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Getting help

For understanding the methods, have a look at our Biogeosciences paper at doi 10.5194/bg-15-5015-2018.

You may search the reddyproc-users list archive for answers. When using google, you may include site:lists.r-forge.r-project.org inurl:reddyproc-users along with your other search criteria.

Or join and post on the email list for general user discussions of the REddyProc package: 'reddyproc-users@lists.r-forge.r-project.org'.

Or emails us your questions.

Please, be patient, if you do not get immediate reply. We are scientists providing this tool for you, but usually have other higher priority tasks.

Please, do not send big data with your e-mail.

When reporting problems with the online tool, please, specify the id hat is assigned to your job. This id appears in the URL of the pages following the upload as ?fileId=<theNumber>.

When reporting problems with the R package, please, specify your operating system, the Version of R, and the version of the REddyProc package.

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Frequently asked questions

How to handle error: "Missing specified columns in dataset"

Most often, the input is not provided in correct format. Carefully reread the documentation on required input format, including case, type, and units of the columns. Also note to provide "tab-delimited or space-delimited ASCII file".

Which output columns should I use?

REddyProc produces a multitude of outputs for different u*thresholds and different methods. The outputs are described at web-menu entry Data Formates/Output format.

We recommend computing statistics across the outputs for different u* thresholds. However, its also save to use output generated using the 50% quantile of u* thesholds, e.g. NEE_U50_f. There are pros and cons for both using nighttime based and daytime based flux partitioning. For comparing to past results, the nighttime based option is probably more suitable: GPP_U50_f and Reco_U50_f.

I obtained some negative GPP, should I remove it?

Due to the random uncertainties in the eddy covariance measurements, the derived GPP fluxes can result in negative fluxes. This is due to the stochastic nature of turbulence and noise in the measurement signal.

With nighttime partitioning, in addition if modelled respiration is too high, GPP might become negative. If this is within the range of NEE uncertainty its normal. If its larger then the fitted respiration~temerature model was not adequate for the data. The partitioning methods only work at sites where respiration is primarily controlled by temperature. They will not work e.g. at some tropical sites, sites controlled by moisture, or at frozen soils.

In other words, though GPP cannot be negative by definition, GPP values derived from EC measurements may also contain (some small) negative values, since these are the GPP values plus their random uncertainty. Hence, the negative values are also correct and should NOT be removed when using the partitioned results. Removing the negative GPP values (e.g. by setting them to zero after processing) would introduce a bias in the derived GPP.

How can I compute uncertainty of daily or annual aggregates?

There are several kinds of uncertainty. First, random uncertainty that decreases in relative terms by aggregating many records. Second, there is systematic uncertainty of using a biased u* threshold that does not decrease during aggregation.

For the random uncertainty, use the equations for error propagation of sums of random variables (adding variances NEE_uStar_fsd^2), but take care for autocorrelations among records (see aggUncertainty vignette).

For systematic uncertainty, repeat all the computation with different values of the distribution of the u* threshold (The default processing setup) including the aggregation for each output columns. Next, compute statistics, i.e. the mean and standard deviation) across the different estimates of the aggregates (see end of use case vignette).

Both kinds of uncertainty are independent of each other and hence, variances add. On annual time scale, often the systematic u*-threshold associated uncertainty dominates and the random uncertainty can be neglected.

I have no incoming solar radiation (Rg) - What can I do?

Incoming radiation (Rg) is used for different purposes in REddyproc. The answer depends on which purpose.

Option 1: Estimate Rg by measured PAR

This should give reasonable results for gap-filling, nighttime partitoning, and daytime partitioning Rg = PAR/0.47

References e.g. Yu 2015 et al. 10.1016/j.enconman.2014.09.038, Britton & Dodd 1976, 10.1016/0002-1571(76)90080-7

Option 2: Use Rg of a geographically not to distant site

  • ok for night-time partitioning,
  • probably reasonable for gap-filling unless the periods where conditions differ much between the sites, and
  • do not use daytime partitioning.

Option 3: net radiation

is not an option for us, but try to convince us with your results.

How to handle error in partitioning "relationship between respiration and temperature could not be established"

Night-time based flux-partitioning estimates respiration by its relationship with temperature. If there is no good relationship you cannot apply night-time partitioning (E.g. with frozen soil, snow cover, or tropical sites with no pronounced temperature differences.)

Sometimes, the relationship is there also with a low temperature variability. Then you can try tuning the the required temperature range constraint to lower than 5 Kelvin:

YourEddyClass$sMRFluxPartition( parsE0Regression = list(TempRange = 3) )

Sometimes, there are just too few good-quality night-time records to estimate the existing relationship. Then you can provide a user-specified temperature sensitivity E0 to use, and be very cautios in interpreting results:

YourEddyClass$sMRFluxPartition( debug = list(fixedE0 = <yourE0Value>) )

Note, that this is an option implemented for debugging. Hence, only use this with great caution.

You can use a value determined at another year at the same site or a value from a very similar site. Or you can specify low, medium, and high values of E0 and inspect how this effects your results.

How can I display the R help page for REddyProc class methods/functions

R help can be request by typing ?functionName at the R command prompt. However, EddyProc is an R5 class and has its functions attached to the class as so called methods.

Use prefix sEddyProc_ before the method name to display the help page. E.g. for sMRFluxPartition type

?sEddyProc_sMRFluxPartition

The help for initializing the class with the call to new is displayed by typing:

sEddyProc_initialize

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