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nu_testing.R
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nu_testing.R
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library(devtools)
setwd("/Users/clunch/GitHub/NEON-utilities/neonUtilities")
#setwd("/Users/clunch/GitHub/utilities-test-suite/neonUtilities/")
#install_github('NEONScience/NEON-utilities/neonUtilities', ref='main')
install('.')
library(neonUtilities)
check()
options(stringsAsFactors = F)
urlchecker::url_check('.')
setwd("/Users/clunch/GitHub/utilities-test-suite/testUtilities")
test()
usera <- paste("neonUtilities/", utils::packageVersion("neonUtilities"), " R/",
R.Version()$major, ".", R.Version()$minor, " ", commandArgs()[1],
" ", R.Version()$platform, sep="")
req <- httr::GET("https://storage.googleapis.com/neon-publication/NEON.DOM.SITE.DP1.20190.001/CARI/20220601T000000--20220701T000000/basic/NEON.D19.CARI.DP1.20190.001.readme.20231102T154855Z.txt", httr::user_agent("test user agent"))
downloader::download("https://storage.googleapis.com/neon-publication/NEON.DOM.SITE.DP1.20190.001/CARI/20220601T000000--20220701T000000/basic/NEON.D19.CARI.DP1.20190.001.readme.20231102T154855Z.txt",
'/Users/clunch/Desktop/testreadme.txt',
mode="wb", quiet=T,
headers=c("User-Agent"=usera,
"X-API-Token"=""))
# empty string works, NA doesn't
# DOIs
dois <- getNeonDOI()
dois <- getNeonDOI(dpID='DP1.10003.001')
dois <- getNeonDOI(dpID='DP1.10098.001', release='RELEASE-2022')
# CERT version?
csd <- loadByProduct(dpID='DP4.00130.001', release='LATEST', stack='cert',
startdate='2021-04', enddate='2021-09',
site=c('BLDE','OKSR','REDB'),
token=Sys.getenv('CERT_LATEST'), check.size=F)
# PARQL from pachy
ql <- loadByProduct(dpID='DP1.00066.001', release='LATEST', stack='cert',
startdate='2022-04', enddate='2022-09',
site=c('HEAL','MOAB','GUAN'),
token=Sys.getenv('CERT_LATEST'), check.size=F)
gg <- ggplot(ql$PARQL_30min, aes(endDateTime, linePARMean, color=horizontalPosition)) +
geom_line() +
facet_wrap(~siteID)
gg
ql <- loadByProduct(dpID='DP1.00066.001', include.provisional=T, stack='cert',
startdate='2023-07', enddate='2023-09',
site=c('HEAL','MOAB','GUAN'),
token=Sys.getenv('CERT_LATEST'), check.size=F)
ql <- loadByProduct(dpID='DP1.00066.001', stack='cert',
startdate='2022-04', enddate='2022-09',
site=c('HEAL','MOAB','GUAN'),
token=Sys.getenv('CERT_LATEST'), check.size=F)
# LATEST accessible?
fsp <- loadByProduct(dpID='DP1.30012.001', package='basic', release='LATEST',
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
brd <- loadByProduct(dpID='DP1.10003.001', release='LATEST',
startdate='2019-01', enddate='2020-12',
site=c('HARV','LAJA','RMNP','TEAK','SJER','WREF'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
pr <- loadByProduct(dpID='DP1.00024.001', release='LATEST',
startdate='2022-09', enddate='2022-10',
site=c('ABBY','BIGC'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
swss <- loadByProduct(dpID='DP1.00094.001', release='LATEST',
startdate='2022-07', enddate='2022-08',
site=c('DSNY','CPER'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
# science review flags
ql <- loadByProduct(dpID='DP1.00066.001', release='LATEST',
startdate='2022-09', enddate='2022-10',
site=c('SERC','WREF'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
pcp <- loadByProduct(dpID='DP1.00006.001', release='LATEST',
startdate='2022-07', enddate='2022-10',
site=c('DSNY','HARV'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
rad <- loadByProduct(dpID='DP1.00023.001', release='LATEST',
startdate='2022-05', enddate='2022-10',
site=c('BLDE','WREF'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
st <- loadByProduct(dpID='DP1.20053.001', release='LATEST',
startdate='2022-01', enddate='2022-02',
site=c('BLDE','ARIK'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
eos <- loadByProduct(dpID='DP1.20016.001', release='LATEST',
startdate='2022-01', enddate='2022-01',
site=c('BIGC','WLOU'),
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
# SRFs
pr <- loadByProduct(dpID='DP1.00024.001', site=c('ABBY','SRER'),
startdate='2022-03', enddate='2022-04',
timeIndex=30, check.size=F)
Sys.time()
pr <- loadByProduct(dpID='DP1.00024.001', site='BARR',
timeIndex=30, check.size=F, include.provisional=T,
token=Sys.getenv('NEON_TOKEN'), package='expanded')
Sys.time()
zipsByProduct(dpID='DP1.00024.001', site='BARR',
timeIndex=30, check.size=F, include.provisional=T,
token=Sys.getenv('NEON_TOKEN'), package='expanded',
savepath='/Users/clunch/Desktop')
Sys.time()
pr <- stackByTable('/Users/clunch/Desktop/filesToStack00024/', savepath='envt')
Sys.time()
# other LATEST
mos <- loadByProduct(dpID='DP1.10043.001', release='LATEST',
startdate='2019-01', enddate='2021-12',
token=Sys.getenv('LATEST_TOKEN'), check.size=F)
asc_LATEST <- neonUtilities::loadByProduct(
dpID='DP1.20194.001',
check.size=F,
startdate = "2018-01",
enddate = "2020-12",
site = "all",
package='expanded',
release = "LATEST",
token = token)
downloader::download("https://data.neonscience.org/api/v0/data/package/DP1.30012.001/GRSM/2015-08?package=basic&release=LATEST",
destfile='/Users/clunch/Desktop/test.zip',
mode="wb", quiet=T,
headers = c('X-API-Token'= Sys.getenv('LATEST_TOKEN')))
dpID <- 'DP1.30012.001'
package <- 'basic'
release <- 'LATEST'
token <- Sys.getenv('LATEST_TOKEN')
site <- 'all'
startdate <- NA
enddate <- NA
timeIndex <- 'all'
tabl <- 'all'
byFileAOP(dpID='DP3.30019.001', site='TREE', year=2017, savepath='/Users/clunch/Desktop')
byFileAOP(dpID='DP3.30019.001', site='TREE', year=2017,
savepath='/Users/clunch/Desktop', include.provisional=T)
byFileAOP(dpID='DP3.30019.001', site='MCDI', year=2020, savepath='/Users/clunch/Desktop')
byTileAOP(dpID = "DP3.30006.001", site = "WREF", year = "2017",
easting = c(571000,578000),
northing = c(5079000,5080000),
savepath='/Users/clunch/Desktop')
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = 2022,
easting = c(571000,578000),
northing = c(5079000,5080000),
savepath='/Users/clunch/Desktop')
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = 2022,
easting = c(571000,578000),
northing = c(5079000,5080000),
include.provisional = T,
savepath='/Users/clunch/Desktop')
zipsByProduct(dpID='DP1.20190.001', site='OKSR',
startdate='2019-01', enddate='2020-12',
package='expanded', savepath='/Users/clunch/Desktop',
check.size=F)
# manually added data frame files
r <- stackByTable('/Users/clunch/Desktop/filesToStack20190/', savepath='envt')
rea <- loadByProduct(dpID='DP1.20190.001', site='SYCA',
startdate='2021-01', enddate='2021-12',
package='expanded', check.size=F,
release='LATEST', token=Sys.getenv('LATEST_TOKEN'))
deflag <- stackEddy('/Users/clunch/Desktop/deflagging/', level='dp01', var='isoCo2', avg=30)
df <- loadByProduct(dpID = 'DP1.20206.001', site = 'ARIK',
startdate = '2021-05', enddate = '2021-05',
check.size = FALSE, package='expanded',
token = Sys.getenv('NEON_TOKEN'))
a<-data.frame(x=1:10,y=1:10)
test<-function(z){
nm <-deparse(substitute(z))
print(nm)
}
# files with release tags
stackByTable('/Users/clunch/Desktop/NEON_temp-soil.zip') # working
st <- stackByTable('/Users/clunch/Desktop/NEON_temp-soil.zip', savepath='envt') # working!
csd <- stackByTable('/Users/clunch/Desktop/NEON_discharge-stream-l4.zip', savepath='envt') # working
cfc <- stackByTable('/Users/clunch/Desktop/NEON_chem-phys-foliar.zip', savepath='envt') # working
stackByTable('/Users/clunch/Desktop/NEON_chem-phys-foliar.zip') # working
stackByTable('/Users/clunch/Desktop/NEON_discharge-stream-l4.zip') # working
stackByTable('/Users/clunch/Desktop/filesToStack00002/')
gch <- stackByTable('/Users/clunch/Desktop/NEON_chem-groundwater.zip', savepath='envt')
stackByTable('/Users/clunch/Desktop/NEON_count-beetles.zip')
bt <- stackByTable('/Users/clunch/Desktop/NEON_temp-bio.zip', savepath='envt')
stackByTable('/Users/clunch/Desktop/NEON_traits-foliar.zip')
stackByTable('/Users/clunch/Desktop/NEON_par.zip')
p <- stackByTable('/Users/clunch/Desktop/NEON_par.zip', savepath='envt')
stackByTable('/Users/clunch/Desktop/NEON_clip-plant-aqu.zip')
aq <- stackByTable('/Users/clunch/Desktop/NEON_clip-plant-aqu.zip', savepath='envt')
# download by release
brd <- loadByProduct(dpID='DP1.10003.001', check.size=F, package='expanded',
release='PROVISIONAL', include.provisional=T,
token=Sys.getenv('NEON_TOKEN'))
inv <- loadByProduct(dpID='DP1.20120.001', package='expanded',
release='RELEASE-2021',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
# no data in release for parameters:
brd.no <- loadByProduct(dpID='DP1.10003.001', check.size=F,
release='RELEASE-2021', startdate='2020-01',
token=Sys.getenv('NEON_TOKEN'))
zipsByProduct(dpID='DP1.10003.001', check.size=F,
site=c('PUUM','NIWO'),
startdate='2018-01', enddate='2022-12',
savepath='/Users/clunch/Desktop',
token=Sys.getenv('NEON_TOKEN'))
stackByTable('/Users/clunch/Desktop/filesToStack10003')
zipsByProduct(dpID='DP1.10033.001', check.size=F,
site=c('HARV','SJER'), package='expanded',
startdate='2018-01', enddate='2022-12',
savepath='/Users/clunch/Desktop',
token=Sys.getenv('NEON_TOKEN'))
stackByTable('/Users/clunch/Desktop/filesToStack10033')
zipsByProduct(dpID='DP1.00005.001', check.size=F,
site=c('PUUM','NIWO'), package='expanded',
startdate='2022-06', enddate='2022-07',
savepath='/Users/clunch/Desktop',
token=Sys.getenv('NEON_TOKEN'))
stackByTable('/Users/clunch/Desktop/filesToStack00005')
# time test
wind <- stackByTable('/Users/clunch/Desktop/NEON_wind-2d.zip', savepath='envt')
# download single table
zipsByProduct(dpID='DP1.10026.001', tabl='cfc_carbonNitrogen',
savepath='/Users/clunch/Desktop',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
cfc.n <- stackByTable('/Users/clunch/Desktop/filesToStack10026', savepath='envt')
cfcc <- loadByProduct(dpID='DP1.10026.001', tabl='cfc_chlorophyll',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
ltr_CN <- loadByProduct(dpID = "DP1.10033.001",
tabl = 'ltr_litterCarbonNitrogen',
release='RELEASE-2021',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
sls_collect <- loadByProduct(dpID = "DP1.10086.001", tabl = 'sls_soilCoreCollection',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
veg <- loadByProduct(dpID='DP1.10098.001', tabl='vst_mappingandtagging',
site=c('WREF','SJER'),
check.size=F, token=Sys.getenv('NEON_TOKEN'))
vn <- loadByProduct(dpID='DP1.10098.001', tabl='vst_non-woody',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
vnl <- loadByProduct(dpID='DP1.10098.001', tabl='vst_non-woody',
release='LATEST', check.size=F, token=Sys.getenv('LATEST_TOKEN'))
nst <- loadByProduct(dpID='DP1.10045.001', tabl='vst_perplotperyear',
release='RELEASE-2021', check.size=F, token=Sys.getenv('LATEST_TOKEN'))
nst <- loadByProduct(dpID='DP1.10045.001', tabl='nst_perindividual',
release='current', check.size=F, token=Sys.getenv('LATEST_TOKEN'))
# lab table error
brdp <- loadByProduct(dpID='DP1.10003.001', tabl='brd_personnel',
package='expanded', site=c('HARV','BLAN','MLBS','LAJA'),
check.size=F, token=Sys.getenv('NEON_TOKEN'))
brdp <- loadByProduct(dpID='DP1.10003.001', tabl='brd_personnel',
release='PROVISIONAL', include.provisional=T,
package='expanded', site=c('HARV','BLAN','MLBS','LAJA'),
check.size=F, token=Sys.getenv('NEON_TOKEN'))
ntrp <- loadByProduct(dpID='DP1.10086.001', tabl='ntr_externalSummary',
package='expanded', site=c('HARV','BLAN','MLBS','LAJA'),
check.size=F, token=Sys.getenv('NEON_TOKEN'))
# table in wrong product error
veg <- loadByProduct(dpID='DP1.10098.001', tabl='bgc_CNiso_externalSummary',
site=c('WREF','SJER'),
check.size=F, token=Sys.getenv('NEON_TOKEN'))
# bad table name
veg <- loadByProduct(dpID='DP1.10098.001', tabl='garbage', site=c('WREF','SJER'),
check.size=F, token=Sys.getenv('NEON_TOKEN'))
dpID <- 'DP1.20093.001'
site <- c('ARIK','POSE','KING')
package <- "expanded"
startdate <- NA
enddate <- NA
tabl <- 'swc_domainLabData'
token <- Sys.getenv('NEON_TOKEN')
dpID <- 'DP1.10003.001'
site <- c('HARV','BLAN','MLBS','LAJA')
package <- "expanded"
startdate <- NA
enddate <- NA
tabl <- 'brd_personnel'
token <- Sys.getenv('NEON_TOKEN')
# time test
Sys.time()
swc <- loadByProduct(dpID='DP1.00094.001', site='RMNP', startdate='2017-05',
enddate='2017-08', check.size=F, token=Sys.getenv('NEON_TOKEN'),
nCores=5)
Sys.time()
# memory test
zipsByProduct(dpID='DP1.00094.001', site='RMNP',
savepath='/Users/clunch/Desktop',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
stackByTable('/Users/clunch/Desktop/filesToStack00094/')
stackByTable('/Users/clunch/Desktop/filesToStack00094/', nCores=4, saveUnzippedFiles = T)
# with 2.0, crashes at 72% of 1 min table
# 1.3.8 crashes at 79% of table. hahahaha
# 2.0 with 4 cores: crashes at 79% - wasn't actually parallelizing
# with parallelization, crashes at 87%
# testing stack set of files
stackByTable(list.files('/Users/clunch/Desktop/filesToStack10053/', full.names = T), saveUnzippedFiles = T)
stackByTable(list.dirs('/Users/clunch/Desktop/filesToStack10053/', full.names = T), saveUnzippedFiles = T)
cfi <- stackByTable(list.dirs('/Users/clunch/Desktop/filesToStack10053/', full.names = T),
saveUnzippedFiles = T, savepath='envt')
# should fail, file paths incomplete
stackByTable(list.files('/Users/clunch/Desktop/filesToStack10053/'), saveUnzippedFiles = T)
# testing stackEddy() on set of files
dum <- stackEddy(c('/Users/clunch/Desktop/filesToStack00200/NEON.D01.HARV.DP4.00200.001.nsae.2018-06.basic.h5',
'/Users/clunch/Desktop/filesToStack00200/NEON.D01.HARV.DP4.00200.001.nsae.2018-07.basic.h5',
'/Users/clunch/Desktop/filesToStack00200/NEON.D13.NIWO.DP4.00200.001.nsae.2018-06.basic.h5',
'/Users/clunch/Desktop/filesToStack00200/NEON.D13.NIWO.DP4.00200.001.nsae.2018-07.basic.h5'))
dum2 <- stackEddy(c('/Users/clunch/Desktop/filesToStack00200/NEON.D01.HARV.DP4.00200.001.2018-06.basic.20190521T201956Z.zip',
'/Users/clunch/Desktop/filesToStack00200/NEON.D01.HARV.DP4.00200.001.2018-07.basic.20190521T201600Z.zip'))
clbj <- stackEddy(c('/Users/clunch/Desktop/NEON.D11.CLBJ.DP4.00200.001.nsae.2021-08-18.expanded.20220511T190125Z.h5.gz',
'/Users/clunch/Desktop/NEON.D11.CLBJ.DP4.00200.001.nsae.2021-08-19.expanded.20220511T190309Z.h5.gz'))
clbj <- stackEddy(c('/Users/clunch/Desktop/NEON.D11.CLBJ.DP4.00200.001.nsae.2021-08-18.expanded.20220511T190125Z.h5',
'/Users/clunch/Desktop/NEON.D11.CLBJ.DP4.00200.001.nsae.2021-08-19.expanded.20220511T190309Z.h5'))
foot <- footRaster(c('/Users/clunch/Desktop/NEON.D11.CLBJ.DP4.00200.001.nsae.2021-08-18.expanded.20220511T190125Z.h5',
'/Users/clunch/Desktop/NEON.D11.CLBJ.DP4.00200.001.nsae.2021-08-19.expanded.20220511T190309Z.h5'))
# methane
meth <- stackEddy('/Users/clunch/Desktop/filesToStack00200', level='dp01',
var='ch4Conc', avg=30)
# Steph incomplete data problem
apl_allTabs <- loadByProduct(dpID = "DP1.20066.001",
site = "TOOK",
package = "expanded",
startdate = "2019-07",
enddate = "2019-07",
check.size = FALSE)
# testing stackFromStore()
library(neonstore)
neon_download(product="DP1.10026.001",
type="expanded",
site=c("TOOL","WREF","GUAN"))
Sys.setenv(NEONSTORE_HOME = '/Users/clunch/Dropbox/data/neonstore')
neon_download(product="DP1.10026.001",
type="expanded",
site=c("BONA","CLBJ","DCFS","DELA","GRSM","KONZ","LENO","MOAB","NOGP","SOAP","UKFS"))
cfcStore <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.10026.001',
site=c('DELA','SOAP','NOGP'), pubdate='2020-12-19',
package='expanded', zipped=F, load=T)
temp <- stackFromStore(filepaths='/Users/clunch/data/neonstore',
dpID="DP1.00002.001",
startdate="2019-03",
enddate="2019-04",
package="basic",
site=c("TOOL","WREF"))
cfc <- stackFromStore(filepaths='/Users/clunch/data/neonstore',
dpID='DP1.10026.001',
package='expanded')
cfc <- stackFromStore(filepaths='/Users/clunch/data/neonstore',
dpID='DP1.10026.001',
package='expanded',
site=c('TOOL','WREF'))
cfc <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.10026.001',
site=c('CLBJ','NOGP'), package='expanded', zipped=T, load=T)
cfc <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.10026.001',
site=c('KONZ','DELA','LENO','SOAP','BONA'), pubdate='2020-10-09',
package='expanded', zipped=F, load=T)
cfc <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.10026.001',
site=c('UNDE','KONA','JERC'), zipped=F, load=T, timeIndex=60)
cfc <- stackByTable(c('/Users/clunch/Dropbox/data/neonstore/NEON.D02.SERC.DP1.10026.001.2016-07.expanded.20200323T154228Z.zip',
'/Users/clunch/Dropbox/data/neonstore/NEON.D05.STEI.DP1.10026.001.2017-08.expanded.20200504T151826Z.zip'),
saveUnzippedFiles = T)
dst <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.00017.001',
package='expanded', zipped=T, load=T) # not working
dst <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.00017.001',
package='expanded', zipped=F, load=T)
dst <- stackFromStore('/Users/clunch/Dropbox/data/neonstore', dpID='DP1.00017.001',
package='expanded', timeIndex=60, zipped=F, load=T)
mam <- stackFromStore(neon_dir(), dpID='DP1.10072.001', package='expanded')
neon_download(product='DP1.10003.001', type='expanded', dir=neon_dir())
brd <- stackFromStore(neon_dir(), dpID='DP1.10003.001', package='expanded')
# confirm same
bird <- loadByProduct(dpID='DP1.10003.001', package='expanded')
flux <- stackFromStore('/Users/clunch/GitHub/utilities-test-suite/testUtilities/inst/extdata/neonstore/',
dpID='DP4.00200.001',
site='TOOL',
package='basic', zipped=F, load=T, level='dp04')
iso <- stackFromStore('/Users/clunch/GitHub/utilities-test-suite/testUtilities/inst/extdata/neonstore/', dpID='DP4.00200.001',
package='basic', zipped=F, load=T, level='dp01', timeIndex=30,
var='dlta13CCo2')
filepaths <- '/Users/clunch/Dropbox/data/neonstore'
dpID <- 'DP1.10026.001'
site <- c('KONZ','DELA','LENO','SOAP','BONA')
zipped <- F
load <- T
pubdate <- "2020-10-07"
package <- "expanded"
startdate <- NA
enddate <- NA
# new download structure for SAE
flux <- stackEddy('/Users/clunch/Desktop/NEON_eddy-flux.zip', level='dp04')
flux <- stackEddy('/Users/clunch/Desktop/PROD_eddy-flux.zip', level='dp04')
flux <- stackEddy('/Users/clunch/Desktop/NEON.D18.TOOL.DP4.00200.001.nsae.2018-07-19.expanded.h5',
level='dp04')
iso <- stackEddy('/Users/clunch/Desktop/NEON.D18.TOOL.DP4.00200.001.nsae.2018-07-19.expanded.h5',
level="dp01", avg=30, var=c("dlta13CCo2","dlta18OH2o"))
del <- stackEddy('/Users/clunch/Desktop/filesToStack00200PUUMAprMay/',
var = 'dlta18OH2oRefe', avg = 9, level = 'dp01')
wnd <- stackEddy(list.files('/Users/clunch/Desktop/filesToStack00200/', pattern='.h5$',
full.names=T),
var = 'soni', avg = 30, level = 'dp01')
filepath <- '/Users/clunch/Desktop/NEON_eddy-flux.zip'
level <- 'dp04'
var <- NA
avg <- NA
# .gz files for SAE
zipsByProduct("DP4.00200.001", site = "PUUM",
startdate = "2021-06",
enddate = "2021-08",
release='LATEST',
savepath = "/Users/clunch/Desktop",
check.size = FALSE,
token=Sys.getenv('LATEST_TOKEN'))
zipsByProduct("DP4.00200.001", site = c("MOAB","PUUM"),
startdate = "2023-10",
enddate = "2023-10",
release = "current",
savepath = "/Users/clunch/Desktop",
check.size = FALSE,
package='expanded',
include.provisional=TRUE,
token=Sys.getenv('LATEST_TOKEN'))
zipsByProduct("DP4.00200.001", site = c("CPER"),
startdate = "2023-11",
enddate = "2023-12",
release = "current",
savepath = "/Users/clunch/Desktop",
check.size = FALSE,
package='expanded',
include.provisional=TRUE,
token=Sys.getenv('LATEST_TOKEN'))
flux <- stackEddy('/Users/clunch/Desktop/filesToStack00200/', level='dp04')
flux <- stackEddy('/Users/clunch/Desktop/PUUM_flux_files/', level='dp04')
flux <- stackEddy(filepath = list.files('/Users/clunch/Desktop/filesToStack00200/',
pattern='[.]h5', full.names = T))
dp1 <- stackEddy('/Users/clunch/Desktop/filesToStack00200/',
level='dp01', avg=2, var='co2Stor')
dp1$HARV$hour <- paste(lubridate::date(dp1$HARV$timeBgn), lubridate::hour(dp1$HARV$timeBgn), sep=".")
Sys.time()
dp1 <- stackEddy('/Users/clunch/Desktop/filesToStack00200/', level='dp01', avg=30)
Sys.time()
# v2.2.3.9000: 11.5 minutes
# with pre-ordering tables: 11 minutes
# using merge.data.table: 5.4 minutes
# moving eddyStampCheck() before stacking: still 5.4 minutes
# join first, then stack: 4.1 minutes
Sys.time()
dp1 <- stackEddy('/Users/clunch/Desktop/filesToStack00200/', level='dp01', avg=30, useFasttime=T)
Sys.time()
# with fasttime: 1.9 minutes
chg <- stackEddy('/Users/clunch/Desktop/filesToStack00200/', level='dp03', avg=30, useFasttime=T)
dp2 <- stackEddy('/Users/clunch/Desktop/filesToStack00200/', level='dp02', avg=30, useFasttime=T)
Sys.time()
isoTest <- stackEddy(filepath = '/Users/clunch/Desktop/filesToStack00200/',
level = "dp01",
var = c("dlta13CCo2","dlta18OH2o"),
avg = "06", metadata=T)
Sys.time()
# 2.3.0.9200: 14 seconds
# v2.2.1: 14 seconds
isoTestP <- stackEddy(filepath = '/Users/clunch/Desktop/filesP/',
level = "dp01",
var = c("dlta13CCo2","dlta18OH2o"),
avg = "06", metadata=T)
Sys.time()
flux <- stackEddy('/Users/clunch/Desktop/expanded00200/',
level='dp04', metadata=T, useFasttime=T)
Sys.time()
iso <- stackEddy('/Users/clunch/Desktop/expanded00200/',
level="dp01", avg=30, var=c("dlta13CCo2","dlta18OH2o"),
metadata=T, useFasttime=T)
Sys.time()
fx <- stackEddy('/Users/clunch/Desktop/NEON_eddy-flux.zip', level='dp04')
fx <- stackEddy('/Users/clunch/Desktop/NEON_eddy-flux/', level='dp04')
# fancy figures for ambassadors
g <- ggplot(subset(dp1$HARV, !verticalPosition %in% c("co2Zero","co2Med","co2Low","co2High") &
timeBgn < as.POSIXct("2021-06-03", format="%Y-%m-%d")),
aes(y=verticalPosition)) +
geom_path(aes(x=data.co2Stor.rtioMoleDryCo2.mean,
group=hour, col=hour)) +
theme(legend.position="none") +
xlab("CO2") + ylab("Tower level")
g
g <- ggplot(subset(flux$HARV, flux$HARV$timeBgn < as.POSIXct("2021-06-05", format="%Y-%m-%d")),
aes(y=data.fluxCo2.nsae.flux, x=timeBgn)) +
geom_point(size=0.7) +
ylim(-35,20)
g
lhflux <- stackEddy("/Users/clunch/Desktop/filesToStack00200", avg = 30, runLocal = F)
lhflux <- stackEddy("/Users/clunch/Desktop/filesToStack00200", avg = 30, runLocal = T)
lhflux <- stackEddy("/Users/clunch/Desktop/filesToStack00200", avg = 30)
lhflux2 <- stackEddy("/Users/clunch/Desktop/filesToStack00200_half_unzipped/", avg = 30)
alldp01 <- stackEddy("/Users/clunch/Desktop/filesToStack00200", level='dp01', avg = 9)
zipsByProduct(site = "SJER",
dpID = "DP4.00200.001",
startdate = "2019-06",
enddate = "2019-07",
package = "basic",
check.size = F,
savepath = '/Users/clunch/Desktop')
isoTest <- stackEddy(filepath = '/Users/clunch/Desktop/filesToStack00200/',
level = "dp01",
var = c("dlta13CCo2","dlta18OH2o"),
avg = "09")
storTest <- stackEddy(filepath = '/Users/clunch/Desktop/filesToStack00200/',
level = "dp01",
var = c("rtioMoleDryCo2","rtioMoleDryH2o"),
avg = "02")
tempTest <- stackEddy(filepath = '/Users/clunch/Desktop/NEON.D16.ABBY.DP4.00200.001.nsae.2022-08.basic.20230223T233702Z.h5',
level = "dp01",
var = c("co2Stor","temp"),
avg = "30")
zipsByProduct(site = "WREF",
dpID = "DP4.00200.001",
startdate = "2019-06",
enddate = "2019-07",
package = "basic",
check.size = F,
savepath = '/Users/clunch/Desktop')
isoTestW <- stackEddy(filepath = '/Users/clunch/Desktop/filesToStack00200/',
level = "dp01",
var = c("dlta13CCo2","dlta18OH2o"),
avg = "09")
# expanded
zipsByProduct(site = "MOAB",
dpID = "DP4.00200.001",
startdate = "2021-06",
enddate = "2021-06",
package = "expanded",
check.size = F,
release = 'RELEASE-2023',
savepath = '/Users/clunch/Desktop')
flux <- stackEddy('/Users/clunch/Desktop/NEON.D03.OSBS.DP4.00200.001.2019-03.expanded.20210118T143742Z/',
level='dp04')
foot <- footRaster('/Users/clunch/Desktop/filesToStack00200/NEON.D13.MOAB.DP4.00200.001.nsae.2023-10-15.expanded.20231024T164932Z.h5')
foot <- footRaster('/Users/clunch/Desktop/filesToStack00200/NEON.D13.MOAB.DP4.00200.001.2021-06.expanded.20230127T120753Z.RELEASE-2023/NEON.D13.MOAB.DP4.00200.001.nsae.2021-06-03.expanded.20221208T043139Z.h5')
foot <- footRaster('/Users/clunch/Desktop/NEON.D16.ABBY.DP4.00200.001.nsae.2022-05-25.expanded.20221206T174118Z.h5')
terra::contour(foot$MOAB.summary, col=topo.colors(24),
levels=0.001*0:24, filled=TRUE)
terra::contour(foot$MOAB.summary, col=topo.colors(24),
levels=0.001*0:24, filled=TRUE,
xlim=c(640500,641500),
ylim=c(4234000,4235000))
# testing for stackEddy() duplication
dp1 <- stackEddy('/Users/clunch/Desktop/filesToStack00200/', level='dp01', avg=30)
which(duplicated(dp1$MOAB[,c('horizontalPosition','verticalPosition','timeBgn')]))
dp1.1 <- stackEddy(c('/Users/clunch/Desktop/filesToStack00200/NEON.D20.PUUM.DP4.00200.001.nsae.2022-06.basic.20221215T172444Z.h5',
'/Users/clunch/Desktop/filesToStack00200/NEON.D20.PUUM.DP4.00200.001.nsae.2022-07.basic.20220808T195138Z.h5'),
level='dp01', avg=1, useFasttime=T)
which(duplicated(dp1.1$PUUM[,c('horizontalPosition','verticalPosition','timeBgn')]))
dp.dup <- dp1.1$PUUM[which(duplicated(dp1.1$PUUM[,c('horizontalPosition','verticalPosition','timeBgn')])),]
isoTest <- stackEddy(filepath = '/Users/clunch/Desktop/filesToStack00200/',
level = "dp01",
var = c("dlta13CCo2","dlta18OH2o"),
avg = "09", useFasttime=T)
isoTest <- stackEddy(filepath = '/Users/clunch/Desktop/NEON_eddy-flux/',
level = "dp01",
var = c("dlta13CCo2","dlta18OH2o"),
avg = 9, useFasttime=T)
which(duplicated(isoTest$SJER[,c('horizontalPosition','verticalPosition','timeBgn')]))
# BAD!
# same in v2.2.1
# this is happening because 13C data have been moved to a 6-min sampling interval, but
# tables are still named 9min. Tables will be renamed in RELEASE-2024
# for 2022-05 to -07 PUUM, the timeBgn stamps also don't match, so it's fine
# citation
stackByTable('/Users/clunch/Desktop/NEON_count-plant-aqu.zip')
stackByTable('/Users/clunch/Desktop/NEON_pressure-air.zip')
stackByTable('/Users/clunch/Desktop/NEON_par-quantum-line.zip')
stackByTable('/Users/clunch/Desktop/NEON_gp.zip')
stackByTable('/Users/clunch/Downloads/NEON_pressure-air (1).zip')
wq <- loadByProduct(dpID = 'DP1.20288.001',
site = c('WALK'), startdate = '2021-03',
enddate = '2021-06', check.size = F,
package = 'expanded',
token=Sys.getenv('NEON_TOKEN'))
zipsByProduct(dpID = 'DP1.20288.001',
site = c('SYCA'), startdate = '2020-02',
enddate = '2020-09', check.size = F,
savepath='/Users/clunch/Desktop',
token=Sys.getenv('NEON_TOKEN'))
# modified file to mimic changing a field name
wq <- stackByTable('/Users/clunch/Desktop/filesToStack20288',
savepath='envt')
# token testing
waq <- loadByProduct(dpID='DP1.20288.001', site=c('ARIK','HOPB'),
startdate='2017-03', enddate='2018-03',
package='expanded', check.size=F, token=Sys.getenv('NEON_TOKEN'))
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = "2017",
easting = c(571000,743000,578000),
northing = c(5079000,3984000,5080000),
savepath='/Users/clunch/Desktop', check.size = FALSE,
token=Sys.getenv('NEON_TOKEN'))
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = "2017",
easting = c(571000,578000),
northing = c(5079000,5080000),
savepath='/Users/clunch/Desktop', check.size = FALSE,
token=Sys.getenv('NEON_TOKEN'))
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = "2017",
easting = c(571000,578000),
northing = c(5079000,5080000),
savepath='/Users/clunch/Desktop', check.size = FALSE,
token=NA)
# fake dpID
byTileAOP(dpID = "DP3.30467.001", site = "WREF", year = "2017",
easting = c(571000,743000,578000),
northing = c(5079000,3984000,5080000),
savepath='/Users/clunch/Desktop', check.size = FALSE,
token=Sys.getenv('NEON_TOKEN'))
# multiple months per year
byFileAOP(dpID='DP3.30015.001', site='KONZ', year=2019,
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
# multiple months per year
byTileAOP(dpID='DP3.30015.001', site='CPER', year=2020,
easting = c(523300,519700),
northing = c(4513400,4518400),
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
byFileAOP(dpID='DP3.30015.001', site='STEI', year=2022,
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
byFileAOP(dpID='DP3.30025.001', site='SCBI', year=2017,
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
byFileAOP(dpID='DP1.30006.001', site='SJER', year=2021,
savepath='/Users/clunch/Dropbox/data/NEON data/AOP/', token=Sys.getenv('NEON_TOKEN'))
zipsByProduct(dpID='DP1.10098.001', site=c('WREF','ABBY'),
startdate='2019-01', enddate='2019-12',
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
stackByTable('/Users/clunch/Desktop/filesToStack10098')
zipsByProduct(dpID='DP1.10098.001', site=c('WREF','ABBY'),
startdate='2019-01', enddate='2019-12', release='RELEASE-2022',
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
stackByTable('/Users/clunch/Desktop/filesToStack10098')
# test Aqu shared site code
pcp <- loadByProduct(dpID='DP1.00006.001', site=c('KING','BLDE','ARIK','MCRA','PRPO'),
startdate='2019-07', enddate='2019-08', timeIndex=30,
check.size=F, token=Sys.getenv('NEON_TOKEN'))
part <- loadByProduct(dpID='DP1.00024.001', site=c('KING','BLWA','ARIK','MCRA','TOMB'),
startdate='2019-07', enddate='2019-08', timeIndex=30,
check.size=F, token=Sys.getenv('NEON_TOKEN'))
# should not alert anything:
part <- loadByProduct(dpID='DP1.00024.001', site=c('KING','ARIK','MCRA'),
startdate='2019-07', enddate='2019-08', timeIndex=30,
check.size=F, token=Sys.getenv('NEON_TOKEN'))
# test chem bundle handling
root <- loadByProduct(dpID='DP1.10102.001') # should error
ntrans <- loadByProduct(dpID='DP1.10078.001', check.size=F, token=Sys.getenv('NEON_TOKEN'))
# 2D wind table name
wind <- loadByProduct(dpID='DP1.00001.001', site='NIWO',
startdate='2020-05', enddate='2020-07',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
# DATA_FRAME handling
scc <- loadByProduct(dpID = 'DP1.10081.001',
startdate = '2018-06',
enddate = '2019-06',
check.size = FALSE,
token = Sys.getenv('NEON_TOKEN'),
package = 'expanded')
scc <- loadByProduct(dpID = 'DP1.10081.002',
startdate = '2021-06',
enddate = '2022-06',
site=c('NIWO','WREF','HARV'),
check.size = FALSE,
token = Sys.getenv('NEON_TOKEN'),
package = 'expanded',
include.provisional = T)
bcc <- loadByProduct(dpID = 'DP1.20086.001',
startdate = '2018-06',
enddate = '2019-06',
check.size = FALSE,
token = Sys.getenv('NEON_TOKEN'),
package = 'expanded')
wcc <- loadByProduct(dpID = 'DP1.20141.001',
startdate = '2018-06',
enddate = '2018-12',
check.size = FALSE,
token = Sys.getenv('NEON_TOKEN'),
package = 'expanded')
fsp <- loadByProduct(dpID='DP1.30012.001',
check.size=F,
package='expanded',
token = Sys.getenv('NEON_TOKEN'))
# more with microbes
smg <- loadByProduct(dpID='DP1.10107.001', startdate='2018-05', enddate='2018-07',
package='expanded', check.size=F, token=Sys.getenv('NEON_TOKEN'))
# LOV files
rea <- loadByProduct(dpID='DP1.20190.001', site='WALK', check.size=F)
zipsByProduct(dpID='DP1.20190.001', savepath='/Users/clunch/Desktop')
tpth <- loadByProduct(dpID='DP1.10092.001', site=c('KONZ','KONA'), startdate='2015-01',
enddate='2019-12', check.size=F, token=Sys.getenv('NEON_TOKEN'),
useFasttime=T)
waq <- loadByProduct(dpID='DP1.20288.001', site=c('ARIK','HOPB'),
startdate='2022-09', enddate='2022-11',
package='expanded', check.size=F, useFasttime=T)
byTileAOP(dpID = "DP3.30006.001", site = "ORNL", year = "2016",
easting = 744000, northing = 983000, check.size = FALSE)
byTileAOP(dpID = "DP3.30006.001", site = "ORNL", year = "2016",
easting = c(743000,747000),
northing = c(3984000,3984000),
savepath='/Users/clunch/Desktop', check.size = FALSE)
byTileAOP(dpID = "DP3.30025.001", site = "ORNL", year = "2016",
easting = c(743000,747000),
northing = c(3984000,3984000),
savepath='/Users/clunch/Desktop', check.size = FALSE)
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = "2017",
easting = c(571000,743000,578000),
northing = c(5079000,3984000,5080000),
savepath='/Users/clunch/Desktop',
check.size = FALSE, token=Sys.getenv('NEON_TOKEN'))
byTileAOP(dpID = "DP3.30025.001", site = "WREF", year = "2017",
easting = c(571000,578000),
northing = c(5079000,5080000),
savepath='/Users/clunch/Desktop',
check.size = FALSE, token='garbage')
byFileAOP(dpID='DP3.30015.001', site='SJER', year=2017, check.size=F,
savepath='/Users/clunch/Desktop')
byFileAOP(dpID='DP3.30019.001', site='OAES', year=2019, check.size=F,
savepath='/Users/clunch/Desktop')
# sites that are flown under another site's name
byFileAOP(dpID='DP3.30015.001', site='TREE', year=2017, check.size=F,
savepath='/Users/clunch/Desktop')
# sites that are flown under another site's name
byTileAOP(dpID='DP3.30025.001', site='SUGG', year=2018,
easting=c(401890,401930), northing=c(3284680,3284690),
savepath='/Users/clunch/Desktop')
# test for Blandy UTM zones
veg <- loadByProduct(dpID='DP1.10098.001', site='BLAN', check.size=F)
veg.loc <- geoNEON::getLocTOS(veg$vst_mappingandtagging, 'vst_mappingandtagging')
veg.temp <- geoNEON::getLocByName(veg$vst_mappingandtagging, locCol='namedLocation', locOnly=T)
ea <- veg.loc$adjEasting[which(!is.na(veg.loc$adjEasting))]
no <- veg.loc$adjNorthing[which(!is.na(veg.loc$adjNorthing))]
ea <- veg.temp$easting
no <- veg.temp$northing
byTileAOP(dpID='DP3.30015.001', site='BLAN', year=2017,
easting=ea, northing=no, buffer=10, savepath='/Users/clunch/Desktop')
# I got 5 tiles. Is that right??
blan1 <- terra::rast('/Users/clunch/Desktop/DP3.30015.001/neon-aop-products/2017/FullSite/D02/2017_BLAN_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D02_BLAN_DP3_752000_4327000_CHM.tif')
blan2 <- terra::rast('/Users/clunch/Desktop/DP3.30015.001/neon-aop-products/2017/FullSite/D02/2017_BLAN_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D02_BLAN_DP3_753000_4327000_CHM.tif')
blan3 <- terra::rast('/Users/clunch/Desktop/DP3.30015.001/neon-aop-products/2017/FullSite/D02/2017_BLAN_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D02_BLAN_DP3_761000_4330000_CHM.tif')
blan4 <- terra::rast('/Users/clunch/Desktop/DP3.30015.001/neon-aop-products/2017/FullSite/D02/2017_BLAN_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D02_BLAN_DP3_762000_4330000_CHM.tif')
blan5 <- terra::rast('/Users/clunch/Desktop/DP3.30015.001/neon-aop-products/2017/FullSite/D02/2017_BLAN_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D02_BLAN_DP3_763000_4330000_CHM.tif')
blan <- terra::merge(blan1, blan2, blan3, blan4, blan5)
terra::plot(blan)
# yes, this is right
# test for data download that should take >1 hour
Sys.time()
byFileAOP(dpID='DP1.30006.001', site='HARV', year=2017, check.size=F,
savepath='/Users/clunch/Desktop')
# with token
byFileAOP(dpID='DP1.30006.001', site='HARV', year=2017, check.size=F,
savepath='/Users/clunch/Desktop', token=Sys.getenv('NEON_TOKEN'))
# test for data download that should take >1 hour
Sys.time()
zipsByProduct(dpID='DP4.00200.001', site='all', check.size=F,
savepath='/Users/clunch/Desktop')
csd <- loadByProduct(dpID='DP4.00130.001', site=c('WLOU','BLUE'),
startdate='2019-04', enddate='2020-03',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
st <- loadByProduct(dpID='DP1.20206.001', token=Sys.getenv('NEON_TOKEN'))
st <- loadByProduct(dpID='DP1.20206.001', startdate='2020-05',
enddate='2021-07', token=Sys.getenv('NEON_TOKEN'),
check.size=F)
fs <- loadByProduct(dpID='DP1.30012.001', check.size=F)
pr <- loadByProduct(dpID='DP1.00024.001', site=c('WREF','ABBY'),
startdate='2019-12', enddate='2020-08')
saat <- loadByProduct(dpID='DP1.00002.001', site=c('CPER','NIWO'),
startdate='2022-05', enddate='2022-08',
check.size=F)
tick <- loadByProduct(dpID='DP1.10093.001', site=c('WREF','ABBY'),
startdate='2021-07', enddate='2022-06', check.size=F)
tick <- loadByProduct(dpID='DP1.10093.001', site=c('WREF','ABBY'),
startdate='2021-01', enddate='2021-12', check.size=F)
tick <- loadByProduct(dpID='DP1.10093.001', site=c('WREF','ABBY'),
startdate='2022-01', enddate='2022-12', check.size=F)
tick <- loadByProduct(dpID='DP1.10093.001', site=c('WREF','ABBY'),
startdate='2021-07', enddate='2022-06',
include.provisional=T, check.size=F)
brd <- loadByProduct(dpID='DP1.10003.001', check.size=F, token=Sys.getenv('NEON_TOKEN'))
brd <- loadByProduct(dpID='DP1.10003.001', site=c('WREF','ABBY'), package='expanded',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
brd.p <- loadByProduct(dpID='DP1.10003.001', site=c('WREF','ABBY'), package='expanded',
include.provisional=TRUE,
check.size=F, token=Sys.getenv('NEON_TOKEN'))
brd.p <- loadByProduct(dpID='DP1.10003.001', site=c('WREF','ABBY'), package='expanded',
include.provisional=TRUE, release='PROVISIONAL',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
fish <- loadByProduct(dpID='DP1.20107.001', site='MART',
include.provisional=T, check.size=F,
token=Sys.getenv('NEON_TOKEN'))
ltr <- loadByProduct(dpID='DP1.10033.001',
startdate='2020-02', enddate='2022-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
div <- loadByProduct(dpID='DP1.10058.001',
startdate='2020-02', enddate='2022-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
veg <- loadByProduct(dpID='DP1.10098.001',
startdate='2020-04', enddate='2020-04',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
veg <- loadByProduct(dpID='DP1.10098.001',
startdate='2020-04', enddate='2020-04',
release='LATEST', include.provisional=T,
check.size=F, token=Sys.getenv('LATEST_TOKEN'))
cfc <- loadByProduct(dpID='DP1.10026.001', package='expanded',
check.size=F, nCores=1, token=Sys.getenv('NEON_TOKEN'))
cfc <- loadByProduct(dpID='DP1.10026.001', package='expanded',
startdate='2020-01', enddate='2022-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'))
gwe <- loadByProduct(dpID='DP1.20100.001', site=c('MART','WLOU'),
startdate='2019-07', enddate='2019-09', check.size=F, nCores=3)
swe <- loadByProduct(dpID='DP1.20016.001', site=c('MART','WLOU'),
startdate='2019-07', enddate='2019-09', check.size=F, nCores=2)
wch <- loadByProduct(dpID='DP1.20093.001', site=c('ARIK','POSE'),
package='expanded', check.size=F)