out.data: Generating TDM output
In the-Hull/TREX: Tree Sap Flow Extractor
out.data R Documentation
Generating TDM output
Description
Generates relevant outputs from the sap flux density (SFD) values.
This function provides both F_{d} (SFD expressed in mmol m^{-2} s^{-1}) and crown conductance values
(G_{C}; an analogue to stomatal conductance) in an easily exportable format.
Additionally, the function can perform environmental filtering on F_{d} and G_{C} and model G_{C} sensitivity to vapour pressure deficit (VPD).
The user can choose between in- (method = "env.filt") or excluding (method = "stat") environmental filtering
on the G_{C} and adjust the filter threshold manually.
Usage
out.data(
input,
vpd.input,
sr.input,
prec.input,
peak.hours = c(10:14),
low.sr = 150,
peak.sr = 300,
vpd.cutoff = 0.5,
prec.lim = 1,
method = "env.filt",
max.quant = 1,
make.plot = TRUE
)
Arguments
input
An is.trex-compliant time series from tdm_cal.sfd outputs
(e.g., X$sfd.mw$sfd)
vpd.input
An is.trex-compliant object an individual series of VPD in kPa (see vpd).
The extent and temporal resolution should be equal to input.
Use dt.steps to correct if needed.
sr.input
An is.trex-compliant object of an individual series of solar irradiance
(e.g. either PAR or global radiation; see sr).
The extent and temporal resolution should be equal to input. Use dt.steps to correct if needed.
This data is only needed when applying the "env.filt" method.
prec.input
An is.trex-compliant object of daily precipitation in mm d-1 (see preci).
The extent should be equal to input with a daily temporal resolution.
Use dt.steps to correct if needed.
This data is only needed when applying the "env.filt" method.
peak.hours
Numeric vector with hours which should be considered as peak-of-the-day hours
(default = c(10:14)).
This variable is only needed when the "stat" method is selected.
low.sr
Numeric threshold value in the unit of the sr.input time-series (e.g., W m-2)
to exclude cloudy days which impact G_{C} (default = 150 W m-2).
This variable is only needed when the "env.filt" method is selected.
peak.sr
Numeric threshold value in the unit of the sr.input time-series (e.g., W m-2)
to exclude hours which are not considered as peak-of-the-day hours (default = 300 W m-2).
This variable is only needed when the "env.filt" method is selected.
vpd.cutoff
Numeric threshold value in kPa for peak-of-the-day mean VPD to eliminate unrealistic
and extremely high values of G_{C} due to low VPD values or high values of G_{C} (default = 0.5 kPa).
prec.lim
Numeric threshold value in mm d-1 for daily precipitation to remove rainy days (default = 1 mm d-1).
This variable is only needed when "env.filt" method is selected.
method
Character string indicating whether precipitation and solar irradiance data should be used
to determined peak-of-the-day G_{C} values and filter the daily G_{C} values ("env.filt")
or not ("stat"; default). When "env.filt" is selected, input, vpd.input, sr.input, prec.input,
peak.sr, low.sr, vpd.cutoff and prec.lim have to be provided.
When "stat" is selected only input, vpd.input and peak.hours.
max.quant
Numeric, defining the quantile of the G_{C} data which should be considered as GC.max (default = 1).
make.plot
Logical; if TRUE, a plot is generated presenting the response of G_{C} to VPD.
Details
Various relevant outputs can be derived from the SFD data.
This function provides the option to recalculate SFD to F_{d} (expressed in mmol m-2 s-1)
and crown conductance (according to Pappas et al. 2018).
G_{C} is estimated per unit sapwood area, where G_{C} = F_{d} / VPD (in kPa), assuming that
i) the stem hydraulic capacitance between the height of sensor and the leaves is negligible, and
ii) that the canopy is well coupled to the atmosphere. In order to reduce the effect of stem hydraulic capacitance,
peak-of-the-day G_{C} are solely considered for calculating daily average G_{C}.
Peak-of-the-day conditions are defined by peak.hours or peak.sr. Moreover, to analyse the relationship between G_{C}
and environmental measurements (e.g., VPD), the daily mean peak-of-the-day G_{C} values can be restricted to:
i) non-cloudy days (see low.sr), to reduce the impact of low irradiance on G_{C},
ii) non-rainy days (see prec.lim), as wet leaves are not well coupled to the atmosphere, and
iii) daily mean peak-of-the-day G_{C} great then a threshold (see vpd.cutoff),
to eliminate unrealistically high G_{C} values due to low F_{d} or VPD values (when method = "env.filt").
Moreover, the sensitivity of the daily mean peak-of-the-day G_{C} to VPD is modelled by fitting the following model:
G_{C} = \alpha + \beta VPD^{-0.5}
Besides using the raw daily mean peak-of-the-day G_{C} values, the function also applies
a normalization where daily mean peak-of-the-day G_{C} is standardized to the maximum conductance (GC.max; see max.quant).
Value
A named list of data.frame objects,
containing the following items:
- raw
A data.frame containing the input data and filtered values. Columns include the timestamp [,"timestamp"]
(e.g., "2012-01-01 00:00:00"), year of the data [,"year"], day of year [,"doy"], input solar radiance data [,"sr"],
daily average radiance data [,"sr"], input vapour pressure deficit data [,"vpd"], isolated peak-of-the-day vapour pressure
deficit values [,"vpd.filt"], input daily precipitation [,"prec.day"], sap flux density expressed in mmol m-2 s-1 [,"fd"],
crown conductance expressed in mmol m-2 s-1 kPa-1 [,"gc"], and the filtered crown conductance [,"gc.filt"]
- peak.mean
A data.frame containing the daily mean crown conductance values.
Columns include the timestamp [,"timestamp"] (e.g., "2012-01-01"), peak-of-the-day vapour pressure deficit [,"vpd.filt"],
the filtered crown conductance mmol m-2 s-1 kPa-1 [,"gc.filt"], and the normalized crown conductance according
to the maximum crown conductance [,"gc.norm"].
- sum.mod
A model summary object (see summary())
of the model between VPD and G_{C}.
- sum.mod.norm
A model summary object (see summary())
of the model between VPD and G_{C}/GC.max.
Examples
## Not run:
#Gc response function
#Gc response function
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="2013-05-01 00:00", end="2013-11-01 00:00",
time.int=15, max.gap=60, decimals=10, df=FALSE)
input[which(input<0.2)]<- NA
input <- tdm_dt.max(input, methods=c("dr"), det.pd=TRUE, interpolate=FALSE,
max.days=10, df=FALSE)
output.data<- tdm_cal.sfd(input,make.plot=TRUE,df=FALSE,wood="Coniferous", decimals = 6)
input<- output.data$sfd.dr$sfd
output<- out.data(input=input, 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)
head(output)
## End(Not run)
the-Hull/TREX documentation built on Feb. 15, 2024, 9:13 a.m.
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| out.data | R Documentation |
Generating TDM output
Description
Generates relevant outputs from the sap flux density (SFD) values.
This function provides both F_{d} (SFD expressed in mmol m^{-2} s^{-1}) and crown conductance values
(G_{C}; an analogue to stomatal conductance) in an easily exportable format.
Additionally, the function can perform environmental filtering on F_{d} and G_{C} and model G_{C} sensitivity to vapour pressure deficit (VPD).
The user can choose between in- (method = "env.filt") or excluding (method = "stat") environmental filtering
on the G_{C} and adjust the filter threshold manually.
Usage
out.data(
input,
vpd.input,
sr.input,
prec.input,
peak.hours = c(10:14),
low.sr = 150,
peak.sr = 300,
vpd.cutoff = 0.5,
prec.lim = 1,
method = "env.filt",
max.quant = 1,
make.plot = TRUE
)
Arguments
input |
An |
vpd.input |
An |
sr.input |
An |
prec.input |
An |
peak.hours |
Numeric vector with hours which should be considered as peak-of-the-day hours
(default = |
low.sr |
Numeric threshold value in the unit of the sr.input time-series (e.g., W m-2)
to exclude cloudy days which impact |
peak.sr |
Numeric threshold value in the unit of the sr.input time-series (e.g., W m-2) to exclude hours which are not considered as peak-of-the-day hours (default = 300 W m-2). This variable is only needed when the "env.filt" method is selected. |
vpd.cutoff |
Numeric threshold value in kPa for peak-of-the-day mean VPD to eliminate unrealistic
and extremely high values of |
prec.lim |
Numeric threshold value in mm d-1 for daily precipitation to remove rainy days (default = 1 mm d-1). This variable is only needed when "env.filt" method is selected. |
method |
Character string indicating whether precipitation and solar irradiance data should be used
to determined peak-of-the-day |
max.quant |
Numeric, defining the quantile of the |
make.plot |
Logical; if |
Details
Various relevant outputs can be derived from the SFD data.
This function provides the option to recalculate SFD to F_{d} (expressed in mmol m-2 s-1)
and crown conductance (according to Pappas et al. 2018).
G_{C} is estimated per unit sapwood area, where G_{C} = F_{d} / VPD (in kPa), assuming that
i) the stem hydraulic capacitance between the height of sensor and the leaves is negligible, and
ii) that the canopy is well coupled to the atmosphere. In order to reduce the effect of stem hydraulic capacitance,
peak-of-the-day G_{C} are solely considered for calculating daily average G_{C}.
Peak-of-the-day conditions are defined by peak.hours or peak.sr. Moreover, to analyse the relationship between G_{C}
and environmental measurements (e.g., VPD), the daily mean peak-of-the-day G_{C} values can be restricted to:
i) non-cloudy days (see low.sr), to reduce the impact of low irradiance on G_{C},
ii) non-rainy days (see prec.lim), as wet leaves are not well coupled to the atmosphere, and
iii) daily mean peak-of-the-day G_{C} great then a threshold (see vpd.cutoff),
to eliminate unrealistically high G_{C} values due to low F_{d} or VPD values (when method = "env.filt").
Moreover, the sensitivity of the daily mean peak-of-the-day G_{C} to VPD is modelled by fitting the following model:
G_{C} = \alpha + \beta VPD^{-0.5}
Besides using the raw daily mean peak-of-the-day G_{C} values, the function also applies
a normalization where daily mean peak-of-the-day G_{C} is standardized to the maximum conductance (GC.max; see max.quant).
Value
A named list of data.frame objects,
containing the following items:
- raw
A
data.framecontaining the input data and filtered values. Columns include the timestamp [,"timestamp"] (e.g., "2012-01-01 00:00:00"), year of the data [,"year"], day of year [,"doy"], input solar radiance data [,"sr"], daily average radiance data [,"sr"], input vapour pressure deficit data [,"vpd"], isolated peak-of-the-day vapour pressure deficit values [,"vpd.filt"], input daily precipitation [,"prec.day"], sap flux density expressed in mmol m-2 s-1 [,"fd"], crown conductance expressed in mmol m-2 s-1 kPa-1 [,"gc"], and the filtered crown conductance [,"gc.filt"]- peak.mean
A
data.framecontaining the daily mean crown conductance values. Columns include the timestamp [,"timestamp"] (e.g., "2012-01-01"), peak-of-the-day vapour pressure deficit [,"vpd.filt"], the filtered crown conductance mmol m-2 s-1 kPa-1 [,"gc.filt"], and the normalized crown conductance according to the maximum crown conductance [,"gc.norm"].- sum.mod
A model summary object (see
summary()) of the model between VPD andG_{C}.- sum.mod.norm
A model summary object (see
summary()) of the model between VPD andG_{C}/GC.max.
Examples
## Not run:
#Gc response function
#Gc response function
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="2013-05-01 00:00", end="2013-11-01 00:00",
time.int=15, max.gap=60, decimals=10, df=FALSE)
input[which(input<0.2)]<- NA
input <- tdm_dt.max(input, methods=c("dr"), det.pd=TRUE, interpolate=FALSE,
max.days=10, df=FALSE)
output.data<- tdm_cal.sfd(input,make.plot=TRUE,df=FALSE,wood="Coniferous", decimals = 6)
input<- output.data$sfd.dr$sfd
output<- out.data(input=input, 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)
head(output)
## End(Not run)
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