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NEON_methods_script.R
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NEON_methods_script.R
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#https://github.com/NEONScience/NEON-water-chemistry-grab-samples/blob/main/linkingSummaryDataScrip/linkSummaryDataToLabData.R
waterChemList <-
neonUtilities::loadByProduct(
dpID = "DP1.20093.001",
site = "CRAM",
package = 'expanded',
check.size = FALSE
)
externalLabData <- waterChemList$swc_externalLabDataByAnalyte
externalSummaryData <- waterChemList$swc_externalLabSummaryData
externalSummaryData$labSpecificEndDate[is.na(externalSummaryData$labSpecificEndDate)] <-
as.POSIXct(Sys.Date())
#Check that the analytes match
externalLabData$analyte[!externalLabData$analyte %in% externalSummaryData$analyte]
#Link the data by analyte
namesToAdd <-
names(externalSummaryData)[!(names(externalSummaryData) %in% names(externalLabData))]
namesToAdd <- namesToAdd[!(namesToAdd %in% c("endDate"))]
externalLabData[, namesToAdd] <- NA
for (i in 1:nrow(externalSummaryData)) {
currStartDate <- externalSummaryData$labSpecificStartDate[i]
currEndDate <- externalSummaryData$labSpecificEndDate[i]
currAnalyte <- externalSummaryData$analyte[i]
currLab <- externalSummaryData$laboratoryName[i]
externalLabData[(
externalLabData$startDate >= currStartDate &
externalLabData$startDate < currEndDate &
externalLabData$analyte == currAnalyte &
externalLabData$laboratoryName == currLab
), namesToAdd] <- externalSummaryData[i, namesToAdd]
}
CRAM<-externalLabData
waterChemList <-
neonUtilities::loadByProduct(
dpID = "DP1.20093.001",
site = "BARC",
package = 'expanded',
check.size = FALSE
)
externalLabData <- waterChemList$swc_externalLabDataByAnalyte
externalSummaryData <- waterChemList$swc_externalLabSummaryData
externalSummaryData$labSpecificEndDate[is.na(externalSummaryData$labSpecificEndDate)] <-
as.POSIXct(Sys.Date())
#Check that the analytes match
externalLabData$analyte[!externalLabData$analyte %in% externalSummaryData$analyte]
#Link the data by analyte
namesToAdd <-
names(externalSummaryData)[!(names(externalSummaryData) %in% names(externalLabData))]
namesToAdd <- namesToAdd[!(namesToAdd %in% c("endDate"))]
externalLabData[, namesToAdd] <- NA
for (i in 1:nrow(externalSummaryData)) {
currStartDate <- externalSummaryData$labSpecificStartDate[i]
currEndDate <- externalSummaryData$labSpecificEndDate[i]
currAnalyte <- externalSummaryData$analyte[i]
currLab <- externalSummaryData$laboratoryName[i]
externalLabData[(
externalLabData$startDate >= currStartDate &
externalLabData$startDate < currEndDate &
externalLabData$analyte == currAnalyte &
externalLabData$laboratoryName == currLab
), namesToAdd] <- externalSummaryData[i, namesToAdd]
}
BARC<-externalLabData
waterChemList <-
neonUtilities::loadByProduct(
dpID = "DP1.20093.001",
site = "LIRO",
package = 'expanded',
check.size = FALSE
)
externalLabData <- waterChemList$swc_externalLabDataByAnalyte
externalSummaryData <- waterChemList$swc_externalLabSummaryData
externalSummaryData$labSpecificEndDate[is.na(externalSummaryData$labSpecificEndDate)] <-
as.POSIXct(Sys.Date())
#Check that the analytes match
externalLabData$analyte[!externalLabData$analyte %in% externalSummaryData$analyte]
#Link the data by analyte
namesToAdd <-
names(externalSummaryData)[!(names(externalSummaryData) %in% names(externalLabData))]
namesToAdd <- namesToAdd[!(namesToAdd %in% c("endDate"))]
externalLabData[, namesToAdd] <- NA
for (i in 1:nrow(externalSummaryData)) {
currStartDate <- externalSummaryData$labSpecificStartDate[i]
currEndDate <- externalSummaryData$labSpecificEndDate[i]
currAnalyte <- externalSummaryData$analyte[i]
currLab <- externalSummaryData$laboratoryName[i]
externalLabData[(
externalLabData$startDate >= currStartDate &
externalLabData$startDate < currEndDate &
externalLabData$analyte == currAnalyte &
externalLabData$laboratoryName == currLab
), namesToAdd] <- externalSummaryData[i, namesToAdd]
}
LIRO<-externalLabData
waterChemList <-
neonUtilities::loadByProduct(
dpID = "DP1.20093.001",
site = "PRLA",
package = 'expanded',
check.size = FALSE
)
externalLabData <- waterChemList$swc_externalLabDataByAnalyte
externalSummaryData <- waterChemList$swc_externalLabSummaryData
externalSummaryData$labSpecificEndDate[is.na(externalSummaryData$labSpecificEndDate)] <-
as.POSIXct(Sys.Date())
#Check that the analytes match
externalLabData$analyte[!externalLabData$analyte %in% externalSummaryData$analyte]
#Link the data by analyte
namesToAdd <-
names(externalSummaryData)[!(names(externalSummaryData) %in% names(externalLabData))]
namesToAdd <- namesToAdd[!(namesToAdd %in% c("endDate"))]
externalLabData[, namesToAdd] <- NA
for (i in 1:nrow(externalSummaryData)) {
currStartDate <- externalSummaryData$labSpecificStartDate[i]
currEndDate <- externalSummaryData$labSpecificEndDate[i]
currAnalyte <- externalSummaryData$analyte[i]
currLab <- externalSummaryData$laboratoryName[i]
externalLabData[(
externalLabData$startDate >= currStartDate &
externalLabData$startDate < currEndDate &
externalLabData$analyte == currAnalyte &
externalLabData$laboratoryName == currLab
), namesToAdd] <- externalSummaryData[i, namesToAdd]
}
PRLA<-externalLabData
waterChemList <-
neonUtilities::loadByProduct(
dpID = "DP1.20093.001",
site = "SUGG",
package = 'expanded',
check.size = FALSE
)
externalLabData <- waterChemList$swc_externalLabDataByAnalyte
externalSummaryData <- waterChemList$swc_externalLabSummaryData
externalSummaryData$labSpecificEndDate[is.na(externalSummaryData$labSpecificEndDate)] <-
as.POSIXct(Sys.Date())
#Check that the analytes match
externalLabData$analyte[!externalLabData$analyte %in% externalSummaryData$analyte]
#Link the data by analyte
namesToAdd <-
names(externalSummaryData)[!(names(externalSummaryData) %in% names(externalLabData))]
namesToAdd <- namesToAdd[!(namesToAdd %in% c("endDate"))]
externalLabData[, namesToAdd] <- NA
for (i in 1:nrow(externalSummaryData)) {
currStartDate <- externalSummaryData$labSpecificStartDate[i]
currEndDate <- externalSummaryData$labSpecificEndDate[i]
currAnalyte <- externalSummaryData$analyte[i]
currLab <- externalSummaryData$laboratoryName[i]
externalLabData[(
externalLabData$startDate >= currStartDate &
externalLabData$startDate < currEndDate &
externalLabData$analyte == currAnalyte &
externalLabData$laboratoryName == currLab
), namesToAdd] <- externalSummaryData[i, namesToAdd]
}
SUGG<-externalLabData
waterChemList <-
neonUtilities::loadByProduct(
dpID = "DP1.20093.001",
site = "TOOK",
package = 'expanded',
check.size = FALSE
)
externalLabData <- waterChemList$swc_externalLabDataByAnalyte
externalSummaryData <- waterChemList$swc_externalLabSummaryData
externalSummaryData$labSpecificEndDate[is.na(externalSummaryData$labSpecificEndDate)] <-
as.POSIXct(Sys.Date())
#Check that the analytes match
externalLabData$analyte[!externalLabData$analyte %in% externalSummaryData$analyte]
#Link the data by analyte
namesToAdd <-
names(externalSummaryData)[!(names(externalSummaryData) %in% names(externalLabData))]
namesToAdd <- namesToAdd[!(namesToAdd %in% c("endDate"))]
externalLabData[, namesToAdd] <- NA
for (i in 1:nrow(externalSummaryData)) {
currStartDate <- externalSummaryData$labSpecificStartDate[i]
currEndDate <- externalSummaryData$labSpecificEndDate[i]
currAnalyte <- externalSummaryData$analyte[i]
currLab <- externalSummaryData$laboratoryName[i]
externalLabData[(
externalLabData$startDate >= currStartDate &
externalLabData$startDate < currEndDate &
externalLabData$analyte == currAnalyte &
externalLabData$laboratoryName == currLab
), namesToAdd] <- externalSummaryData[i, namesToAdd]
}
TOOK<-externalLabData
all_data<-rbind(CRAM,BARC,LIRO,PRLA,TOOK,SUGG)
unique(all_data$laboratoryName)
write.csv(all_data,"NEON_chemandmethods_data.csv")