TREXr
allows to assimilate, process and analyse sap flow data obtained with the thermal dissipation method (TDM).
The package includes functions for gap filling time-series data, detecting outliers, calculating data-processing uncertainties and generating uniform data output and visualisation.
The package is designed to deal with large quantities of data and apply commonly used data-processing methods.
The functions have been validated on data collected from different tree species across the northern hemisphere (Peters et al. 2018 ).
A development version of TREXr
can be installed and used via
remotes::install_github("the-Hull/TREXr")
library(TREXr)
# load raw data
raw <- is.trex(example.data(type="doy"),
tz="GMT",
time.format="%H:%M",
solar.time=TRUE,
long.deg=7.7459,
ref.add=FALSE)
# adjust time steps
input <- dt.steps(input=raw,
start="2013-05-01 00:00",
end="2013-11-01 00:00",
time.int=15,
max.gap=60,
decimals=10,
df=FALSE)
# remove obvious outliers
input[which(input<0.2)]<- NA
Three methods can be applied to calculate ΔT (or ΔV for voltage differences between TDM probes):
pd
: pre-dawnmw
: moving-windowdr
: double-regressioninput <- tdm_dt.max(input,
methods = c("pd", "mw", "dr"),
det.pd = TRUE,
interpolate = FALSE,
max.days = 10,
df = FALSE)
plot(input$input, ylab = expression(Delta*italic("V")))
lines(input$max.pd, col = "green")
lines(input$max.mw, col = "blue")
lines(input$max.dr, col = "orange")
output.data<- tdm_cal.sfd(input,make.plot=TRUE,df=FALSE,wood="Coniferous")
plot(output.data$sfd.pd$sfd[1:1000, ], ylim=c(0,10))
# see estimated uncertainty
lines(output.data$sfd.pd$q025[1:1000, ], lty=1,col="grey")
lines(output.data$sfd.pd$q975[1:1000, ], lty=1,col="grey")
lines(output.data$sfd.pd$sfd[1:1000, ])
sfd_data <- output.data$sfd.dr$sfd
Here we generate outputs based on environmental filters and calculate crown conductance (Gc) values.
output<- out.data(input=sfd_data,
vpd.input=vpd,
sr.input=sr,
prec.input=preci,
low.sr = 150,
peak.sr=300,
vpd.cutoff= 0.5,
prec.lim=1,
method="env.filt",
max.quant=0.99,
make.plot=TRUE)
TREXr
TREXr
TREXr
was introduced and demonstrated in detail in a workshop during the Ecological Society of America's 2020 AGM.
The workshop description can be found here, and all materials on the dedicated page.Any scripts or data that you put into this service are public.
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