| Type: | Package |
| Title: | Granier's Sap Flow Sensors (TDP) Analysis |
| Version: | 1.0 |
| Date: | 2020-02-28 |
| Author: | Maxime Durand |
| Maintainer: | Maxime Durand <duran1211@gmail.com> |
| Description: | Set of functions designed to help in the analysis of TDP sensors. Features includes dates and time conversion, weather data interpolation, daily maximum of tension analysis and calculations required to convert sap flow density data to sap flow rates at the tree and plot scale (For more information see : Granier (1985) <doi:10.1051/forest:19850204> & Granier (1987) <doi:10.1093/treephys/3.4.309>). |
| Imports: | stats, plyr, graphics |
| Depends: | R (≥ 2.10) |
| Encoding: | UTF-8 |
| LazyData: | true |
| License: | GPL-2 |
| RoxygenNote: | 7.0.2 |
| NeedsCompilation: | no |
| Packaged: | 2020-02-28 07:22:06 UTC; Localadmin_durandma |
| Repository: | CRAN |
| Date/Publication: | 2020-02-28 07:40:02 UTC |
Sap flow dataset
Description
Exemple dataset exemple for the TDPanalysis package
Usage
SpFl
Format
An object of class data.frame with 432 rows and 4 columns.
Details
"DATE" is dates in dd/mm/yyyy format. "TIME" is time in hh:mm:ss format, "ID" is sub-groups and "tension" is the measured tension from the TDP probe.
Sapwood area calculation
Description
Calculate sapwood area based on diameter, heartwood diameter and sapwood fraction
Usage
SpWd_Area_calc(diam, SpWd_frac = 1, HtWd_diam = 0)
Arguments
diam |
Vector with diameter. |
SpWd_frac |
Numerical (from 0 to 1). Indicate the fraction of the diameter which is sapwood |
HtWd_diam |
Vector with diameter of the heartwood. |
Details
If SpWD_frac and HtWd_diam are both entered, the function will return an error. Units of "diam" and "HtWd_diam" should be the same.
Value
Return a numerical vector containing the sapwood area
Examples
diam = c(12,14,16,13,15)
SpWd_Area_calc(diam=diam, SpWd_frac=0.2)
Find Tmax
Description
Find the daily maximum of tension
Usage
Tmax.find(tension, dates, ID)
Arguments
tension |
Vector with tension. |
dates |
Vector with dates in the DOY format. |
ID |
Character vector for specifying which group the tension is assigned to (e.g. trees) |
Value
Return a vector containing daily Tmax for each group specified in the ID argument
Examples
tension = c(1:20)
dates = c(rep(102, times=10), rep(103, times=10))
ID = c(rep("A", times=5), rep("B", times=5), rep("A", times=5), rep("B", times=5))
Tmax.find(tension=tension, dates=dates, ID=ID)
Calculate a mean of Tmax
Description
Calculate a mean Tmax for each sub-group
Usage
Tmax.mean(df)
Arguments
df |
Data frame containing all Tmax for each sub-group. |
Details
The data frame should contain a column named "Tmax" whith all Tmax and a column named "ID" to identify which Tmax belong to which sug-group.
Value
Return the inputed data frame with a new column names "Tmax_mean".
Examples
ID = c(rep("A", times=5), rep("B", times=5), rep("A", times=5), rep("B", times=5))
Tmax = c(rep(2.5, times=5), rep(2.7, times=5), rep(3.2, times=5), rep(3.4, times=5))
DOY = c(rep(102, times=10), rep(103, times=10))
df <- data.frame(DOY, ID, Tmax)
Tmax.mean(df)
Plot the Tmax
Description
Plot the Tmax with indications of extreme values
Usage
Tmaxplot(df)
Arguments
df |
Data frame containing Tmax, identification of sub-groups and DOY. |
Details
The dataframe should contain at least 3 columns named "Tmax" (daily maximums of tension), "DOY" (day of the year) and "ID" (sub-groups). The red horizontal lines reprensents 3 times the inter-quartile range (3*IQR) of all the Tmax of the data. The blue horizontal line reprensent the 1.5*IQR without the Tmax outside the red lines.
Value
Return a plot of Tmax by days for each sub-group
Examples
DOY = c(rep(102, times=10), rep(103, times=10))
ID = c(rep("A", times=5), rep("B", times=5), rep("A", times=5), rep("B", times=5))
Tmax = c(rep(0.7512, times=5), rep(0.7359, times=5),rep(0.7644, times=5),rep(0.7666, times=5))
df <- data.frame(DOY, ID, Tmax, stringsAsFactors = FALSE)
Tmaxplot(df)
Calculate daily transpiration
Description
Calculate daily transpiration for each sub-group inputed
Usage
Wat.transp(Sapflow, days, ID)
Arguments
Sapflow |
Vector with sap flow. |
days |
Vector containg the days for which to calculate transpiration |
ID |
Character vector containing identification for each sub-group |
Details
!!Beware of the units!! The Granier formula usually convert tension into sap flow density (in kg.dm-2.h-1). So, you should first convert sap flow density into sap flow (in kg.h-1). Moreover, if you take measurment every 30 minutes sap flow should be corrected by dividing the value by 2.
Value
Return a data frame with transpiration for each day and sub-group inputed
Examples
ID = c(rep("A", times=5), rep("B", times=5), rep("A", times=5), rep("B", times=5))
Sapflow = c(rep(2.5, times=5), rep(2.7, times=5), rep(3.2, times=5), rep(3.4, times=5))
days = c(rep(102, times=10), rep(103, times=10))
Wat.transp(Sapflow=Sapflow, days=days, ID=ID)
Date conversion
Description
Convert dates from the DD/MM/YYYY format to day of the year (DOY)
Usage
date.to.DOY(dates, format = "dd/mm/yyyy")
Arguments
dates |
Vector with dates to convert. |
format |
Format of the date (support DD/MM/YYYY MM/DD/YYYY and YYYY/MM/DD). |
Value
Return a vector containing the corresponding DOY.
Examples
dates = c("01/01/2000", "03/03/2000", "03/03/1999")
date.to.DOY(dates=dates)
Time & dates conversion
Description
Convert DOY and time into a single numerical variable
Usage
datetime(dates, Time)
Arguments
dates |
Vector with dates in the DOY format. |
Time |
Vector with time |
Details
time vector should be numerical (e.g. as outputed by the time.to.cont function)
Value
Return a vector containing DOY and time as a single numerical variable
Examples
dates = c(102,102,102,102,103,103,103,103)
Time = c(22, 22.5, 23, 23.5, 0, 0.5, 1, 1.5)
datetime(dates=dates, Time=Time)
Remove unwanted dates
Description
Remove all data for the corresponding date argument
Usage
remove.fun(df, dates)
Arguments
df |
Data frame containing a DOY column named "DOY". |
dates |
Character vector containing the DOY to remove from the data frame. |
Details
This function is primarely used to remove days for which Tmax is too extreme.
Value
Return the inputed data frame without the date corresponding the the "dates" argument.
Examples
DOY = c(rep(102, times=10), rep(103, times=10))
ID = c(rep("A", times=5), rep("B", times=5), rep("A", times=5), rep("B", times=5))
Tmax = c(rep(2.5, times=5), rep(2.7, times=5), rep(3.2, times=5), rep(3.4, times=5))
df <- data.frame(DOY, ID, Tmax)
dates = c("103")
remove.fun(df=df, dates=dates)
Convert tension into sap flow density
Description
Use the Granier formula to convert tension into sap flow density using daily or mean Tmax
Usage
tens.to.sapflow(tension, Tmax)
Arguments
tension |
Vector with tension. |
Tmax |
Vector with corresponding maximums of tension. |
Value
Return a numerical vector containing the sap flow density
References
Granier A. 1985. A new method of sap flow measurement in tree stems. Annales Des Sciences Forestieres 42(2): 193-200.
Granier A. 1987. Evaluation of transpiration in a douglas-fir stand by means of sap flow measurements. Tree Physiology 3(4): 309-319.
Examples
Tmax = c(rep(2.5, times=5), rep(2.7, times=5), rep(3.2, times=5), rep(3.4, times=5))
tension = c(5:25)
tens.to.sapflow(tension=tension, Tmax=Tmax)
Time conversion
Description
Convert time from the HH:MM:SS format to a numerical
Usage
timecont(Time, sep = ":")
Arguments
Time |
Vector with time to convert. |
sep |
Character element containing regular expression(s) to use to splitting. |
Details
time vector should be in the HH:MM:SS format.
Value
Return a vector containing the corresponding time.
Examples
Time = c("14:30:00", "20:45:00", "05:00:00")
timecont(Time=Time)