tdm_hw.cor: Heartwood correction
In TREXr: Tree Sap Flow Extractor

Description Usage Arguments Details Value References Examples

The function corrects for the proportion of the probe that is installed within the non-conductive heartwood according to Clearwater et al. (1999). The function requires Δ Tmax, the probe length and the sapwood thickness. The correction is applied on the Δ T (or Δ V) values and K is recalculated accordingly. When an is.trex-compliant object is provided, the K values for each method are determined (see tdm_dt.max.

1 2	tdm_hw.cor (input, dt.max, probe.length = 20, sapwood.thickness = 18, df = FALSE)

`input`	A `tdm_dt.max` ouput or `is.trex`-compliant object of Δ T (or Δ V) values containing a timestamp and a value column.
`dt.max`	Optional `zoo` object or `data.frame` (columns = “timestamp” or “value”) containing the Δ Tmax when no `is.trex`-compliant object is provided.
`probe.length`	Numeric, the length of the TDM probes in mm.
`sapwood.thickness`	Numeric, the sapwood thickness in mm.
`df`	Logical; If `TRUE`, output is provided in a `data.frame` format with a timestamp and a value column. If `FALSE`, output is provided as a `zoo` vector object (default = `FALSE`).

The function applied the correction provided by Clearwater et al. 1999. Δ T (or Δ V) was corrected (denoted as Δ Tsw) for the proportion of the probe that was inserted into the conducting sapwood vs the proportion of the probe that was inserted into the nonconductive heartwood (γ in mm mm-1). Together with Δ Tmax, Δ T was corrected according to the following equation:

Δ Tsw = (Δ T – (1 – γ) Δ Tmax) / γ

Δ Tsw together with Δ Tmax is then recalculated to K.

A zoo object or data.frame in the appropriate format for other functionalities. See tdm_dt.max for output specifications. All K values for each method are provided when an output from tdm_dt.max was provided. If individual time series are provided for input and tdm_dt.max an alternative output is provided:

input: = Δ T input data.
dt.max: Δ T_{max}{Δ Tmax} input data.
dtsw: Corrected Δ T data.
k.value: K values calculated according to Clearwater et al. (1999).
settings: data.frame of the applied probe.length and sapwood.thickness

Clearwater MJ, Meinzer FC, Andrade JL, Goldstein G, Holbrook NM. 1999. Potential errors in measurement of nonuniform sap flow using heat dissipation probes. Tree Physiology 19:681–687 doi: 10.1093/treephys/19.10.681

#correct for probes being inserted into the heartwood
raw   <-is.trex(example.data(type="doy"),
          tz="GMT",time.format="%H:%M",solar.time=TRUE,
          long.deg=7.7459,ref.add=FALSE)
input <- dt.steps(input=raw,
                   start="2014-05-08 00:00",
                   end="2014-07-25 00:50",
                  time.int=15,max.gap=60,decimals=6,df=F)
input[which(input<0.2)]<-NA
input <-tdm_dt.max(input, methods=c("pd","mw","dr"),
                 det.pd=TRUE,interpolate=FALSE,max.days=10,df=FALSE)
output.data<-tdm_hw.cor(input,probe.length=20,
                   sapwood.thickness=18,df=FALSE)
plot(output.data$k.dr,col="orange")
lines(input$k.dr)