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no_testing.R
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library(devtools)
library(urlchecker)
library(neonUtilities)
setwd("~/GitHub/NEON-OS-data-processing/neonOS")
install('.')
library(neonOS)
check()
url_check()
# removeDups() testing
cfc <- loadByProduct(dpID='DP1.10026.001', check.size=F,
startdate='2017-05', enddate='2019-08',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
cfc.cn <- removeDups(cfc$cfc_chlorophyll, variables=cfc$variables_10026, table='cfc_chlorophyll')
# only one field in primary key
secchi <- loadByProduct(dpID='DP1.20252.001', check.size=F,
startdate='2017-05', enddate='2019-08',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
list2env(secchi, .GlobalEnv)
sec.d <- removeDups(dep_secchi, variables=variables_20252)
# test expanded package error
cfc <- loadByProduct(dpID='DP1.10026.001', check.size=F,
startdate='2017-05', enddate='2019-08',
token=Sys.getenv('NEON_TOKEN'))
cfc.cn <- removeDups(cfc$cfc_chlorophyll, variables=cfc$variables_10026, table='cfc_chlorophyll')
cfc.dum <- removeDups(cfc$cfc_chlorophyll, variables=cfc$variables_10026, table='cfc_elements')
bird <- loadByProduct(dpID='DP1.10003.001', check.size=F,
startdate='2022-05', enddate='2023-08',
include.provisional = T,
package='expanded', token=Sys.getenv('NEON_TOKEN'))
list2env(bird, .GlobalEnv)
brd.d <- removeDups(brd_countdata, variables=variables_10003)
fish <- loadByProduct(dpID='DP1.20107.001', check.size=F,
startdate='2017-05', enddate='2019-08',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
fish.d <- removeDups(fish$fsh_fieldData, variables=fish$variables_20107, table='fsh_fieldData')
fish.p <- removeDups(fish$fsh_perPass, variables=fish$variables_20107, table='fsh_perPass')
fish.f <- removeDups(fish$fsh_perFish, variables=fish$variables_20107, table='fsh_perFish')
dust <- loadByProduct(dpID='DP1.00101.001', check.size=F, startdate='2017-05', enddate='2019-06')
dpm.d <- removeDups(dust$dpm_lab, variables=dust$variables_00101, table='dpm_lab')
# mammals
mam <- loadByProduct(dpID='DP1.10072.001', site='JERC', startdate='2016-01', enddate='2017-12',
package='expanded', check.size=F, token=Sys.getenv('NEON_TOKEN'))
mam.dup.plot <- removeDups(mam$mam_perplotnight, variables=mam$variables_10072, table='mam_perplotnight')
mam.dup.trap <- removeDups(mam$mam_pertrapnight, variables=mam$variables_10072, table='mam_pertrapnight')
# joinTableNEON() testing
mam.all <- joinTableNEON(mam.dup.plot, mam.dup.trap,
name1="mam_perplotnight",
name2="mam_pertrapnight")
# error for incorrect name inputs
mam.all <- joinTableNEON(mam.dup.plot, mam.dup.trap,
name1=mam_perplotnight,
name2=mam_pertrapnight)
# no names when they're needed
mam.all <- joinTableNEON(mam.dup.plot, mam.dup.trap)
cfc <- loadByProduct(dpID='DP1.10026.001', check.size=F,
startdate='2019-05', enddate='2021-08',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
list2env(cfc, .GlobalEnv)
tst <- joinTableNEON(cfc_fieldData, cfc_elements)
tst <- joinTableNEON(cfc_fieldData, cfc_carbonNitrogen)
# left join special case
tst <- joinTableNEON(cfc_fieldData, vst_mappingandtagging)
# override left join
tst <- joinTableNEON(cfc_fieldData, vst_mappingandtagging, left.join=F)
bird <- loadByProduct(dpID='DP1.10003.001', check.size=F,
startdate='2017-05', enddate='2019-08',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
list2env(bird, .GlobalEnv)
tst <- joinTableNEON(brd_countdata, brd_personnel)
tst <- joinTableNEON(brd_perpoint, brd_personnel)
tst <- joinTableNEON(brd_references, brd_personnel)
tst <- joinTableNEON(brd_countdata, brd_perpoint)
# location fields = F special case
sdg <- loadByProduct(dpID='DP1.20097.001', check.size=F,
startdate='2019-05', enddate='2019-10',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
list2env(sdg, .GlobalEnv)
tst <- joinTableNEON(sdg_fieldDataProc, sdg_fieldDataAir)
# recent data only special case
tck <- loadByProduct(dpID='DP1.10092.001', check.size=F,
startdate='2020-01',
package='expanded', token=Sys.getenv('NEON_TOKEN'))
list2env(tck, .GlobalEnv)
tst <- joinTableNEON(tck_pathogen, tck_pathogenqa)
tck_pathogen <- tck_pathogen[tck_pathogen$collectDate>as.POSIXct("2021-01-01"),] # no 2021 data yet
mos <- loadByProduct(dpID="DP1.10043.001",
site="TOOL",
release="RELEASE-2022",
token=Sys.getenv('NEON_TOKEN'),
check.size=F)
inv <- loadByProduct(dpID="DP1.20120.001",
site="TOOK",
release="RELEASE-2022",
token=Sys.getenv('NEON_TOKEN'),
check.size=F)
# getSampleTree() testing
sampleNode <- "BLDE.SS.20181002"
idType <- "tag"
sampleClass <- "swc.asi.sdg.amc"
token <- Sys.getenv('NEON_TOKEN')
algs <- getSampleTree(sampleNode='BLDE.SS.20181002', idType='tag',
sampleClass='swc.asi.sdg.amc', token=Sys.getenv('NEON_TOKEN'))
# should exit with sampleClass info:
algs <- getSampleTree('BLDE.SS.20181002', idType='tag',
token=Sys.getenv('NEON_TOKEN'))
# plant div
div <- loadByProduct(dpID='DP1.10058.001', site='ABBY',
startdate='2019-01', enddate='2019-12',
package='expanded', check.size=F,
token=Sys.getenv('NEON_TOKEN'))
div.all <- merge(div$div_1m2Data, div$div_10m2Data100m2Data, by='eventID') # NOPE
## taxa
t <- getTaxonList('FISH')
t <- getTaxonList('FISH', verbose='true')
p <- getTaxonList('PLANT', verbose='true', recordReturnLimit=15)
m <- getTaxonList('SMALL_MAMMAL', stream='false')
m <- getTaxonList('SMALL_MAMMAL', stream='true')
# join recursion
mamdat <- loadByProduct(dpID="DP1.10072.001",
site=c("SCBI", "SRER", "UNDE"),
package="basic",
check.size = FALSE,
startdate = "2021-01",
enddate = "2022-12")
list2env(mamdat, .GlobalEnv)
mam_perplotnight <- removeDups(mam_perplotnight, variables=variables_10072)
mam_pertrapnight <- removeDups(mam_pertrapnight, variables=variables_10072)
mam.f <- joinTableNEON(mam_perplotnight, mam_pertrapnight)
apc_allTabs <- loadByProduct(
dpID='DP1.20072.001',
check.size=F,
site = "all",
package='expanded',
startdate = '2021-07',
enddate = '2021-07',
token = Sys.getenv('NEON_TOKEN'))
list2env(apc_allTabs, envir=.GlobalEnv)
removeDups(data = apc_taxonomyRaw, variables = variables_20072)
View(apc_taxonomyRaw)
veg <- loadByProduct(dpID='DP1.10098.001',
startdate='2019-01', enddate='2020-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'),
include.provisional=T)
vdup <- removeDups(veg$vst_apparentindividual, variables=veg$variables_10098,
table='vst_apparentindividual')
veg2021 <- loadByProduct(dpID='DP1.10098.001',
startdate='2021-01', enddate='2021-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'),
include.provisional=T)
vdup2021 <- removeDups(veg2021$vst_apparentindividual, variables=veg2021$variables_10098,
table='vst_apparentindividual')
vdup2021 <- removeDups(veg2021$vst_apparentindividual, variables=veg2021$variables_10098,
table='vst_apparentindividual', ncores=5)
saveRDS(vdup2021, '/Users/clunch/Desktop/vdups.rds')
vdups <- readRDS('/Users/clunch/Desktop/vdups.rds')
all(vdups==vdup2021, na.rm=T)
vsub <- vdups[which(vdups$duplicateRecordQF!=0),]
vpsub <- vdup2021[which(vdup2021$duplicateRecordQF!=0),]
vkeys <- unique(vsub[,c('eventID', 'individualID', 'tempStemID')])
vpkeys <- unique(vpsub[,c('eventID', 'individualID', 'tempStemID')])
vkeys <- vkeys[order(vkeys$individualID),]
vpkeys <- vpkeys[order(vpkeys$individualID),]
all(vkeys==vpkeys)
which(vkeys!=vpkeys, arr.ind=T)
vkeys[263:265,]
max(veg$vst_apparentindividual$date[which(!is.na(veg$vst_apparentindividual$tempStemID))])
length(which(!is.na(veg$vst_apparentindividual$tempStemID)))
nrow(veg$vst_apparentindividual)
max(veg$vst_apparentindividual$date[which(is.na(veg$vst_apparentindividual$tempStemID))])
temp <- veg$vst_apparentindividual[which(is.na(veg$vst_apparentindividual$tempStemID)),]
mam <- loadByProduct(dpID='DP1.10072.001', site=c('HARV','BART','SJER','SOAP','HEAL'),
startdate='2015-01', enddate='2021-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'),
include.provisional=T)
mdup <- removeDups(mam$mam_pertrapnight, variables=mam$variables_10072,
table='mam_pertrapnight', ncores=5)
mdup1 <- removeDups(mam$mam_pertrapnight, variables=mam$variables_10072,
table='mam_pertrapnight')
all(mdup==mdup1, na.rm=T)
saveRDS(mdup, '/Users/clunch/Desktop/mamdups.rds')
mamdups <- readRDS('/Users/clunch/Desktop/mamdups.rds')
unique(mam$mam_pertrapnight$trapStatus)
gr <- mam$mam_pertrapnight[grep("X", mam$mam_pertrapnight$trapCoordinate),]
mult <- mam$mam_pertrapnight[grep("4", mam$mam_pertrapnight$trapStatus),]
# parallel
phe <- loadByProduct(dpID='DP1.10055.001', site='SJER',
startdate='2023-01', enddate='2023-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'),
include.provisional=T)
Sys.time()
pdup <- removeDups(phe$phe_statusintensity, variables=phe$variables_10055,
table='phe_statusintensity', ncores=6)
Sys.time()
saveRDS(pdup, '/Users/clunch/Desktop/phedups.rds')
phedups <- readRDS('/Users/clunch/Desktop/phedups.rds')
all(pdup$duplicateRecordQF==phedups$duplicateRecordQF)
all(pdup==phedups, na.rm=T)
fish <- loadByProduct(dpID='DP1.20107.001', package='expanded',
startdate='2016-01', enddate='2018-12',
check.size=F, token=Sys.getenv('NEON_TOKEN'),
include.provisional=T)
fpdup <- removeDups(fish$fsh_perFish, variables=fish$variables_20107,
table='fsh_perFish', ncores=6)
fpdup1 <- removeDups(fish$fsh_perFish, variables=fish$variables_20107,
table='fsh_perFish')
all(fpdup==fpdup1, na.rm=T)
saveRDS(fpdup, '/Users/clunch/Desktop/fishdups.rds')
fpdup <- readRDS('/Users/clunch/Desktop/fishdups.rds')