<div dir="ltr">Carl --<div><br></div><div>Sorry I'm just getting back to this from my email backlog. You raise a number of important issues that again would represent areas where we could improve EML. Currently, EML documents data and, outside of the methods section, does not have a machine readable way of differentiating the data source (e.g., observation versus simulation). This would be valuable. And even more so if it were a community standard way of flagging the source, i.e., a standard vocabulary. I haven't searched for such a vocabulary, but I'll bet there has been some work done. Once we had a vocabulary, we could decide if it merits a new field in EML, should be put in 'additionalMetadata' (with its drawbacks), or if there is an existing field that is appropriate.</div>
<div><br></div><div>For the case of 'arbitrary abundance units', I think your model has some form of abundance unit, implied by the unit of the initial abundance input (X_t where t=0) -- everything else derives from that, right? In any case, either the derived values have physical units (e.g., kg), or they are dimensionless numbers -- both of which can be indicated with EML's standard units. I don't think you should need any custom units just because its a simulation result.</div>
<div><br></div><div>Whether the data should be archived is largely a pragmatic issue. For complex models, its certainly valuable to archive the sim output and cite it in your papers along with the code that generated it. Some simulation data is too large to archive conveniently, but my guess is that is not the case for most fisheries simulations.</div>
<div><br></div><div>Good luck!</div><div><br></div><div>Matt</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 1, 2013 at 2:56 PM, Carl Boettiger <span dir="ltr"><<a href="mailto:cboettig@gmail.com" target="_blank">cboettig@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi eml-dev,<br><br></div>I am looking to document a simple simulated time series appropriately in EML and am unclear how to best describe units used. For example, perhaps one data set generates stock abundance from a stochastic Ricker model: <br>
<br></div><div>X_{t+1} = Z_t X_t exp(r (1 - X_t / K))<br><br></div><div>and the data consist then of time t, abundance X, and metadata stating the parameters. <br></div><div><br></div>One approach is to document the data in the same way comparable 'real-world' data might be documented. For instance, declaring that the simulated dynamics pertain to a particular species such as Anchovy, declaring the the abundance is in units of tonnes, time in years, the geography restricted to the Peruvian current, etc. This raises several issues. <br>
<br>While such assignments may best reflect the intended representation of the data, perhaps we want to be able to still distinguish these from real observations (programmatically, without consulting the methods section of the EML). What would be the best way to indicate that these are simulated instead of true observations? <br>
<br></div>Second, for many simulations such specificity is mere fiction, as the example may be intended to represent a certain species but the abundance has not been calibrated to any meaningful unit scale and would be better described merely as "arbitrary abundance units". On the other hand, a proliferation of customUnits seems undesirable as well. <br clear="all">
<div><div><div><div><div><br></div><div>Third, one might argue that such data should not be archived at all, but documented only by the code required to re-generate it (including random number seed, etc). Obviously this approach faces non-trivial challenges of computational replication (architecture, compiler, etc). <br>
<br><br></div><div>Thanks for any input and suggestions. <br><br><br>Cheers,<br><br>Carl<span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888"><div><br>-- <br><div dir="ltr">
Carl Boettiger<br>UC Santa Cruz<br><a href="http://carlboettiger.info/" target="_blank">http://carlboettiger.info/</a><br>
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