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gn_testing.R
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library(devtools)
library(neonUtilities)
library(geoNEON)
setwd("/Users/clunch/GitHub/NEON-geolocation/geoNEON")
options(stringsAsFactors = F)
install('.')
check()
test()
loc <- getLocBySite('ARIK', type='AQU')
loc <- getLocBySite('SYCA', type='all', history=T, token=Sys.getenv('NEON_TOKEN'))
loc.is <- getLocBySite('ARIK', type='site', token='garbage')
loc.os <- getLocBySite('HARV', type='all')
loc <- getLocBySite('ABBY', type='TIS')
loc <- getLocBySite('BART', type='TOS')
loc <- getLocBySite('GUIL', type = "all", history = T)
# wtf people are using this below the site level
nogp <- geoNEON::getLocBySite("NOGP_037.mosquitoPoint.mos", token = Sys.getenv('NEON_TOKEN'))
nogp <- geoNEON::getLocBySite("NOGP_037.mosquitoPoint.mos", history=T, token = Sys.getenv('NEON_TOKEN'))
# no lat-long calculation
bird <- loadByProduct(dpID='DP1.10003.001', site='WREF', check.size=F)
perpoint.loc <- getLocByName(bird$brd_perpoint)
countdata.loc <- getLocTOS(bird$brd_countdata, 'brd_countdata', token=Sys.getenv('NEON_TOKEN'))
# lat-long calculation using Sarah's function
phe <- loadByProduct(dpID='DP1.10055.001', site='MOAB', check.size=F)
phe.loc <- getLocTOS(phe$phe_perindividual, 'phe_perindividual')
phe.name <- getLocByName(phe$phe_perindividual)
# lat-long calculation using my function
root <- loadByProduct(dpID='DP1.10067.001', site=c('TREE','TALL'), check.size=F)
root.loc <- getLocTOS(root$bbc_percore, 'bbc_percore')
sls <- loadByProduct(dpID='DP1.10086.001', site='UNDE', check.size=F)
bet <- loadByProduct(dpID='DP1.10022.001', site='TALL', check.size=F)
mos <- loadByProduct(dpID='DP1.10043.001', site='NIWO', check.size=F)
tick <- loadByProduct(dpID='DP1.10093.001', site=c('TALL','CLBJ'), check.size=F)
dhp <- loadByProduct(dpID='DP1.10017.001', check.size=F, token=Sys.getenv('NEON_TOKEN'))
dhp.loc <- getLocTOS(dhp$dhp_perimagefile, 'dhp_perimagefile', token=Sys.getenv('NEON_TOKEN'))
herb <- loadByProduct(dpID='DP1.10023.001', check.size=F, token=Sys.getenv('NEON_TOKEN'))
herb.loc <- getLocTOS(herb$hbp_perbout, 'hbp_perbout', token=Sys.getenv('NEON_TOKEN'))
herb.W <- loadByProduct(dpID='DP1.10023.001', site='WOOD',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
herb.W.loc <- getLocTOS(herb.W$hbp_perbout, 'hbp_perbout', token=Sys.getenv('NEON_TOKEN'))
cdw.tally <- loadByProduct(dpID='DP1.10010.001', check.size=F)
cdw.density <- loadByProduct(dpID='DP1.10014.001', check.size=F)
divJ <- loadByProduct(dpID='DP1.10058.001', site='JERC',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
divJ.loc <- getLocTOS(divJ$div_1m2Data, 'div_1m2Data', token=Sys.getenv('NEON_TOKEN'))
# testing subplot updates
vst <- loadByProduct(dpID='DP1.10098.001', site='ABBY',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
vst.loc <- getLocTOS(vst$vst_mappingandtagging, 'vst_mappingandtagging', token=Sys.getenv('NEON_TOKEN'))
vst.shrub <- getLocTOS(vst$vst_shrubgroup, 'vst_shrubgroup', token=Sys.getenv('NEON_TOKEN'))
vst.nw <- getLocTOS(vst$`vst_non-woody`, 'vst_non-woody', token=Sys.getenv('NEON_TOKEN'))
vst.ind <- getLocTOS(vst$vst_apparentindividual, 'vst_apparentindividual', token=Sys.getenv('NEON_TOKEN'))
library(ggplot2)
gg <- ggplot(data=vst.ind, aes(x=adjEasting, y=adjNorthing,
size=adjCoordinateUncertainty)) + # size is relative, not absolute
geom_point(shape=0) +
geom_point(data=vst.shrub, aes(x=adjEasting, y=adjNorthing),
shape=0, color='olivedrab') +
geom_point(data=vst.nw, aes(x=adjEasting, y=adjNorthing),
shape=0, color='darkblue') +
geom_point(data=vst.loc, aes(x=adjEasting, y=adjNorthing),
shape='.', color='green')
gg
vst <- loadByProduct(dpID='DP1.10098.001', site='STEI', check.size=F)
vst.loc <- getLocTOS(vst$vst_mappingandtagging, 'vst_mappingandtagging')
byTileAOP(dpID='DP3.30015.001', site='STEI', year=2017,
easting=vst.loc$adjEasting, northing=vst.loc$adjNorthing,
savepath='/Users/clunch/Desktop')
veg <- loadByProduct(dpID='DP1.10098.001', check.size=F)
veg.loc <- getLocTOS(veg$vst_mappingandtagging, 'vst_mappingandtagging')
badpoints <- veg.loc$points[which((!is.na(veg.loc$pointID)) & is.na(veg.loc$adjEasting) &
(!is.na(veg.loc$stemDistance)) & (!is.na(veg.loc$stemAzimuth)))]
badpoints <- unique(badpoints)
write.table(badpoints, '/Users/clunch/Desktop/vegpoints.csv', sep=',', quote=F, row.names=F)
req <- httr::GET("http://data.neonscience.org/api/v0/locations/SCBI")
req <- httr::GET("http://data.neonscience.org/api/v0/locations/ARIK")
loc <- jsonlite::fromJSON(httr::content(req, as='text', encoding='UTF-8'))
req <- httr::GET("http://data.neonscience.org/api/v0/locations/S2LOC100103")
# megapit locations
mp <- loadByProduct(dpID='DP1.00096.001')
mpl <- getLocByName(mp$mgp_permegapit, locCol='pitNamedLocation', locOnly=T)
# #SOILAR100590 TOWER100594
# req <- httr::GET("http://data.neonscience.org/api/v0/locations/CFGLOC103160")
# loc <- jsonlite::fromJSON(httr::content(req, as='text', encoding='UTF-8'))
loc$data$locationChildrenUrls[which(substring(loc$data$locationChildren, 1, 4)!='SCBI')]
req <- httr::GET("http://data.neonscience.org/api/v0/locations/S2LOC111011?history=true")
loc <- jsonlite::fromJSON(httr::content(req, as='text', encoding='UTF-8'))
req <- httr::GET("http://data.neonscience.org/api/v0/locations/GWWELL112553?history=true")
loc <- jsonlite::fromJSON(httr::content(req, as='text', encoding='UTF-8'))