No subject
Fri Jan 14 16:09:15 CET 2011
Modelling summary
-----------------------------------
Number of species modelled : 1
redwood
numerical variables : RAIN1, RAIN2, RAIN3, RAIN4, RAIN5,
RAIN6, RAIN7, RAIN8, RAIN9, RAIN10, RAIN11, RAIN12, TMAX1, TMAX2, TMAX3,
TMAX4, TMAX5, TMAX6, TMAX7, TMAX8, TMAX9, TMAX10, TMAX11, TMAX12, TMEAN1,
TMEAN2, TMEAN3, TMEAN4, TMEAN5, TMEAN6, TMEAN7, TMEAN8, TMEAN9, TMEAN10,
TMEAN11, TMEAN12, TMIN1, TMIN2, TMIN3, TMIN4, TMIN5, TMIN6, TMIN7, TMIN8,
TMIN9, TMIN10, TMIN11, TMIN12
number of evaluation repetitions : 3
number of pseudo-absences runs : 2
models selected : ANN, CTA, GAM, GBM, GLM, MARS, RF,
SRE
total number of model runs : 64
-----------------------------------
##### redwood #####
##### pseudo-absence run 1 #####
Model=Artificial Neural Network
3 Fold Cross Validation + 3 Repetitions
Calibration and evaluation phase: Nb of cross-validations: 3
*Error in xzfile(file, "wb", compression = 9) : cannot open the connection*
*In addition: There were 15 warnings (use warnings() to see them)*
This code used to work for me so not sure what has changed. When I try it
using the sample data given in the manual, I get the error about 50% of the
time. When I use my data, I get the error every time.
Any help on the "xzfile" error and how to avoid it would be great.
Thanks!
Sarah
Center for Applied Biodiversity Informatics
California Academy of Sciences
--0016368330640af185049a6636aa
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Dear BIOMODers,<br><br>I am having some trouble with the models() function =
in BIOMOD and was hoping to get some help.=A0 <br><br>Here is the relevant =
info:<br>- R version 2.12.1<br>- I re-downloaded the BIOMOD package a few d=
ays ago so it should be up to date.<br>
- code:<br><br>
<p class=3D"MsoNormal" style=3D"margin-bottom: 0.0001pt; line-height: norma=
l; font-family: courier new,monospace; margin-left: 40px;"><span style=3D"f=
ont-size: 10pt;">TrialDF<-data.frame(XCoord=3Dx,
YCoord=3Dy, RAIN1=3DRAIN1scan, RAIN2=3DRAIN2scan, RAIN3=3DRAIN3scan,
RAIN4=3DRAIN4scan, RAIN5=3DRAIN5scan, RAIN6=3DRAIN6scan, RAIN7=3DRAIN7scan,
RAIN8=3DRAIN8scan, RAIN9=3DRAIN9scan, RAIN10=3DRAIN10scan, RAIN11=3DRAIN11s=
can,
RAIN12=3DRAIN12scan, TMAX1=3DTMAX1scan, TMAX2=3DTMAX2scan, TMAX3=3DTMAX3sca=
n,
TMAX4=3DTMAX4scan, TMAX5=3DTMAX5scan, TMAX6=3DTMAX6scan, TMAX7=3DTMAX7scan,
TMAX8=3DTMAX8scan, TMAX9=3DTMAX9scan, TMAX10=3DTMAX10scan, TMAX11=3DTMAX11s=
can,
TMAX12=3DTMAX12scan, TMEAN1=3DTMEAN1scan, TMEAN2=3DTMEAN2scan, TMEAN3=3DTME=
AN3scan,
TMEAN4=3DTMEAN4scan, TMEAN5=3DTMEAN5scan, TMEAN6=3DTMEAN6scan, TMEAN7=3DTME=
AN7scan,
TMEAN8=3DTMEAN8scan, TMEAN9=3DTMEAN9scan, TMEAN10=3DTMEAN10scan, TMEAN11=3D=
TMEAN11scan, TMEAN12=3DTMEAN12scan, TMIN1=3DTMIN1scan, TMIN2=3DTMIN2scan, T=
MIN3=3DTMIN3scan,
TMIN4=3DTMIN4scan, TMIN5=3DTMIN5scan, TMIN6=3DTMIN6scan, TMIN7=3DTMIN7scan,
TMIN8=3DTMIN8scan, TMIN9=3DTMIN9scan, TMIN10=3DTMIN10scan, TMIN11=3DTMIN11s=
can, TMIN12=3DTMIN12scan,<span style=3D"">=A0 </span>LOCALITY=3Dlocalitysca=
n)</span></p>
<div style=3D"margin-left: 40px;"><br style=3D"font-family: courier new,mon=
ospace;"></div>
<p style=3D"font-family: courier new,monospace; margin-left: 40px;" class=
=3D"MsoNormal">Initial.State(Response=3DTrialDF[,51],
Explanatory=3DTrialDF[,3:50], IndependentResponse=3DNULL,
IndependentExplanatory=3DNULL, <a href=3D"http://sp.name">sp.name</a>=3D=
9;spp1')</p>
<p style=3D"font-family: courier new,monospace; margin-left: 40px;" class=
=3D"MsoNormal"><br></p><p style=3D"font-family: courier new,monospace; marg=
in-left: 40px;" class=3D"MsoNormal">Models(GLM=3DT, TypeGLM=3D"poly&qu=
ot;,
Test=3D"AIC", GBM=3DT, No.trees=3D2000, GAM=3DT, CTA=3DT, CV.tree=
=3D50, ANN=3DT,
CV.ann=3D3, SRE=3DT, MARS=3DT, RF=3DT, NbRunEval=3D3, DataSplit=3D80, NbRep=
PA=3D2,
strategy=3D"circles", coor=3DTrialDF[,1:2], distance=3D.5,
nb.absences=3D220, Yweights=3DNULL, VarImport=3DT, Roc=3DT, Optimized.Thres=
hold.Roc=3DT,
Kappa=3DT, TSS=3DT, KeepPredIndependent=3DT)</p>
<br>From this, I get the following:<br><br>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">Modelling
summary </span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">-----------------------------------
</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">Number
of species modelled :<span style=3D"">=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 </s=
pan>1</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">redwood</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">numerical
variables :<span style=3D"">=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0 </span>RAIN1,
RAIN2, RAIN3, RAIN4, RAIN5, RAIN6, RAIN7, RAIN8, RAIN9, RAIN10, RAIN11, RAI=
N12,
TMAX1, TMAX2, TMAX3, TMAX4, TMAX5, TMAX6, TMAX7, TMAX8, TMAX9, TMAX10, TMAX=
11,
TMAX12, TMEAN1, TMEAN2, TMEAN3, TMEAN4, TMEAN5, TMEAN6, TMEAN7, TMEAN8, TME=
AN9,
TMEAN10, TMEAN11, TMEAN12, TMIN1, TMIN2, TMIN3, TMIN4, TMIN5, TMIN6, TMIN7,
TMIN8, TMIN9, TMIN10, TMIN11, TMIN12</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">=A0</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">number
of evaluation repetitions :<span style=3D"">=A0=A0=A0=A0=A0 </span>3</span>=
</p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">number
of pseudo-absences runs :<span style=3D"">=A0=A0=A0=A0=A0=A0=A0 </span>2</s=
pan></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">models
selected :<span style=3D"">=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0 </span>ANN,
CTA, GAM, GBM, GLM, MARS, RF, SRE</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">total
number of model runs :<span style=3D"">=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 </=
span>64</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">-----------------------------------
</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">=A0</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">#####<span style=3D"">=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 </span>redwood<span style=3D"">=A0=A0=
=A0=A0=A0=A0=A0=A0=A0 </span><span style=3D"">=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0</span>#####</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">#####<span style=3D"">=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0 </span>pseudo-absence run 1<span style=3D"">=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 </span>#####</span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">Model=3DArtificial
Neural Network </span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";"><span style=3D"">=A0=A0=A0=A0=A0=A0=A0=A0 <=
/span>3 Fold Cross Validation + 3
Repetitions </span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><span style=3D"font-fa=
mily: "Courier New";">Calibration
and evaluation phase: Nb of cross-validations:<span style=3D"">=A0
</span>3 </span></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><b><span style=3D"font=
-family: "Courier New";">Error
in xzfile(file, "wb", compression =3D 9) : cannot open the connec=
tion</span></b></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><b><span style=3D"font=
-family: "Courier New";">In
addition: There were 15 warnings (use warnings() to see them)</span></b></p=
><p class=3D"MsoNormal" style=3D"margin-left: 0.5in;"><br><span style=3D"fo=
nt-family: "Courier New";"></span></p><p class=3D"MsoNormal" styl=
e=3D"margin-left: 0.0866in; font-family: arial,helvetica,sans-serif;">
<font size=3D"2">This code used to work for me so not sure what has changed=
.=A0 </font><font size=3D"2">When I try it using the sample data given in t=
he manual, I=20
get the error about 50% of the time.=A0 When I use my data, I get the=20
error every time.</font></p><p class=3D"MsoNormal" style=3D"margin-left: 0.=
0866in; font-family: arial,helvetica,sans-serif;"><font size=3D"2"><br></fo=
nt></p><p class=3D"MsoNormal" style=3D"margin-left: 0.0866in; font-family: =
arial,helvetica,sans-serif;">
<font size=3D"2">Any help on the "xzfile" error and how to avoid =
it would be great.=A0 <br></font></p><p class=3D"MsoNormal" style=3D"margin=
-left: 0.0866in; font-family: arial,helvetica,sans-serif;"><font size=3D"2"=
><br></font></p>
<p class=3D"MsoNormal" style=3D"margin-left: 0.0866in; font-family: arial,h=
elvetica,sans-serif;"><font size=3D"2">Thanks!</font></p><p class=3D"MsoNor=
mal" style=3D"margin-left: 0.0866in; font-family: arial,helvetica,sans-seri=
f;"><font size=3D"2">Sarah<br>
</font></p><p class=3D"MsoNormal" style=3D"margin-left: 0.0866in; font-fami=
ly: arial,helvetica,sans-serif;"><font size=3D"2"><br></font></p><p class=
=3D"MsoNormal" style=3D"margin-left: 0.0866in; font-family: arial,helvetica=
,sans-serif;">
<span style=3D"font-family: "Courier New";"><font style=3D"font-f=
amily: arial,helvetica,sans-serif;" size=3D"2"><br></font></span></p><p cla=
ss=3D"MsoNormal" style=3D"margin-left: 0.0866in; font-family: arial,helveti=
ca,sans-serif;">
<span style=3D"font-family: "Courier New";"><font style=3D"font-f=
amily: arial,helvetica,sans-serif;" size=3D"2">Center for Applied Biodivers=
ity Informatics</font></span></p><p class=3D"MsoNormal" style=3D"margin-lef=
t: 0.0866in; font-family: arial,helvetica,sans-serif;">
<span style=3D"font-family: "Courier New";"></span><font size=3D"=
2">California Academy of Sciences</font></p><p class=3D"MsoNormal" style=3D=
"margin-left: 0.0866in;"><span style=3D"font-family: "Courier New"=
;;"><br>
</span></p>
<br>
--0016368330640af185049a6636aa--
More information about the Biomod-commits
mailing list