NEON_workshop_day_1
D. S. Fernandez del Viso
9/19/2019
Contact information
address: ORCID
Packages installed:
- neonUtilities
- raster
- BiocManager
- devtools
Script to download NEON data
Instalation instructions
Activate packages and set global options
# load packages
library(neonUtilities)
library(geoNEON)
library(raster)## Loading required package: splibrary(rhdf5)
# Set global option to NOT convert all character variables to factors
options(stringsAsFactors=F)put together files with stack
Put the downloaded zip file in the working directory.
If the folder is un-zipped, use the folder name without the .zip extension.
stackByTable(filepath="NEON_par.zip")## Unpacking zip files
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## Stacking table PARPAR_1min
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## Stacking table PARPAR_30min
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## Finished: All of the data are stacked into 2 tables!
## Copied the first available variable definition file to /stackedFiles and renamed as variables.csv
## Stacked PARPAR_1min which has 803520 out of the expected 803520 rows (100%).
## Stacked PARPAR_30min which has 26784 out of the expected 26784 rows (100%).
## Stacking took 29.58059 secs
## All unzipped monthly data folders have been removed.download data via API
Need the DataProduct ID the API does not need token authentication.
# woody plant vegetation structure
zipsByProduct(dpID = "DP1.10098.001", site = "WREF", startdate = "2012-01", enddate = "2019-09", check.size = F)## Warning in dir.create(filepath): '/Users/dsfernandez/Documents/R/NEON/
## filesToStack10098' already exists## Downloading 2 files
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## 2 files downloaded to /Users/dsfernandez/Documents/R/NEON/filesToStack10098# stack the zip
stackByTable("filesToStack10098", folder = T)## Unpacking zip files
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## T): error 1 in extracting from zip file## Warning in file.remove(p): cannot remove file 'filesToStack10098/
## stackedFiles', reason 'Directory not empty'##
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## Stacking table vst_apparentindividual
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## Stacking table vst_mappingandtagging
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## Stacking table vst_perplotperyear
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## Finished: All of the data are stacked into 3 tables!
## Copied the first available variable definition file to /stackedFiles and renamed as variables.csv
## Copied the first available validation file to /stackedFiles and renamed as validation.csv
## Stacked vst_apparentindividual which has 2431 out of the expected 2431 rows (100%).
## Stacked vst_mappingandtagging which has 2263 out of the expected 2263 rows (100%).
## Stacked vst_perplotperyear which has 20 out of the expected 20 rows (100%).
## Stacking took 0.147789 secs
## All unzipped monthly data folders have been removed.Using R project
create object veg (a list) with the files
veg <- loadByProduct(dpID = "DP1.10098.001", site = "WREF", startdate = "2012-01", enddate = "2019-09", check.size = F)## Downloading 2 files
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## Unpacking zip files
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## Stacking table vst_apparentindividual
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## Stacking table vst_mappingandtagging
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## Stacking table vst_perplotperyear
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## Finished: All of the data are stacked into 3 tables!
## Copied the first available variable definition file to /stackedFiles and renamed as variables.csv
## Copied the first available validation file to /stackedFiles and renamed as validation.csv
## Stacked vst_apparentindividual which has 2431 out of the expected 2431 rows (100%).
## Stacked vst_mappingandtagging which has 2263 out of the expected 2263 rows (100%).
## Stacked vst_perplotperyear which has 20 out of the expected 20 rows (100%).
## Stacking took 0.1308298 secs
## All unzipped monthly data folders have been removed.mapping <- veg$vst_mappingandtagging
View(mapping)## Warning in system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE):
## running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/
## Resources/modules/R_de.so'' had status 1remote sensing data
No function to download data directly to R, could be an overload. Use selected tiles to download.
# savepath default is the current directory
byTileAOP(dpID = "DP3.30015.001", site = "WREF", year = "2017", easting=580000, northing=5075000, check.size = F)## Downloading 6 files
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## Successfully downloaded 6 files.
## NEON_D16_WREF_DP3_580000_5075000_CHM.tif downloaded to /Users/dsfernandez/Documents/R/NEON/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/L3/DiscreteLidar/CanopyHeightModelGtif
## NEON_D16_WREF_DP1_580000_5075000_classified_point_cloud.prj downloaded to /Users/dsfernandez/Documents/R/NEON/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/Metadata/DiscreteLidar/TileBoundary/shps
## NEON_D16_WREF_DP1_580000_5075000_classified_point_cloud.shx downloaded to /Users/dsfernandez/Documents/R/NEON/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/Metadata/DiscreteLidar/TileBoundary/shps
## NEON_D16_WREF_DP1_580000_5075000_classified_point_cloud.kml downloaded to /Users/dsfernandez/Documents/R/NEON/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/Metadata/DiscreteLidar/TileBoundary/kmls
## NEON_D16_WREF_DP1_580000_5075000_classified_point_cloud.shp downloaded to /Users/dsfernandez/Documents/R/NEON/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/Metadata/DiscreteLidar/TileBoundary/shps
## NEON_D16_WREF_DP1_580000_5075000_classified_point_cloud.dbf downloaded to /Users/dsfernandez/Documents/R/NEON/DP3.30015.001/2017/FullSite/D16/2017_WREF_1/Metadata/DiscreteLidar/TileBoundary/shps# to get all data for a site and year
## byFileAOP(dpID = "DP3.30015.001", site = "WREF", year = "2017") #very big 1GB
chm <- raster("DP3.30015.001/2017/FullSite/D16/2017_WREF_1/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D16_WREF_DP3_580000_5075000_CHM.tif")
plot(chm)