trex's Introduction

TREX

TREX 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 <doi: 10.1111/nph.15241>), and an accompanying manuscript has been published in Methods in Ecology and Evolution as (Peters et al. 2020 <doi: 10.1111/2041-210X.13524>)

1. Installation

The latest version of TREX can be installed and used via

remotes::install_github("the-Hull/TREX")

library(TREX)

If you want to use CRAN, we have a stable release version used for the MEE manuscript available named TREXr:

install.packages("TREXr")

2. Basic use and workflow

Load data

# 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

Calculate maximum ΔT-Values

Three methods can be applied to calculate ΔT (or ΔV for voltage differences between TDM probes):

pd: pre-dawn
mw: moving-window
dr: double-regression

input <- 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")

Calculate Sap Flux Density

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

Generate Outputs

Here we generate outputs based on environmental filters and calculate crown conductance (G_c) 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)

3. More on `TREX`

Workshops using `TREX`

ESA 2020: TREX 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.

4. Citing this work

Please cite TREX when you apply it in your own work as:

Peters, RL, Pappas, C, Hurley, AG, et al. Assimilate, process and analyse thermal dissipation sap flow data using the TREX r package. Methods Ecol Evol. 2021; 12: 342– 350. https://doi.org/10.1111/2041-210X.13524

A reference is available in R using:

citation("TREX")

#or

citation("TREXr")

trex's People

Contributors

Stargazers

Watchers

trex's Issues

Error when running tdm_cal.sfd()

Hey.

First of all, thank you and the team for all the great work you did on the sap flow package.

While going through the package functionalists with the supplied example.data() from README.md I ran into an error while running the tdm_cal.sfd():

Error in xtfrm.data.frame(x) : cannot xtfrm data frames

It seams to be an ordering issue.

I'm using R version 4.3.2 on RStudio version 2023.9.1.494

Swap CI from Travis to GitHub Actions

TravisCI is changing its business model and will not include a free option.

To do:

Set up GitHub Actions for package testing

Release TREX 1.0.0

Prepare for release:

Submit to CRAN:

usethis::use_version('major')
devtools::submit_cran()
Approve email

Wait for CRAN...

Recommend Projects

the-hull / trex Goto Github PK