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<font face="Times New Roman, Times, serif">Dear Chris,</font><br>
<blockquote
cite="mid:OF13D117B7.0BDA960B-ON852575FA.0065D033-852575FA.0065DE4B@usgs.gov"
type="cite"><font size="3">We have two questions: <br>
</font><font face="sans-serif" size="2"><br>
1) The first question about BIOMOD deals with the independent
explanatory
and independent response inputs. Since we have the "truth" in
the shrub census data and are sampling from it, we would like to
compare
the sample against the "truth." In other words, instead of splitting
our sample data into training and testing sets, the split would be the
sample and the "truth." I have been reading in the manual about
the independent inputs, and I am confused as to whether or not this is
where we would place the "truth" data. I have included an example
of the initial.state below:</font><font size="3"> <br>
</font><font face="sans-serif" size="2"><br>
> Initial.State(Response = sample[,c(27, 28, 29, 30, 31,32,)],
Explanatory
= sample[,15:26],</font><font size="3"> </font><font face="sans-serif"
size="2"><br>
+ IndependantResponse = alldata[,c(27, 28, 29, 30, 31,32,)],
IndependentExplanatory
= alldata[,15:26]</font><font size="3"> <br>
</font><font face="sans-serif" size="2"><br>
so the object "sample" is a table of our sample of the census,
and the object "alldata" is the census dataset. Is this correct?
If not, is there a way to use the census data set to test the sampled
data
in the models?</font><font size="3"> <br>
</font></blockquote>
This is perfectly correct.<br>
<blockquote
cite="mid:OF13D117B7.0BDA960B-ON852575FA.0065D033-852575FA.0065DE4B@usgs.gov"
type="cite"><font size="3"></font>
<font size="3">2) We are running multiple batches in a simulation and
errors caused by small sample sizes are causing the simulations to
crash.
We would like to allow the modeling to stop but the simulation to loop
to the next larger sample size and continue. Is there a way to trap the
errors and prevent the modeling package from stopping all together?</font>
<br>
</blockquote>
Unfortunately R does not handle errors as far as I know, as you can do
in C or Java. I am curious to hear if someone has an idea. <br>
<br>
One way to cope with this problem, is to have a filter based on
prevalence. You first estimate the sample size of the species. If the
species has a sample size smaller than 10 or 15 points, remove it
before running BIOMOD. <br>
Quite primitive but probably efficient. <br>
<br>
Best<br>
Wilfried<br>
<br>
<br>
<br>
<blockquote
cite="mid:OF13D117B7.0BDA960B-ON852575FA.0065D033-852575FA.0065DE4B@usgs.gov"
type="cite"><br>
<font face="sans-serif" size="2">Chris</font>
<br>
<br>
<font face="sans-serif" size="2">Christopher A. Walter <br>
Biological Science Technician <br>
USGS Leetown Science Center <br>
11649 Leetown Road <br>
Kearneysville, WV 25430 <br>
Phone: 304 724-4479 <br>
<br>
"Its easy not to think when you're not told that much."<br>
-Justin Pierre</font>
<pre wrap="">
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
--
Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR-CNRS 5553
Université J. Fourier
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0)4 76 63 54 53
Fax: +33 (0)4 76 51 42 79
Email: <a class="moz-txt-link-abbreviated" href="mailto:wilfried.thuiller@ujf-grenoble.fr">wilfried.thuiller@ujf-grenoble.fr</a>
Home page: <a class="moz-txt-link-freetext" href="http://www.will.chez-alice.fr">http://www.will.chez-alice.fr</a>
Website: <a class="moz-txt-link-freetext" href="http://www-leca.ujf-grenoble.fr/equipes/tde.htm">http://www-leca.ujf-grenoble.fr/equipes/tde.htm</a>
FP6 European MACIS project: <a class="moz-txt-link-freetext" href="http://www.macis-project.net">http://www.macis-project.net</a>
FP6 European EcoChange project: <a class="moz-txt-link-freetext" href="http://www.ecochange-project.eu">http://www.ecochange-project.eu</a></pre>
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