f1.gt3[i], 
                              df1$f2.pnt5to3[i] + df1$f2.gt3[i],
                              df1$f3.pnt5to3[i] + df1$f3.gt3[i]))
}

# below this point, change filter date as required and add one-off data point 
# corrections as necessary.
df2 <- filter(df1, date > "2016-03-01")
# do all site ids match known twb2 sites?
df2$site.id[!(df2$site.id %in% twb2_sites$site.id)]
# what known twb2 sites are missing from this collection?
twb2_sites$site.id[!(twb2_sites$site.id %in% df2$site.id)]

df2[df2$site.id=="1618", ]$site.id <- "1618A"
df2[df2$site.id=="1619", ]$site.id <- "1619A"
df2[df2$site.id=="1620", ]$site.id <- "1620A"
df2[df2$site.id=="1621", ]$site.id <- "1621A"
df2[df2$site.id=="1615", ]$site.id <- "1615B"

write.csv(df2, file=paste0("./output/twb2_", Sys.Date(), ".csv"), 
          row.names=FALSE)