flux (version 0.1-2)

flux.calib: Determine calibration measurement ranges according to the dates of real measurements

Description

Preliminary! The function basically takes a huge amount of calibration gas measurements and extracts the calibration gas measurements that have been carried out temporally close to a real data measurement and calculates the standard deviation of the calibration gas measurements. The obtained range limits can be used in flux as a quality parameter (via range.lim).

Usage

flux.calib(dat, columns, calib, format = "%d.%m.%Y", calib.max = 12000, 
range.ext = 200, window = 7, calib.gas.defaults = c(300, 1000, 2000, 
6000, 10000))

Arguments

dat

Object returned by conz.prep containing gas concentration measurements for several chamber measurements.

columns

Character vector giving the names of the two columns that shall be taken from dat and from calib for extracting the calibration measurements. Typically one date and one concentration column. This also implies that they carry the

calib

data.frame with concentration measurements of calibration gases that have been carried out at least in part during the time the concentration measurements in dat have been achieved.

format

Character string specifying the format of dates in dat as well as in calib. Internally dates are converted to a date format R can handle (see strptime for details and format o

calib.max

Numeric value. Maximum accepted concentration measurement for a calibration gas. All calibration gas measurements are filtered and any values above this limit are skipped.

range.ext

Numeric value. Used to extent the range of the concentration measurements per chamber placement. Therefore it is in the same units as the concentration measurements themselves (typicall ppm for CO2 and ppb for CH4 and N2O).

window

Integer value. Window around the date of measurement of the field greenhouse gas concentrations at the measurement device (e.g. a GC) that shall be considered for the inclusion of calibration gas measurements.

calib.gas.defaults

Numeric or integer vector giving the pre-configured concentrations of the respective gas in the calibration gases. What really comes from the calibration gas bottles will presumably change according to fill level and other external parameters. Therefore t

Value

• Returns a named vector with the range limits of the measurement device (as needed within flux) per chamber measurement.

encoding

UTF-8

Details

The function automatically detects the single species of calibration gases that have been measured. It calculates the standard deviations of the measurements per calibration gas species and than gives back an average of the calculated range limit values if there are more than one calibration gas concentrations covered by the range within the field concentration measurements per chamber placement. However, this is rather academic because a chamber measurements for which concentrations develop over the range of two or more calibration concentrations will typically not have a range limit problem.

In its actual form it is possible that there are no valid calibration measurements found for certain chamber data because the range of the chamber data (even with range extension) does not cover any of the calibration gas concentrations. One could try to increase the range.ext argument to achieve better results.

See Also

conz.prep, flux

Examples

## load example data
data(tt.pre)

## extract field concentration measurements
gcd <- tt.pre[tt.pre$sampletype_a=="P",]

## partition the data into data tables per chamber measurement
# first tell which columns of the data you want to carry on
columns <- c("date", "veg", "spot", "time_min", "temp_dC", "cham_area", 
"cham_vol", "CO2ppm", "CO2Code", "CH4ppb", "CH4Code", "N2Oppb", "N2OCode")
# then do the partitioning
gcd.parts <- conz.prep(gcd, columns, factors = c("date", "spot", "veg"), 
nmes = c("date", "veg", "spot"))

## calculate range limits according to the data and the accompanying 
## calibration gas measurements
# extract and prepare calibration measurements
cal <- tt.pre[tt.pre$sampletype_a=="E",c("date_gc", "CH4ppb", "CH4Code", 
"CO2ppm", "CO2Code", "N2Oppb", "N2OCode")]
names(cal)[1] <- "date"
cal$date <- "2011-03-16"
# calculate the range limits per gas (makes no real sense with such
# a small dataset.
# CH4 range limits 
CH4.lims <- flux.calib(gcd.parts, columns = c("date", "CH4ppb"), 
calib = cal, format="%Y-%m-%d")
# N2O range limits 
N2O.lims <- flux.calib(gcd.parts, columns = c("date", "N2Oppb"), 
calib = cal, format="%Y-%m-%d")
# CO2 range limits 
CO2.lims <- flux.calib(gcd.parts, columns = c("date", "CO2ppm"), 
calib = cal, format="%Y-%m-%d")