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Curate_spectral_datasets.R
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Curate_spectral_datasets.R
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####################################################################################################
#
# --- Last updated: 04.02.2021 By Shawn P. Serbin <sserbin@bnl.gov>
####################################################################################################
#---------------- Close all devices and delete all variables. -------------------------------------#
rm(list=ls(all=TRUE)) # clear workspace
graphics.off() # close any open graphics
closeAllConnections() # close any open connections to files
#--------------------------------------------------------------------------------------------------#
#--------------------------------------------------------------------------------------------------#
# Load libraries
devtools::install_github(repo = "TESTgroup-BNL/spectratrait", dependencies=TRUE)
list.of.packages <- c("devtools","readr","RCurl","httr","dplyr","spectratrait")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages, dependencies=c("Depends", "Imports",
"LinkingTo"))
invisible(lapply(list.of.packages, library, character.only = TRUE))
# not in
`%notin%` <- Negate(`%in%`)
#--------------------------------------------------------------------------------------------------#
#--------------------------------------------------------------------------------------------------#
### output location
output_dir <- file.path("~/Data/Dropbox/MANUSCRIPTS/BNL_TEST/SSerbin_NGEEArctic_Spectra_Trait/data/compiled_data/")
#--------------------------------------------------------------------------------------------------#
#--------------------------------------------------------------------------------------------------#
###### Barrow datasets
#NGEE Arctic Leaf Spectral Reflectance Utqiagvik (Barrow) Alaska 2013
ecosis_id <- "224c23b4-9e85-4275-b5f4-308db02547b3"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
names(dat_raw)[1:45]
# clean up
dat_raw[dat_raw==-9999]=NA
head(dat_raw)
dat_raw$Sample_ID <- lapply(dat_raw$Sample_ID, function(x) paste0('BNL', x))
dat_raw$Sample_ID <- as.character(dat_raw$Sample_ID)
head(dat_raw)
names(dat_raw)[1:45]
nga_2013_barrow_leaf_spec <- dat_raw %>%
select(Sample_ID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,Instrument=`Instrument Model`,
`350`:`2500`)
head(nga_2013_barrow_leaf_spec)
spectra <- nga_2013_barrow_leaf_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- nga_2013_barrow_leaf_spec[,names(nga_2013_barrow_leaf_spec) %notin% seq(350,2500,1)]
if (max(spectra)<1) {
spectra <- spectra*100
}
nga_2013_barrow_leaf_spec_out <- data.frame(spec_info,spectra)
head(nga_2013_barrow_leaf_spec_out)[,1:5]
#plot(seq(350,2500,1), nga_2013_barrow_leaf_spec_out[1,5:dim(nga_2013_barrow_leaf_spec_out)[2]])
write.csv(nga_2013_barrow_leaf_spec_out,
file = file.path(output_dir,"NGEE-Arctic_Utqiagvik_2013_Leaf_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic Leaf Spectral Reflectance and Transmittance Data 2014 to 2016 Utqiagvik (Barrow) Alaska
ecosis_id <- "bf41fff2-8571-4f34-bd7d-a3240a8f7dc8"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
names(dat_raw)[1:40]
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)
nga_20142016_barrow_leaf_spec <- dat_raw %>%
filter(Measurement=="Reflectance") %>%
select(Sample_ID=BNL_Barcode,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(nga_20142016_barrow_leaf_spec)
spectra <- nga_20142016_barrow_leaf_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- nga_20142016_barrow_leaf_spec[,names(nga_20142016_barrow_leaf_spec) %notin% seq(350,2500,1)]
if (mean(spectra$Wave_850, na.rm=T)<1) {
spectra <- spectra*100
}
nga_20142016_barrow_leaf_spec_out <- data.frame(spec_info,spectra)
head(nga_20142016_barrow_leaf_spec_out)[,1:5]
write.csv(nga_20142016_barrow_leaf_spec_out,
file = file.path(output_dir,"NGEE-Arctic_Utqiagvik_2014_2016_Leaf_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic BNL Canopy Spectral Reflectance Utqiagvik (Barrow) Alaska 2014 to 2016
ecosis_id <- "ae1463cc-9984-4a0e-8277-0ba784eda5fd"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
names(dat_raw)[1:40]
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)
nga_20142016_barrow_canopy_spec <- dat_raw %>%
select(Sample_ID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=Instrument,`350`:`2500`)
head(nga_20142016_barrow_canopy_spec)
spectra <- nga_20142016_barrow_canopy_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- nga_20142016_barrow_canopy_spec[,names(nga_20142016_barrow_canopy_spec) %notin% seq(350,2500,1)]
if (mean(spectra$Wave_850, na.rm=T)<1) {
spectra <- spectra*100
}
nga_20142016_barrow_canopy_spec_out <- data.frame(spec_info,spectra)
head(nga_20142016_barrow_canopy_spec_out)[,1:5]
write.csv(nga_20142016_barrow_canopy_spec_out,
file = file.path(output_dir,"NGEE-Arctic_Utqiagvik_2014_2016_Canopy_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
###### SewPen datasets
#NGEE Arctic 2016 Leaf Spectral Reflectance Kougarok Road Seward Peninsula Alaska 2016
ecosis_id <- "960dbb0c-144e-4563-8117-9e23d14f4aa9"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
nga_2016_sewpen_leaf_spec <- dat_raw %>%
select(Sample_ID=BNL_Barcode,Sample_Date=`Sample Collection Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(nga_2016_sewpen_leaf_spec)[,1:6]
spectra <- nga_2016_sewpen_leaf_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- nga_2016_sewpen_leaf_spec[,names(nga_2016_sewpen_leaf_spec) %notin% seq(350,2500,1)]
if (mean(spectra$Wave_850, na.rm=T)<1) {
spectra <- spectra*100
}
nga_2016_sewpen_leaf_spec_out <- data.frame(spec_info,spectra)
head(nga_2016_sewpen_leaf_spec_out)[,1:5]
write.csv(nga_2016_sewpen_leaf_spec_out,
file = file.path(output_dir,"NGEE-Arctic_SewardPeninsula_2016_Leaf_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic 2016 Averaged Canopy Spectral Reflectance Seward Peninsula Alaska
ecosis_id <- "d4d3e843-3cf9-4441-83bd-731595cdb181"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
sewpen_2016_canopy_spec <- dat_raw %>%
select(Sample_ID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(sewpen_2016_canopy_spec)[,1:6]
spectra <- sewpen_2016_canopy_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- sewpen_2016_canopy_spec[,names(sewpen_2016_canopy_spec) %notin% seq(350,2500,1)]
sewpen_2016_canopy_spec_out <- data.frame(spec_info,spectra)
head(sewpen_2016_canopy_spec_out)[,1:5]
# for now only keep those samples that have barcode sample ids that link with trait data
remove <- which(is.na(sewpen_2016_canopy_spec_out$USDA_Species_Code))
sewpen_2016_canopy_spec_out <- sewpen_2016_canopy_spec_out[-remove,]
head(sewpen_2016_canopy_spec_out)[,1:5]
write.csv(sewpen_2016_canopy_spec_out,
file = file.path(output_dir,"NGEE-Arctic_SewardPeninsula_2016_Avg_Canopy_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic 2017 Canopy Spectral Reflectance Seward Peninsula Alaska
ecosis_id <- "2074ef11-d43c-4cb9-bf2b-19d4fc57dc4e"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
sewpen_2017_canopy_spec <- dat_raw %>%
select(Sample_ID=SampleID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(sewpen_2017_canopy_spec)[,1:6]
spectra <- sewpen_2017_canopy_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- sewpen_2017_canopy_spec[,names(sewpen_2017_canopy_spec) %notin% seq(350,2500,1)]
sewpen_2017_canopy_spec_out <- data.frame(spec_info,spectra)
head(sewpen_2017_canopy_spec_out)[,1:5]
# for now only keep those samples that have barcode sample ids that link with trait data
remove <- which(is.na(sewpen_2017_canopy_spec_out$USDA_Species_Code))
sewpen_2017_canopy_spec_out <- sewpen_2017_canopy_spec_out[-remove,]
head(sewpen_2017_canopy_spec_out)[,1:5]
write.csv(sewpen_2017_canopy_spec_out,
file = file.path(output_dir,"NGEE-Arctic_SewardPeninsula_2017_Avg_Canopy_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic 2017 Leaf Spectral Reflectance Teller Watershed Seward Peninsula Alaska
ecosis_id <- "b64174d0-c426-4e90-b9ed-c3afdcb8bb73"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
sewpen_2017_leaf_spec <- dat_raw %>%
select(Sample_ID=SampleID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(sewpen_2017_leaf_spec)[,1:6]
spectra <- sewpen_2017_leaf_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- sewpen_2017_leaf_spec[,names(sewpen_2017_leaf_spec) %notin% seq(350,2500,1)]
sewpen_2017_leaf_spec_out <- data.frame(spec_info,spectra)
head(sewpen_2017_leaf_spec_out)[,1:5]
write.csv(sewpen_2017_leaf_spec_out,
file = file.path(output_dir,"NGEE-Arctic_SewardPeninsula_2017_Leaf_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic 2018 Canopy Spectral Reflectance Kougarok Watershed Seward Peninsula Alaska
ecosis_id <- "2a9cce28-3f20-44a2-9d3f-2af1fa353231"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
sewpen_2018_canopy_spec <- dat_raw %>%
select(Sample_ID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(sewpen_2018_canopy_spec)[,1:6]
spectra <- sewpen_2018_canopy_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- sewpen_2018_canopy_spec[,names(sewpen_2018_canopy_spec) %notin% seq(350,2500,1)]
sewpen_2018_canopy_spec_out <- data.frame(spec_info,spectra)
head(sewpen_2018_canopy_spec_out)[,1:5]
write.csv(sewpen_2018_canopy_spec_out,
file = file.path(output_dir,"NGEE-Arctic_SewardPeninsula_2018_Canopy_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic 2019 Leaf Spectral Reflectance Seward Peninsula Alaska
ecosis_id <- "dd3d1e06-9411-4b7a-a3bb-99657e6e9a0c"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
sewpen_2019_leaf_spec <- dat_raw %>%
select(Sample_ID=SampleID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(sewpen_2019_leaf_spec)[,1:6]
spectra <- sewpen_2019_leaf_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- sewpen_2019_leaf_spec[,names(sewpen_2019_leaf_spec) %notin% seq(350,2500,1)]
sewpen_2019_leaf_spec_out <- data.frame(spec_info,spectra)
head(sewpen_2019_leaf_spec_out)[,1:5]
write.csv(sewpen_2019_leaf_spec_out,
file = file.path(output_dir,"NGEE-Arctic_SewardPeninsula_2019_Leaf_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
# NGEE Arctic 2019 Canopy Spectral Reflectance Seward Peninsula Alaska
ecosis_id <- "8d575b12-4c5c-4397-98b0-43e6f5b8c765"
dat_raw <- get_ecosis_data(ecosis_id = ecosis_id)
head(dat_raw)
# clean up
dat_raw[dat_raw==-9999]=NA
names(dat_raw)[1:40]
sewpen_2019_canopy_spec <- dat_raw %>%
select(Sample_ID=SampleID,Sample_Date=`Measurement Date`,USDA_Species_Code=`USDA Symbol`,
Instrument=`Instrument Model`,`350`:`2500`)
head(sewpen_2019_canopy_spec)[,1:6]
spectra <- sewpen_2019_canopy_spec %>%
select(`350`:`2500`) %>%
setNames(paste0('Wave_', names(.)))
spec_info <- sewpen_2019_canopy_spec[,names(sewpen_2019_canopy_spec) %notin% seq(350,2500,1)]
sewpen_2019_canopy_spec_out <- data.frame(spec_info,spectra)
head(sewpen_2019_canopy_spec_out)[,1:5]
write.csv(sewpen_2019_canopy_spec_out,
file = file.path(output_dir,
"NGEE-Arctic_SewardPeninsula_2019_Canopy_Spectral_Reflectance.csv"),
row.names = F)
rm(spec_info,spectra)
#--------------------------------------------------------------------------------------------------#
#--------------------------------------------------------------------------------------------------#
rm(list=ls(all=TRUE)) # clear workspace
graphics.off() # close any open graphics
closeAllConnections() # close any open connections to files
### Combine datasets
input_dir <- file.path("~/Data/Dropbox/MANUSCRIPTS/BNL_TEST/SSerbin_NGEEArctic_Spectra_Trait/data/compiled_data/")
Utqiagvik_2013_Leaf_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_Utqiagvik_2013_Leaf_Spectral_Reflectance.csv"))
orig_names <- names(Utqiagvik_2013_Leaf_Reflectance)
Utqiagvik_2013_Leaf_Reflectance$Location <- rep("Utqiagvik",times=dim(Utqiagvik_2013_Leaf_Reflectance)[1])
Utqiagvik_2013_Leaf_Reflectance <- Utqiagvik_2013_Leaf_Reflectance %>%
select(Location,paste(orig_names))
head(Utqiagvik_2013_Leaf_Reflectance)[,1:10]
Utqiagvik_2014_2016_Leaf_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_Utqiagvik_2014_2016_Leaf_Spectral_Reflectance.csv"))
orig_names <- names(Utqiagvik_2014_2016_Leaf_Reflectance)
Utqiagvik_2014_2016_Leaf_Reflectance$Location <- rep("Utqiagvik",times=dim(Utqiagvik_2014_2016_Leaf_Reflectance)[1])
Utqiagvik_2014_2016_Leaf_Reflectance <- Utqiagvik_2014_2016_Leaf_Reflectance %>%
select(Location,paste(orig_names))
head(Utqiagvik_2014_2016_Leaf_Reflectance)[,1:10]
SewardPeninsual_2016_Leaf_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2016_Leaf_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2016_Leaf_Reflectance)
SewardPeninsual_2016_Leaf_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2016_Leaf_Reflectance)[1])
SewardPeninsual_2016_Leaf_Reflectance <- SewardPeninsual_2016_Leaf_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2016_Leaf_Reflectance)[,1:10]
SewardPeninsual_2016_Canopy_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2016_Avg_Canopy_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2016_Canopy_Reflectance)
SewardPeninsual_2016_Canopy_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2016_Canopy_Reflectance)[1])
SewardPeninsual_2016_Canopy_Reflectance <- SewardPeninsual_2016_Canopy_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2016_Canopy_Reflectance)[,1:10]
SewardPeninsual_2016_Canopy_Reflectance <- SewardPeninsual_2016_Canopy_Reflectance %>%
mutate(Instrument = recode(Instrument,
"HR-1024i"="SVC_HR-1024i") )
head(SewardPeninsual_2016_Canopy_Reflectance)[,1:10]
Utqiagvik_2014_2016_Canopy_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_Utqiagvik_2014_2016_Canopy_Spectral_Reflectance.csv"))
orig_names <- names(Utqiagvik_2014_2016_Canopy_Reflectance)
Utqiagvik_2014_2016_Canopy_Reflectance$Location <- rep("Utqiagvik",times=dim(Utqiagvik_2014_2016_Canopy_Reflectance)[1])
Utqiagvik_2014_2016_Canopy_Reflectance <- Utqiagvik_2014_2016_Canopy_Reflectance %>%
select(Location,paste(orig_names))
head(Utqiagvik_2014_2016_Canopy_Reflectance)[,1:10]
SewardPeninsual_2017_Leaf_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2017_Leaf_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2017_Leaf_Reflectance)
SewardPeninsual_2017_Leaf_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2017_Leaf_Reflectance)[1])
SewardPeninsual_2017_Leaf_Reflectance <- SewardPeninsual_2017_Leaf_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2017_Leaf_Reflectance)[,1:10]
SewardPeninsual_2017_Leaf_Reflectance <- SewardPeninsual_2017_Leaf_Reflectance %>%
mutate(Instrument = recode(Instrument,
"HR-1024i"="SVC_HR-1024i") )
head(SewardPeninsual_2017_Leaf_Reflectance)[,1:10]
SewardPeninsual_2017_Canopy_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2017_Avg_Canopy_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2017_Canopy_Reflectance)
SewardPeninsual_2017_Canopy_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2017_Canopy_Reflectance)[1])
SewardPeninsual_2017_Canopy_Reflectance <- SewardPeninsual_2017_Canopy_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2017_Canopy_Reflectance)[,1:10]
SewardPeninsual_2017_Canopy_Reflectance <- SewardPeninsual_2017_Canopy_Reflectance %>%
mutate(Instrument = recode(Instrument,
"HR-1024i"="SVC_HR-1024i") )
head(SewardPeninsual_2017_Canopy_Reflectance)[,1:10]
SewardPeninsual_2018_Canopy_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2018_Canopy_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2018_Canopy_Reflectance)
SewardPeninsual_2018_Canopy_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2018_Canopy_Reflectance)[1])
SewardPeninsual_2018_Canopy_Reflectance <- SewardPeninsual_2018_Canopy_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2018_Canopy_Reflectance)[,1:10]
SewardPeninsual_2018_Canopy_Reflectance <- SewardPeninsual_2018_Canopy_Reflectance %>%
mutate(Instrument = recode(Instrument,
"HR-1024i"="SVC_HR-1024i") )
head(SewardPeninsual_2018_Canopy_Reflectance)[,1:10]
# [2019 datasets still missing]
input_dir <- file.path("~/Data/Dropbox/MANUSCRIPTS/BNL_TEST/SSerbin_NGEEArctic_Spectra_Trait/data/compiled_data/")
SewardPeninsual_2019_Leaf_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2019_Leaf_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2019_Leaf_Reflectance)
SewardPeninsual_2019_Leaf_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2019_Leaf_Reflectance)[1])
SewardPeninsual_2019_Leaf_Reflectance <- SewardPeninsual_2019_Leaf_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2019_Leaf_Reflectance)[,1:10]
SewardPeninsual_2019_Leaf_Reflectance <- SewardPeninsual_2019_Leaf_Reflectance %>%
mutate(Instrument = recode(Instrument,
"HR-1024i"="SVC_HR-1024i") )
head(SewardPeninsual_2019_Leaf_Reflectance)[,1:10]
input_dir <- file.path("~/Data/Dropbox/MANUSCRIPTS/BNL_TEST/SSerbin_NGEEArctic_Spectra_Trait/data/compiled_data/")
SewardPeninsual_2019_Canopy_Reflectance <- read.csv(file = file.path(input_dir,"NGEE-Arctic_SewardPeninsula_2019_Canopy_Spectral_Reflectance.csv"))
orig_names <- names(SewardPeninsual_2019_Canopy_Reflectance)
SewardPeninsual_2019_Canopy_Reflectance$Location <- rep("Seward_Peninsula",times=dim(SewardPeninsual_2019_Canopy_Reflectance)[1])
SewardPeninsual_2019_Canopy_Reflectance <- SewardPeninsual_2019_Canopy_Reflectance %>%
select(Location,paste(orig_names))
head(SewardPeninsual_2019_Canopy_Reflectance)[,1:10]
SewardPeninsual_2019_Canopy_Reflectance <- SewardPeninsual_2019_Canopy_Reflectance %>%
mutate(Instrument = recode(Instrument,
"HR-1024i"="SVC_HR-1024i") )
head(SewardPeninsual_2019_Canopy_Reflectance)[,1:10]
# leaf data
NGEEArctic_leaf_reflectance <- rbind(Utqiagvik_2013_Leaf_Reflectance,Utqiagvik_2014_2016_Leaf_Reflectance,
SewardPeninsual_2016_Leaf_Reflectance, SewardPeninsual_2017_Leaf_Reflectance,
SewardPeninsual_2019_Leaf_Reflectance)
head(NGEEArctic_leaf_reflectance)[,1:10]
unique(NGEEArctic_leaf_reflectance$Location)
unique(NGEEArctic_leaf_reflectance$USDA_Species_Code)
unique(NGEEArctic_leaf_reflectance$Instrument)
NGEEArctic_canopy_reflectance <- rbind(Utqiagvik_2014_2016_Canopy_Reflectance, SewardPeninsual_2016_Canopy_Reflectance,
SewardPeninsual_2017_Canopy_Reflectance, SewardPeninsual_2018_Canopy_Reflectance,
SewardPeninsual_2019_Canopy_Reflectance)
NGEEArctic_Reflectance <- list(Leaf_Reflectance=NGEEArctic_leaf_reflectance,
Canopy_Reflectance=NGEEArctic_canopy_reflectance)
head(NGEEArctic_Reflectance$Leaf_Reflectance)[,1:5]
head(NGEEArctic_Reflectance$Canopy_Reflectance)[,1:5]
save(NGEEArctic_Reflectance, file = file.path(input_dir,"NGEEArctic_Leaf_and_Canopy_Reflectance.RData"))
#--------------------------------------------------------------------------------------------------#
#--------------------------------------------------------------------------------------------------#
output_dir <- file.path("~/Data/Dropbox/MANUSCRIPTS/BNL_TEST/SSerbin_NGEEArctic_Spectra_Trait/data/compiled_data/")
load(file.path(output_dir,"NGEEArctic_Leaf_and_Canopy_Reflectance.RData"))
fig_dir <- file.path("~/Data/Dropbox/MANUSCRIPTS/BNL_TEST/SSerbin_NGEEArctic_Spectra_Trait/figures_and_tables/spectra")
if (! file.exists(fig_dir)) dir.create(fig_dir,recursive=TRUE)
lr <- NGEEArctic_Reflectance$Leaf_Reflectance
names(lr)[1:6]
pdf(file.path(fig_dir,"NGEEArctic_Leaf_Reflectance.pdf"),height=7,width=10)
df <- as.data.frame(lr[,6:dim(lr)[2]])
matplot(seq(350,2500,1),t(df), type = "l", lty = 1, xlab="Wavelength (nm)", ylab = "Reflectance (%)",
ylim=c(0,70))
box(lwd=2.2)
dev.off()
cr <- NGEEArctic_Reflectance$Canopy_Reflectance
names(cr)[1:6]
pdf(file.path(fig_dir,"NGEEArctic_Canopy_Reflectance.pdf"),height=7,width=10)
df <- as.data.frame(cr[,6:dim(cr)[2]])
matplot(seq(350,2500,1),t(df), type = "l", lty = 1, xlab="Wavelength (nm)", ylab = "Reflectance (%)",
ylim=c(0,85))
box(lwd=2.2)
dev.off()
#--------------------------------------------------------------------------------------------------#
#--------------------------------------------------------------------------------------------------
### EOF