GUIDELINES FOR MAKING EDDY COVARIANCE FLUX MEASUREMENTS

Munger JW, Loescher HW

[**Rationale**](#rationale)

[**1.0 TOWER PLACEMENT**](#tower-placement)

[**2.0 EDDY COVARIANCE FLUXES -- CO~2~ H~2~O, heat and
momentum**](#eddy-covariance-fluxes-co2-h2o-heat-and-momentum)

**2.1 Required equipment**

**2.2 Closed-path IRGA arrangement**

**2.3 Open-path IRGA arrangement**

[**3.0 DATA ACQUISITION EQUIPMENT AND
PROCESSING**](#data-acquisition-equipment-and-processing)

**3.1 Signal** **measurement** **frequency**

**3.2 Data** **processing** **programs**

**3.3 Flux** **calculations**

**3.4 Quality** **control**

[**4.0 CALIBRATION PROCEDURES**](#calibration-procedures)

**4.1 IRGA calibration**

**4.2 Sonic anemometer-thermometer calibration**

**4.3 Temperature and Humidity**

**4.4 Radiation sensors**

**4.5 Wind speed** **and** **direction**

**4.6 Precipitation**

[**5.0 PROFILE AND CO~2~ and H~2~O
CONCENTRATIONS**](#profile-and-co2-and-h2o-concentrations)

### Rationale 

Measurement consistency is essential for realizing the potential of
AmeriFlux as a network. In general there is not a single perfect method
that can be recommended. Instead the benefits, drawbacks, and costs of
various methodologies must be evaluated to define an optimum solution
that best meets the precision and accuracy requirements of the site and
network science goals. Whatever the level of accuracy, site data need to
include results of ***ongoing quality assurance tests*** that verify
whether a particular measurement system ***as installed*** is operating
within its stated accuracy and precision limits over time. Accuracy
goals depend on the questions being addressed and the inherent
variability of the quantity being measured. Generally as the flux data
record lengthens the importance of small variations in flux responding
to the subtle shifts in weather pattern or successional change
increases. Ultimately, the science team at each site is responsible for
setting and implementing a quality assurance program for their
particular site. Measurement uncertainty needs to be small enough for
instance that hypotheses can be accepted or rejected with confidence, or
meaningful comparisons can be made among sites, between years, or to
model predictions. The essential element is for measurements to include
a traceable record to demonstrate their consistency and accuracy in
order to allow comparisons across the network and to include complete
documentation of the QA/QC procedures in a site description. This
document updates the core and desired measurement lists as well as
providing specific recommendations for their implementation and some
quality assurance measures. The guidelines presented here are a
distillation of collective experience making long-term flux measurements
and have incorporated many of the recommendations adopted by Fluxnet
Canada (Margolis *et al*. <http://www.fluxnet-canada.ca/home>). [Tables
1](#table-1.-core-ameriflux-measurements) and
[2](#table-2.-additional-desired-measurements) list the core and desired
measurement, its ID, and technique. Guidelines for site setup and
measurement techniques are described in subsequent sections.

### 1.0 TOWER PLACEMENT

Site requirements

The EC technique was established over uniform vegetative canopies with
short roughness lengths on flat terrain and large fetch. But our
interest in measuring net ecosystem carbon fluxes forces us to work in
ecosystems with aerodynamically rough canopies and challenging terrain.
Site requirements vary depending on the research questions, some general
guidelines and quality requirements apply in all cases. The tower should
be sited to maximize the time with winds blowing from the desired
landcover type, and with the longest upwind fetch attainable. If the
surroundings are not of a uniform cover type there needs to be some
analysis of prevailing winds to demonstrate that the desired sectors are
sampled uniformly through time. Consider the extreme example of a site
with two different forest types and a consistent daily wind cycle that
blew from one forest type and in the day and the other at night. Daily
integrated NEE in this situation would be uninterpretable. This extreme
condition is unlikely, but many sites could have more subtle wind
direction biases that need to be examined and considered in data
interpretation. All systems are subject to horizontal flux divergence,
advective motions and drainage of air sheds. The question becomes, how
much do these motions affect measured fluxes, and at what timescales. If
the terrain is complex and below-canopy drainage or advection is a
concern, placement of the tower should be on a relatively flat portion
of the fetch to minimize flows to- or away from the site. Regular
motions due to orographic effects or circulations associated with large
bodies of water should either be well studied and quantified, or
avoided. For further discussion see Loescher *et al.* in review).
Footprint analyses to determine the source area under different
stabilities, wind speeds and direction provide valuable guidance for
appropriate tower placement, documentation of site characteristics, and
definition of data acceptance criteria (Foken and Leclerc 2004, Schmid
1994, Schuepp *et al.* 1990).

The tower needs to be high enough to place the sensors well above the
surrounding canopy, but not so high that the footprint during stable
night-time conditions extends beyond the boundary of the ecosystem type
of interest. The tower should be constructed with minimum disturbance to
the adjacent ecosystem, but without compromise to safety or tower
reliability. Extensive clearing or use of large construction equipment
should be avoided as much as possible. Regularly scheduled tower
inspection and preventative maintenance according to tower manufacturer
recommendations are essential for assuring site reliability and safety
of personnel. .

In many locations lightning is common and measures need to be taken to
minimize the potential for instrument damage and loss of data. Proper
grounding of the tower, guywires, anchors, and buildings is an essential
component of construction. Local experts in the grounding of radio and
cell-phone towers may be the best source of specific designs appropriate
for the tower site. Induced voltages can occur in long signal wires from
sensors to data acquisition systems. It is inexpensive insurance to
place surge voltage protectors (i.e., breakaway fuses) on each signal
line (e.g., model SVP48 Campbell Scientific, Logan UT). Serial
communications and short haul modem s should also be protected, e.g.
with optical isolation. Obviously, site personnel should never risk
their lives by working on or around a tower when lightning storms are
nearby.

### 2.0 EDDY COVARIANCE FLUXES -- CO~2~ H~2~O, heat and momentum

**2.1 Required equipment**

Basic required equipment includes a three-dimensional sonic
anemometer-thermometer (SAT) and a fast response infrared gas analyzer
(IRGA).

AmeriFlux has not made specific recommendations for which SAT to use.
Available choices include ATI, Campbell, Metek, R.M. Young,
Koshin-Denki, and Gill Instruments (contact info listed on equipment
sources webpage). Each has their own advantages and disadvantages.
Comparison between the Campbell and other sonic thermometers suggest a 5
-- 10 % discrepancy in sonic temperature (Hollinger pers comm.), and may
be due to Campbell accounting for the temperature dependency of the
sonic transducers to measure the speed of sound (Tanner pers comm.).
Comparisons of wind statistics between the different SATs have shown
reasonable agreement. Available evidence suggests that bias due to
choice of SAT is less than 10% in favorable weather conditions
(Hollinger *et al.* in review).

Proper installation, maintenance, and data assurance of the SAT are more
important than choice of manufacturer. However, sensor configurations
that place the transducer array at the end of a horizontal boom are the
best choice. Vertically oriented transducer arrays appear to have
significant errors when the attach angle of wind is very steep (Gash and
Dolman, 2003). The SAT should be installed on a firm and steady support
(mast or post) facing into mean wind direction to minimize disturbances
and flow distortions caused by the tower structure itself (i.e., winds
through and around the tower) that require data to be rejected. SATs
should be clean and free of debris (i.e., bird droppings). Manufacturers
often require a zero (wind) offset to be periodically calibrated. For
example, ATI supplies zero air chambers and suggest that zero offset
calibrations be made for specific humidity and temperature operating
ranges. SAT fail when wet or when the path is obstructed, as in the case
with hoar frost or freezing rain. SATs may have to be heated when frozen
over with frost. Age and wear of sonic transducers may require
replacement. Rain, dew (water droplets), snow and frost on the end of
the sonic transducer changes the path length to estimate speed of sound.
Each SAT model reacts differently to light rain events, but all fail in
heavy precipitation. Many SATs report data quality flags, which need to
be recorded and interpreted. Independent checks on air temperature and
wind statistics are essential for demonstrating long-term accuracy of
the SAT and for identifying periods for which the SAT data are
unreliable. The SAT should be kept level to reduce uncertainties in wind
direction and minimize errors associated with large rotation angles.
Each time the SATs are moved rotation angles have to be recalculated if
planar fit rotation schemes are used. The importance of tower stiffness
and guy-tension adjustment becomes apparent when considering long-term
maintenance of SAT level.

Two types of gas analyzers can be used to simultaneously measure high
frequency CO~2~ and H~2~O concentrations, (i) closed-path and (ii)
open-path. The first has an internal sample cell (optical bench) through
which sampled air must be drawn. Temperature and pressure within the
sample cell are different from the ambient condition and with
appropriate plumbing configuration can be precisely controlled to
constant values. The open-path sensor makes a measurement in situ where
the gas density is affected by ambient pressure and temperature. In both
cases the analyzer consists of a light source and detector. In the
closed path analyzer, a second, or reference cell, with gas having zero
or a known concentration of the analyte is used to account for
variability in the light source and detector. For the open path sensor,
an adjacent non-absorbing wavelength is used as reference. Models
Li-6262 and Li-7000 (Li-Cor Inc., Lincoln NE) are examples of the first
and model Li-7500 (Li-Cor Inc., Lincoln NE) is an example of the second.
The krypton hygrometer (model KH20, Campbell Scientific, Logan UT, or
model BLR Lyman- hygrometer, Electromagnetic Research Inc.) are common
alternatives to measure high frequency H~2~O concentrations. The LI-7000
has a higher frequency response (real 10 Hz or greater) than the LI-6262
(DAC and 0.1s channels operate at \~ 8 and \~ 5 hz for CO~2~ and H~2~O,
respectively). In order to minimize zero calibration drift (discussed
further below), either closed-path instrument should be enclosed in a
temperature-controlled environment. Pressure within the sample cell
should also be accounted for. Li-7000 has pressure sensor factory
installed, and the Li-6262 it is an accessory (model Li-6262-03,). The
pressure correction can either be applied by the instrument's software,
or if raw signals are recorded the pressure is recorded as well and the
correction term is applied off-line during data reduction. The inlet
tube required to bring ambient sample from the outside into the analysis
cell will have an affect on frequency response in the closed-path
analyzers. Selection of tubing material, design of the overall plumbing
configuration, and maintenance of tube cleanliness can mitigate the
attenuation of high frequency components. Examination of signal spectra
and co-spectra is necessary to identify and quantify the magnitude of
high frequency attenuation and its affect on the computed fluxes for an
individual site.

Open-path analyzers (e.g. Li-7500) have the advantage of an excellent
high frequency response but do not operate when the windows are wet or
icy. Furthermore, the open-path analyzers are not amenable to automated
routine calibrations and are not suitable for measuring high-precision
high-accuracy CO~2~ concentrations.

If high-frequency response were the only consideration, open-path
sensors would be the ideal solution. However, the gain in high frequency
response is made at the expense of increased down time (from rain and
inclement weather), and the need to include heat fluxes in the
calculation of CO~2~ and H~2~O fluxes (Webb *et al.* 1980, Luening *et
al*. 2003), which add additional uncertainties. At sites with frequent
precipitation, or large heat fluxes this may not be an acceptable
tradeoff. If high-frequency flux components are observed to be
negligible the open path sensor has less advantage.

**2.2 Closed-path IRGA arrangement**

**Temperature control**. Temperature should be controlled to minimize
the zero signal drift in the IRGA. For instruments that are mounted
outdoors a temperature controlled housing with a setpoint at few ºC
above ambient maximum is ideal. Maintaining temperature above ambient
allows heat loss to the environment to be used for temperature control
and ensures that non-condensing conditions within the system are
maintained at all times. Obviously this approach is not universally
applicable, as it would require instruments in hot climates to operate
above the acceptable range for the IRGA. Placement of the instrument
inside a climate-controlled building reduces the need for an actively
temperature-controlled enclosure; however, the IRGA needs to be placed
where air conditioning and space heating will not cause rapid
temperature variations. Signal drift that is not avoided by temperature
control will need to be compensated for through frequent calibrations.
For instruments inside air-conditioned buildings in humid climates
pressure drop in the sample line along with heating the inlet lines is
needed to prevent condensation. Damping the temperature fluctuations in
the tubing before entering the IRGA is essential. (see Webb *et al.*
1980). Often the tubing is insulated and heated to a constant
temperature for a few meters before the IRGA inlet. An alternative to
this approach is using a few meters of metal (non-reactive) tubing
before the IRGA inlet as a heat sink.

**Evaluate frequency response.** The Li-7000 has an inherently higher
frequency response than the Li-6262, which makes it preferable for
low-stature or aerodynamically smooth sites. Spectra (IRGA signals) and
cospectra (between IRGA and SAT signals) need to be examined to
demonstrate that the selected instrument in its deployed configuration
responds to all relevant frequencies. The use of ogive analyses
(integrated cospectra) can assess the time periods needed to capture low
frequency flux (e.g., the effects of local and mesoscale motions), thus
determining the appropriate averaging times (Berger *et al.* 2001).

**Tubing choice and Flow rates**. Best choices of tubing have been found
to be Dekoron, Teflon or stainless steel. These materials have
acceptably low H~2~O and CO~2~ adsorption if kept clean and above
dew-point temperature (see below), and they are resistant to UV damage
and embrittlement in cold temperatures. Evaluation of tubing by
examination of spectra and periodic testing by introducing step changes
in H~2~O and CO~2~ concentrations is required to confirm continued data
quality. Turbulent flow is desired in order to insure maximum frequency
response of the gas analysis system, typically indicated by a Reynold's
number (***Re***) \> 2300, eq 1.

$\text{Re} = \frac{\text{ud}}{\nu}$ Eq. 1

where ***u*** is mean free stream velocity (cm s^-1^), ***v*** is
kinematic viscosity of air (cm^2^ s^-1^), and ***d*** is characteristic
dimension and in this case, the tubing inner diameter (cm). Selection of
tubing diameter and flow rate requires for a given inlet length requires
optimization. High flow rate reduces sample delay (sensor separation)
and maintains turbulent flow. Analytical sensitivity however, is
sacrificed as pressure drop increases. In practice, the frequency
response continues to improve with increasing Re, Re = 3000 to 3,500 is
recommended. Dead volumes, sharp bends, and restrictions in the tubing,
that introduce mixing will attenuate high-frequency variability and
should be minimized as much as practical. Flow rate through the Li-6262
should not surpass 10 L min^-1^ because it exceeds the time constant
within the sensor. To achieve large flow rates needed to minimize delay
and ensure turbulent conditions without exceeding the flow limits of the
sample cell set up a bypass pump to draw a large volume of air through a
relatively large diameter tubing and take a subsample of air through the
analyzer

The entrance to the sampling tube should be positioned as close to the
center of the sonic transducer array as possible and slightly behind the
transducers so that there is no distortion of wind flow from prevailing
winds. The SAT should be oriented facing the direction of prevailing
winds. Directing the inlet downward and inserting it through a small
funnel or drip-tip will minimize the chance of ingesting liquid during
rain. A mosquito mesh over the mouth of funnel is also helpful if
insects are prevalent. Fine particles should be kept out of the sample
line and instrument using a filter An open face filter will act as the
rain shield and introduces less of a mixing volume than many inline
filters do. Filters should be changed often enough so that flow rates
are not decreased below desired values and there is no evidence of
degradation of high frequency responses for water vapor by sample air
interacting with collected dust. Likewise, replacement of the inlet tube
can be determined by monitoring the high-frequency response for water
vapor.

**2.3 Open-path IRGA arrangement**

When an open -path IRGA (e.g. LI-7500) is used, an independent method of
determining absolute CO~2~ concentrations with high accuracy is
required. The open path instrument is useful where high frequency
fluctuations contribute significantly to flux. It is valuable to compare
open- and closed-path systems to assess the high frequency losses
associated with closed-path systems.

The open-path IRGA should be mounted following the recommendations for
positioning the entrance of the sampling tube in the closed--path IRGA
arrangement (see above), e.g., such that the open-path should be
co-located with the sonic volume without causing flow distortions in the
wind velocity measurements. Orienting the main axis of the instrument
15° - 30° with respect to the horizontal helps drain water from rain or
dew off the light-source (lower) window. An inexpensive rubber o-ring
(1.875") placed over the detector head (upper) can also act as a
drip-tip, shedding water from light rains from migrating over the
window. Because the open-path IRGA does not measure during precipitation
it is not recommended as the sole instrument for long-term CO~2~ flux
measurements. The open-path IRGA is ideal when power supply is low. They
can run for long periods of time unattended on 12 vdc, eliminating the
need for pumps and climate control of a closed-path IRGA.

### 3.0 DATA ACQUISITION EQUIPMENT AND PROCESSING

**3.1 Signal** **measurement** **frequency**

Sampling frequency should be as high as practical, and high enough to
demonstrate that the full range of frequencies carrying the turbulent
flux has been sampled. The necessary sampling frequency will depend on
site characteristics, with lower sampling frequencies being acceptable
over tall rough canopies than over smooth short-stature vegetation.

The choice of data collection hardware does not directly influence the
data quality as long as the hardware configuration is sufficiently
reliable to avoid data loss and has enough resolution to capture the
relevant signal fluctuations. Linking the SAT and IRGA data stream
together often utilizes some configuration of A2D processing. The A2D
resolution limits the available concentration range that can be
measured. For example to achieve resolution of 0.1 ppm with a 12-bit A2D
the range between maximum and minimum concentration can be 400 ppm,
which is probably adequate for most situations. For greater resolution
or a wider concentration range a higher resolution A2D may be required.
Obviously, if the data system can directly store the serial data from
the IRGA, A2D resolution issues are eliminated. However, serial data
introduces the need for a system that can read multiple serial inputs,
and software to ensure that the data streams are time synchronized.

**3.2 Data** **processing** **programs**

Periodic comparisons of data processing software have shown that
differences in the processing do not significantly affect the final
results as long as the same rotation, averaging routines, and correction
terms are applied. A standard set of raw closed-path data file developed
by the Euroflux network ('gold files'
<http://cdiac.esd.ornl.gov/ftp/ameriflux/gold/info.html>) has been used
to intercompare results of existing processing codes. Whenever new
processing routines are developed they should be compared to
pre-existing routines by processing the same data. The gold files should
be analyzed to intercompare processing between groups. New gold files
developed by Ameriflux for open-path sensors can be found at
<http://cdiac.esd.ornl.gov/ftp/ameriflux/gold>. Results to each of the
'gold' files can be acquired by writing hank.loescher@oregonstate.edu

**3.3 Flux** **calculations**

Basic equations and conversions for calculating flux densities of
sensible, latent and carbon dioxide from eddy covariances follows. The
standard properties of air are from List (1951). Of course, the units of
scalar quantities may be different depending on the type of instrument
and its configuration for the data had been collected.

***Sensible Heat***

$H = \left( \frac{M_{a}C_{p}}{V} \right)\left( \overline{w't_{s}'} - \left( 0\text{.}\text{000321}T_{k}\overline{w'q'} \right) \right)$
Eq. 2

where

***H*** is sensible heat (W m^-2^), ***M~a~*** is the molecular weight
of dry air (0.0289644 kg mol^-1^), ***C~p~*** is the specific heat of
dry air (1004.84 J K^-1^ kg^-1^), ***V*** is the molar volume of air (Eq
3, m^3^ mol^-1^), $\overline{w't'}$ is the time-averaged (i.e., 30-min)
covariance of vertical wind velocities (m ºC s^-1^), ***w*** (m s^-1^)
and sonic temperature, ***t~s~***, (Eq 4, º C), ***T~k~*** is the actual
air temperature (º K) estimated from the sonic temperature (Eq 5, Kaimal
and Gaynor 1991), and $\overline{w'q'}$is the time-averaged covariance
(m mmol water s-1 mol air-1) of w and water vapor, q (mmol mol^-1^).

$V = \frac{\text{RT}_{k}}{P}$ Eq. 3

where, ***R*** is the ideal gas constant (0.082 L atm K^-1^ mol^-1^),
and ***P*** is atmospheric pressure (1.10325 atm).

$T_{s} = \frac{c^{2}}{\left\lbrack \text{430}\left( 1 + \frac{0\text{.}\text{32}q}{P} \right) \right\rbrack}$
Eq. 4

where, ***c*** is the measured speed of sound (m s^-1^) ***403*** is the
product of ***R*** (287.04 J K^-1^ mol^-1^) and the ratio of the
specific heats of moist air at constant pressure and constant volume
(C~p~\*/C~v~\*). This ratio is very close to that for dry air, thus
C~p~\*/C~v~\* \~ C~p~/C~v~ = 1.4.

T~K~ is the actual air temperature, estimated by,

$T_{k} = \frac{T_{s}}{\left( 1 + 0\text{.}\text{000321}q \right)} + \text{273}\text{.}\text{15}$
Eq. 5

If a correction for crosswind effects on the temperature measurement
(typically derived from the vertical wind velocity component) is
required, then the above equation should be modified as follows (Kaimal
and Gaynor 1991).

$$$H = \left( \frac{M_{a}C_{p}}{V} \right)\left( \overline{w't_{s}'} - \left( 0\text{.}\text{000321}T_{k}\overline{w'q'} \right) + \frac{2\overline{u}\overline{u'w'}}{\text{403}} \right)$
Eq. 6

where, is the time-averaged horizontal wind velocity (m s^-1^), is the
time-average covariance of u and w (m2 s-2). Correction for crosswind
effects are not required for ATI probes, Campbell CSAT3 or Gill R series
SATS)

***Latent Heat***

$\lambda E = \frac{{\lambda M}_{w}\overline{w'q'}}{V \cdot \text{1000}}$
Eq. 7

where, ***E*** is the latent energy flux (W m^-2^), is the latent heat
of vaporization of water (2500.8 - 2.3668 T~s~, J g^-1^, List 1951),
***M~w~*** is the molecular weight of water (18.015 g mol^-1^).

***CO~2~ Flux***

$\text{FCO}_{2} = \frac{\overline{w'c'}}{V}$ Eq. 8

where, ***FCO~2~*** is the estimated carbon flux (mol m^-2^ s^-1^), and
$\overline{w'c'}$ is the measured covariance (m s^-1^ mol C mol^-1^).

**3.4 Quality** **control**

Eddy covariance and profile data are typically screened for validity and
removed when either i) SAT or IRGA data flags indicate problem data, ii)
SAT or IRGA signals were out-of-range (Hollinger *et al*. 1995, Anthoni
*et al*. 1999), iii) rain occurred, or, iv) 30-min data collection
periods were incomplete. Other diagnoses often include i) variance
filters (i.e., when signals are outside a preset, physically meaningful
variance threshold, assuming a Guassian distribution), ii) stability
parameter (either monin-obukov stability parameter, eq. 2, or Richardson
number eq.3), or iii) some indication of non-stationarity (time series
for wind statistics in steady state, Foken *et al.* 2004, Foken and
Wichura 1996).

$l = (z - d)\frac{- {\rho C}_{p}T_{a}u^{3}}{\text{gkH}}$ Eq. 2

where ***z*** is the measurement height (m), ***d*** is zero plane
displacement (m), is the density of air (kg m^-3^), ***C~p~*** is the
specific heat capacity of air (J kg^-1^ K^-1^), ***T~a~*** is air
temperature in Kelvin (K), **u\*** is friction velocity (m s^-1^),
***g*** is acceleration due to gravity (m s^-2^), **k** is the von
Karmen constant (0.41, dimensionless), and ***H*** is the sensible heat
flux density (J m^-2^ s^-1^, Rosenberg *et al*. 1983, Montieth and
Unsworth 1990, Pahlow *et al*. 2000).

$\text{Ri} = \left( \frac{g}{T_{a}}\frac{\partial T_{a}}{\partial z} \right)/\left( \frac{\partial u}{\partial z} \right)^{2}$
Eq. 3

Where u is horizontal wind velocity (m s^-1^).

Assumptions in the eddy covariance technique require turbulent
conditions, i.e., shear stress and surface heating. Researchers have
found that empirical relationships between u\* and scalar fluxes can
determine 'well-mixed' conditions. Hence, a u\* threshold is often
employed to remove data during stable conditions when vertical
turbulence is not the dominant transport pathway. This is an active area
of research though, and use of a u\* threshold must be rigorously
examined. Further discussion on u\* and its role in estimated of
turbulent exchange can be found in Loescher *et al.* (in review). There
is no set standard for data removal, or recommendations that work
universally across sites.

Gaps in the data sets are unavoidable. Filling or averaging routines are
required for providing integrated fluxes over longer intervals. Falge
*et al*. (2001) discuss three methods for gap filling carbon flux data;
mean diurnal variation, non-linear regressions, and look-up tables based
on meteorological and seasonal conditions. Unfilled data need to be
presented for use in comparing responses to environmental forcing over
time or between sites. Integrated, or gap-filled data is not suitable
for instance to compare light-response curves among sites because the
filling routine may have imposed a light response.

### 4.0 CALIBRATION PROCEDURES 

**4.1 IRGA calibration**

Ultimately, measurement data are only as good as the calibrations. It is
encouraged that all sites make their measurements with the highest level
of precision and accuracy that is practical. The level of precision and
accuracy\--and frequency of calibrations to achieve these desired levels
rely on the Principle Investigators experience to capture the abiotic
and biotic events needed to answer their research questions (*e.g.*,
synoptic-to-local circulations, punctuated rain events, soil CO~2~
pulses, etc..), and rely on those in the network that use these data for
among-site research questions.

Independent verification by periodic calibration (lab, factory and *in
situ*) is required to demonstrate that calibration drift, artifacts, or
other interferences do not affect the data. External desiccants and
filters need to be inspected frequently, \~ 7 d and exchanged when
necessary. Internal filters and desiccants should be replaced every 6
months, regardless of contamination. It is also important to recognize
that measurements of concentration and flux face different sources of
uncertainty. CO~2~ flux measurements are mainly dependent on the
accuracy with which the instrument's gain (span) is determined.
Variations in the zero over time scales longer than the flux-averaging
interval (typically 30-min) are less important because they are removed
by the averaging operator (*i.e*., block average, detrending, etc.).
Calibration to within ±0.2% accuracy will generally be sufficient to
meet the needs for flux measurements. Both the zero and span affect
concentration measurements, and the accuracy requirements become more
stringent. A 2% error in concentration of a purchased standard gives an
associated uncertainty of 7 ppm or more\--which is unacceptable when
analyzing spatial gradients between sites across a network, or vertical
gradients between surface sites and aircraft which can be ≤ 1 ppm.
Moreover, when flux and concentration measurements are made available to
the greater flux community, they have a great utility in developing
ongoing research questions (*i.e.,* data assimilation projects, regional
constraints, etc.).

There are measurement uncertainties caused by i) the factory polynomial
that determines the instrument response to the scalar, ii) the
repeatability of the measurement, and iii) the reproducibility of the
instrument (zero and gain function). Each of these uncertainties have
more than one contributing factor (*cf*. Ocheltree and Loescher 2006).
The first two sources of uncertainty are often determined by the
manufacturer. Even though the factory calibrations are not adequate by
themselves as a measurement standard, the polynomials and
reproducibility can be estimated in the lab with the proper equipment
and scalar standards. Hence, IRGA polynomials and reproducibility should
be checked, and changed if necessary every 3-12 months depending on the
application (regardless of either open- or closed-path design). *In
situ* calibrations that adjust the zero and span (gain) of the IRGA
addresses the third source of uncertainty, *i.e.*, reproducibility.
AmeriFlux recommends that the gain does not change more than 5% across a
10 ppm range between *in situ* calibrations. The frequency between *in
situ* calibrations can be different for open- and closed path designs,
and should be determined dependent on the specific research questions to
be answered. Manual *in situ* calibrations for closed-path IRGAs are
typically more frequent than open-path designs, every 3-7 d. A better
alternative is to automate zero and span calibrations to every 4-10 h to
assess the drift in gain (see below). Open-path IRGAs tend to be less
accurate while maintaining similar high levels of precision compared to
closed-path designs. But they are also subject to ambient conditions
that may affect its operation, *e.g.*, wet and dry deposition. At
minimum, inspection of the windows, diagnostic flags should occur ca.
every7 d, and *in situ* open-path calibrations should be checked and
changed if necessary every 21- 42 d.

Additional information on CMDL gas standards see;
<http://www.cmdl.noaa.gov/ccgg/refgases/>

And on making high precision CO~2~ measurements see, Zhao *et al.*1997
and <http://rflux.psu.edu/>

Closed-path instruments should be configured for automatic routine
calibrations. The simplest approach is to supply an excess of CO~2~-free
air (N~2~) or working standards that bracket the range of observed
concentrations to the sample inlet. An excess flow of 20-30% assures
that no ambient air is drawn into the optic bench during the
calibration. The calibration needs to run long enough that the entire
volume of tubing and analyzer cell is flushed completely and data from
the end of calibration interval are collected for a sufficiently long
period to return valid statistics. By delivering calibration gas to the
inlet and venting it to the atmosphere there is no need for pressure and
flow control, but excess gas is consumed. If the pressure and flow in
the analyzer are actively controlled it is preferable to calibrate by
operating a valve to switch between ambient sample and calibration
source. A needle valve, frit, or mass flow controller can be used to
provide pressure drop between the high pressure standard tank and the
low pressure analyzer cell. If only the instrument gain needs to be
determined, a standard addition calibration by adding a small known
volume of high concentration CO~2~ to the main flow is an option. Two
mass flow meters are required to measure the flow of sample and of
calibration gas. Any calibration approach that involves introduction of
a calibration gas near the inlet has the added benefit of providing a
test of wall interactions and mixing in the inlet tube by evaluating the
rise and fall of signal when the calibration is turned on and off.

There are differing opinions on whether it is better to configure the
CO~2~ analyzer in absolute mode, using CO~2~-free air or N~2~ as a zero
reference gas or in differential mode using a near-ambient CO~2~ in air
as the reference. Differential mode requires that the analyzer is
configured to maintain the same pressure in sample and reference cell
but the concentration range between 'zero' and sample that must be
recorded is narrower. Absolute mode reduces the dependence on pressure
in the reference cell because there are no gases that absorb IR,
however, the data system will need to have adequate resolution to record
the entire span between 0 and ambient CO~2~ concentrations in order to
include a zeroing in the calibration sequence.

**4.2 Sonic anemometer-thermometer calibration**

Each flux station should attempt to carry out short-term (3 - 10 day)
comparisons of their operating field sonic anemometers with their spare
unit. The spare unit should be mounted at the same level as the field
unit. An important goal of the cross-site EC calibration program is to
assess the performance of the sonic anemometer operating at the main
site of each flux station. Another important daily check is the
comparison of half-hour values of \"cup wind speed\" and wind direction
calculated from horizontal wind vector components (*u* and *v*) measured
by the sonic anemometer (2*uv*2+) with wind speed/direction measured
independently by a wind-vane and anemomter. The agreement should be
within 5%.

Air temperature (T~a~) and sonic temperature (T~s~), differ due to the
contribution of water vapor to air density. T~a~ should be measured
using an aspirated shield (discussed below). T~s~ may also have to be
adjusted to approximate T~a~ and subject to cross-wind effects. For
further discussion see Kaimal and Gaynor (1991) and Schotanus *et al.*
(1983).

**4.3 Temperature and Humidity**

In principle, temperature and humidity these are simple measurements to
make, yet, as experience tells us, they have high disagreement between
site sensors and those in the AmeriFlux portable EC system site. To
avoid errors due to solar heating, temperature and humidity sensors need
to be protected by an aspirated radiation shield. If temperature sensors
are used in conjunction with flux profile measurements, sample inlets
can be collocated with temperature sensors inside a radiation shield to
quasi-aspirate the sensor. Platinum resistance probes, thermistors, or
thermocouples can all be used to measure with sufficient precision and
accuracy. If Pt100 probes are used, they should be connected according
to manufacturer's recommendation for using the 4-wire output to
compensate for resistance changes in the cable and linearizing the
signal. Thermistors (e.g., 30k ohm) have high enough resistance that
variations due to the cable length are insignificant. Thermocouples are
inexpensive and need an independent reference temperature. In all cases,
temperature sensors should be calibrated initially at known
temperatures. An insulated ice bath and water vapor at boiling point are
two suitable standards (procedures can be found in chemistry texts).
Periodic comparisons to a calibrated thermometer can be made *in situ*
to verify performance over time.

Capacitance sensor chips (e.g. Vaisala HMP45) are suitable for long-term
humidity measurement. Factory calibration should be verified
periodically by comparison to in situ measurements such as wet-bulb
psychrometer, a chilled-mirror instrument, or measurement of humidity
over a series of saturated salt solutions.

**4.4 Radiation sensors**

Net radiation is frequently measured with a net radiation sensor, which
utilizes two optically black thermopiles to detect the difference in
total incoming and outgoing radiation (e.g., Kipp and Zonen NR lite,
REBS Q\*7.1). Preferably the individual components of up- and
down-welling short- and long-wave radiation are measured separately to
derive the net radiation, albedo, and effective surface temperature
(e.g., Kipp and Zonen CNR1, Eppley PSP). These data are primarily used
for understanding surface energy budgets and are reported in W-m^-2^.
Some of these black thermopiles are sealed and require little
maintenance besides cleaning. Others are housed inside glass or plastic
domes and can require heating and dried air to prevent condensation. As
in the case with the REBS Q\*7.1, the domes may be particularly prone to
attack by birds. The portion of solar radiation utilized by vegetation
(photosynthetically active radiation) is measured as a
photosynthetically active photon flux density (PPFD) by quantum sensors.
The fraction of light absorbed by the canopy is also a critical
parameter for evaluating CO~2~ uptake over time, across sites, or
between models and observations. Sites should include a PPFD sensor
below the canopy, but the optimum strategy for quantifying spatial
variability beneath the canopy is highly site dependent.

Because radiation sensors age, cross-site comparisons or long-term
trends in surface energy properties or photosynthetic light-use
efficiency are critically dependent on maintaining accurate calibrations
to ensure that the radiation measurements are comparable through time.
To detect a 10% change in photosynthetic efficiency between different
growing seasons requires that the PPFD calibration is constant to better
than 10%. Sensor placement must be made so that upward facing sensors
are not subject to shadowing from the tower. Downward facing sensors
should be as high above the canopy and extend as far from the tower
structure as possible to provide a maximum field of view and minimize
the portion of their viewing area that is tower structure and not
canopy. Calibration using a transfer standard instrument is required at
least annually. The transfer standard is only exposed for a few days at
a time during calibration and should be calibrated at the factory or
suitable radiation facility periodically. Intersite comparisons require
shared transfer standards or that all the calibrations are referenced to
a common scale.

**4.5 Wind speed** **and** **direction**

Although the Sonic anemometer provides wind speed and direction, it is
preferable to have an independent measurement with which to compare the
sonic data. Standard meteorological wind vanes and cup anemometers
should be installed according to routine meteorological guidelines.
Single units that include wind vane and propeller anemometer are
convenient, but separate wind vanes and spinning cup anemometers are
suitable as well. All mechanical anemometers need a minimal wind speed
to overcome inertia; this break through volume should be as low as money
permits. Proper placement of the wind monitor is crucial. Wake
turbulence (flow distortions) from trees and other tall structures
upwind can greatly influence measurements. To get meaningful
measurements, situate the wind monitor well above (including the tower
on which it is installed) or upwind of major obstacles. A single
measurement at an arbitrary height above the canopy has limited value as
a network measurement. More useful is to determine a vertical profile of
wind speed that can be used to define drag coefficients and zero plane
displacement height. For meaningful comparisons across sites it is
essential that data below minimum wind speed threshold be treated
consistently. Data documentation for each site must include information
on the wind sensor performance specifications and define the procedures
for treating low wind speeds. Frequent inspection of the raw data to
evaluate the windspeed cutoff is required to detect any sensor
degradation. Mechanical anemometers will need periodic maintenance
(bearing replacement).

**4.6 Precipitation**

Precipitation is another seemingly trivial measurement that is in fact
prone to large uncertainty. Significant differences in precipitation may
be observed between a gauge mounted above the canopy on the tower and
one at the ground in a nearby clearing. Collection efficiency is
dependent on wind speed. Spatial variability may be significant for
small rain showers or at sites with orographic precipitation. The best
approach for precipitation measurements that can be compared across the
network is to adopt standard precipitation protocols for National
Weather Service observing stations, or rely on NWS observations made
nearby, particularly if there is a spatially dense network of
cooperative observation sites in the region. Rain gauges should be
cleaned and leveled often. Throughfall, the precipitation that reaches
the ground below-canopy, is extremely heterogeneous. Methodologies
should embody the spatial variability inherent in the ecosystem in
question. For more on throughfall see Roberts *et al.* (in press) and
Loescher *et al.* (2002).

### 5.0 PROFILE AND CO~2~ and H~2~O CONCENTRATIONS

The change of CO~2~ storage between the EC measurement height and the
ground would be close to zero over a daily cycle if there are not net
losses due to advection. The small change in storage from variations in
the mean concentration are likely insignificant. Over short intervals,
particularly at the dusk and dawn transitions, storage is important and
Net Ecosystem Exchange is unequal to the vertical eddy flux of CO~2~.
The storage term is derived as the time derivative of the column
integral of concentration. An ideal measurement of storage would use a
vertically integrating inlet to get a true column average between the
ground and eddy sensor height. In practice, the shape of the
concentration profile can be of interest for quantification of source
and sink structure in the canopy. The profile is determined from
individual inlets that are sampled sequentially. The number of inlets
and their spacing need to be designed to adequately capture the shape of
the concentration profile. Exact spacing and number are site dependent.
Typical installations deploy 6 - 8 inlets per 30 m and a separate
closed-path IRGA to measure the CO~2~ and H~2~O concentrations.
Calibration and quality assurance protocols need to be consistent with
consistent with those for the eddy CO~2~ measurements. Changes in
pressure will affect the CO~2~ signal, so pressure differences should be
eliminated by matching the inlet lengths or installing an active
pressure control system.

### Table 1. Core AmeriFlux Measurements

+-----------------------+-----------------------+-----------------------+
| Parameter/Variable    | ID                    | Note                  |
+-----------------------+-----------------------+-----------------------+
| Biosphere-atmosphere  |                       |                       |
| interface CO~2~,      |                       |                       |
| water vapor, and      |                       |                       |
| energy flux           |                       |                       |
+-----------------------+-----------------------+-----------------------+
| CO~2~ flux            | Fc30 or Fc60          | Eddy Covariance       |
+-----------------------+-----------------------+-----------------------+
| Sensible heat flux    | H30 or H60            | Eddy Covariance       |
+-----------------------+-----------------------+-----------------------+
| Water vapor flux      | E30 or E60            | Eddy Covariance       |
+-----------------------+-----------------------+-----------------------+
| Latent heat flux      | LE30 or LE60          | Eddy Covariance       |
+-----------------------+-----------------------+-----------------------+
| Momentum flux\        | TAU30 or TAU60\       | Eddy Covariance       |
| measured as\          | Uwcvar                |                       |
| Kinematic momentum    |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Meteorological data   |                       |                       |
| and consequences      |                       |                       |
| (e.g. wetness)        |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Air temperature       | Ta30 or Ta60          | Aspirated/Shielded    |
|                       |                       | temperature sensor    |
+-----------------------+-----------------------+-----------------------+
| Relative humidity\    | Rh30 or Rh60          | Aspirated/shielded    |
| Direct measure, or    |                       | humidity sensor, or   |
| computed from         |                       | absolute water vapor  |
| absolute humidity     |                       | measurement           |
+-----------------------+-----------------------+-----------------------+
| Vapor pressure        | VPD30 or VPD60        | Calculated            |
| deficit               |                       |                       |
|                       |                       |                       |
| (calculated)          |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Net radiation         | Rn30 or Rn60          | Net radiation sensor  |
|                       |                       | or sum of components  |
+-----------------------+-----------------------+-----------------------+
| Global Radiation      | Rg30 or Rg60          | Global Radiation      |
|                       |                       | sensor                |
+-----------------------+-----------------------+-----------------------+
| Photosynthetic Active | PPFD30 or PPFD60      | Quantum sensor        |
| Radiation\            |                       |                       |
| (Photosynthetic       |                       |                       |
| active Photon Flux    |                       |                       |
| Density, Incident     |                       |                       |
| PAR)                  |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Wind speed            | WS30 or WS60          | Sonic or cup          |
|                       |                       | anemometer            |
+-----------------------+-----------------------+-----------------------+
| Wind direction        | WD30 or WD60          | Sonic anemometer or   |
+-----------------------+-----------------------+-----------------------+
| Friction Velocity\    | USt \*                | Calculated            |
| (calculated from      |                       |                       |
| u'w\')                |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Atmospheric stability | ZL30 or ZL60          | Calculated            |
| parameter\            |                       |                       |
| (calculated)          |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Precipitation         | P30 or P60            | Standard rain gauge   |
+-----------------------+-----------------------+-----------------------+
| Within canopy data,   |                       |                       |
| e.g. profiles         |                       |                       |
+-----------------------+-----------------------+-----------------------+
| CO~2~ concentration   | Co30 or Co60          | CO~2~ analyzer with   |
| profile               |                       | inlet manifold        |
+-----------------------+-----------------------+-----------------------+
|                       |                       |                       |
+-----------------------+-----------------------+-----------------------+
|                       |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Humidity              | Ho30 or Ho60          | H~2~O analyzer with   |
|                       |                       | inlet manifold        |
+-----------------------+-----------------------+-----------------------+
| Dew-point temperature | T0dew30 or Tdew60 \*  | Calculate from        |
|                       |                       | humidity and          |
| (Calculated or\       |                       | temperature, or       |
| direct measure)       |                       | direct measure using  |
|                       |                       | wet-bulb or chilled   |
|                       |                       | mirror                |
+-----------------------+-----------------------+-----------------------+
| Need a sub-canopy     |                       |                       |
| light msmt.           |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Derived variables:    |                       |                       |
| CO~2~, water vapor    |                       |                       |
| and energy storage    |                       |                       |
+-----------------------+-----------------------+-----------------------+
| CO~2~ storage in      | Sc30 or Sc60          | Calculate from        |
| canopy air layer      |                       | profile,or measure as |
|                       |                       | concentration from    |
|                       |                       | integrating inlet     |
+-----------------------+-----------------------+-----------------------+
| Soil efflux of CO~2~, |                       |                       |
| water vapor, and      |                       |                       |
| energy in addition to |                       |                       |
| soil moisture and     |                       |                       |
| temperature profiles  |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Soil CO~2~ flux, Soil | FCSOIL30 or FCSOIL60  | Soil respiration      |
| respiration           |                       | chamber\              |
|                       |                       | protocols discussed   |
|                       |                       | elsewhere             |
+-----------------------+-----------------------+-----------------------+
| Soil heat flux        | G30 or G60            | Heat Flux plates      |
+-----------------------+-----------------------+-----------------------+
| Soil temperature      | Tscm30 or Tscm060 \*  | Buried temperature    |
| (profile) (5/10/20    |                       | probes                |
| etc cm)               |                       |                       |
+-----------------------+-----------------------+-----------------------+
|                       |                       |                       |
+-----------------------+-----------------------+-----------------------+
| Soil water potential  | SWP \*                | In units of MPa       |
+-----------------------+-----------------------+-----------------------+

### Table 2. Additional desired measurements

  ----------------------- ----------------------- -----------------------
  Canopy air temperature  Tap30 or Tap60 \*       Multiple temperature
  profile                                         sensors

  Relative humidity       Rhp30 or Rhp60          Multiple humidity
  profile                                         sensors

  Short-wave Radiation    Rgs30 or Rgs60          Solar radiation sensor

  Long-wave Radiation     Rgl30 or Rgl60          Solar radiation sensor

  Reflected Radiation     Rr30 or R360            Downward facing
                                                  radiation sensor(s).

  Direct Radiation        Rb30 or Rb60 \*         Part of global
                                                  radiation, which is due
                                                  to the relatively
                                                  unmodified parallel
                                                  radiation in the direct
                                                  beam W m-2. (Pearcy
                                                  1991)

  Diffuse Radiation       Rd30 or Rd60            Part of global
                                                  radiation, which
                                                  includes reflected and
                                                  scattered radiation
                                                  from all portions of
                                                  the sky in units of W
                                                  m-2. (Pearcy 1991)

  UV Radiation            Ru30 or Ru60            Radiation of
                                                  wave-lengths between
                                                  0.1 and 0.4 m m. In
                                                  units of mW m-2 nm-1

  Absorbed PPFD           APAR30 or APAR60        Compute from incident,
                                                  reflected and subcanopy
                                                  PPFD

  Percent (Fraction)      FIPAR30 or FIPAR60      Compute from above
  Intercepted Radiation                           

  Barometric pressure     Pa30 or Pa60            Pressure transducer

  Throughfall             TF30 or TF60            Below canopy
                                                  precipitation
                                                  collection

  Stem flow               SF30 or SF60            Stem flow collars

  Snow depth              SNOWD30 or SNOWD60      Depth of the snow at
                                                  the ground, averaged
                                                  over the observed time
                                                  period in mm

  Canopy wetness          CW30 or CP60            Wetness sensor

  Light profile/tram data Rprof30 or Rprof60      In W m-2

  Soil Albedo             SAlb                    ???

  Litter Albedo           LAlb \*                 ???

  Canopy Albedo           CAlb \*                 Derive from up/down
                                                  radiation measurements

  Within canopy process                           
  parameters (Not                                 
  addressed in this                               
  document                                        

  Pre-dawn water          PSI                     (Note time of day:
  potential                                       dawn, pre-dawn) in
                                                  units of MPa (Strongly
                                                  suggested)

  Leaf water potential    LWP \*                  In units of MPa

  Stomatal conductance    Gs                      (minimum, spring) (vpd
                                                  response, vpd in kPa at
                                                  stomatal closure). The
                                                  gas exchange
                                                  measurement systems
                                                  usually provide
                                                  temperature, humidity,
                                                  and light. In mmol m-2
                                                  s-1

  Leaf net photosynthesis Psat                    Light response curves
                                                  (maximum photosynthetic
                                                  rate at light
                                                  saturation, A/Ci
                                                  curves). The gas
                                                  exchange measurement
                                                  systems usually provide
                                                  temperature, humidity,
                                                  and light. In µmol m-2
                                                  s-1

  Foliar respiration      RLD                     In units of µmol m-2
                                                  leaf area s-1

  Bole respiration        RB                      In units of µmol m^-2^
                                                  bole area s^-1^

  Xylem sapflow           TR30 or TR60            (transpiration) in
                                                  units of mm hr-1

  CO~2~ Drift             FcD30 or FcD60 \*       In units of µmol m-2
                                                  s-1

  Heat storage in canopy  Sa30 or Sa60            Compute from integral
  air layer                                       of density and heat
                                                  capacity with delta T
                                                  profile

  Heat storage in canopy  Sb30 or Sb60            Scale from deltaT and
  biomass                                         density and heat
                                                  capacity in the biomass

  Latent heat in canopy   Sw30 or Sw60            Compute from profile of
  air layer                                       dq/dt
  ----------------------- ----------------------- -----------------------

Poorly defined measurements that need some work

  ----------------------- ----------------------- -----------------------
  Bole temperature        Tbole30 or Tbole60      Inserted temperature
                                                  probes

  Soil water vapor flux   ESOIL30 or ESOIL60      ???

  Soil moisture (0-30cm/  SWCcm                   Gravimetric or TDR type
  etc)                                            probes
  ----------------------- ----------------------- -----------------------

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