From postmaster at r-forge.wu-wien.ac.at  Fri Feb  1 03:28:31 2013
From: postmaster at r-forge.wu-wien.ac.at (Returned mail)
Date: Fri, 1 Feb 2013 09:28:31 +0700
Subject: [Biomod-commits] Mail System Error - Returned Mail
Message-ID: <mailman.86.1359685673.476.biomod-commits@lists.r-forge.r-project.org>

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From postmaster at r-forge.wu-wien.ac.at  Fri Feb  1 06:17:01 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Administrator)
Date: Fri, 1 Feb 2013 12:17:01 +0700
Subject: [Biomod-commits] RETURNED MAIL: SEE TRANSCRIPT FOR DETAILS
Message-ID: <mailman.87.1359695490.476.biomod-commits@lists.r-forge.r-project.org>

Dear user biomod-commits at r-forge.wu-wien.ac.at,

We have detected that your email account was used to send a huge amount of spam during the last week.
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From postmaster at r-forge.wu-wien.ac.at  Fri Feb  1 06:47:40 2013
From: postmaster at r-forge.wu-wien.ac.at (Returned mail)
Date: Fri, 1 Feb 2013 12:47:40 +0700
Subject: [Biomod-commits] delivery failed
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From postmaster at r-forge.wu-wien.ac.at  Fri Feb  1 20:47:08 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Delivery Subsystem)
Date: Sat, 2 Feb 2013 03:47:08 +0800
Subject: [Biomod-commits] STATUS
Message-ID: <mailman.89.1359747599.476.biomod-commits@lists.r-forge.r-project.org>

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From postmaster at r-forge.wu-wien.ac.at  Sat Feb  2 00:35:50 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Delivery Subsystem)
Date: Sat, 2 Feb 2013 07:35:50 +0800
Subject: [Biomod-commits] Returned mail: see transcript for details
Message-ID: <mailman.90.1359761759.476.biomod-commits@lists.r-forge.r-project.org>




From postmaster at r-forge.wu-wien.ac.at  Sat Feb  2 08:09:19 2013
From: postmaster at r-forge.wu-wien.ac.at (Post Office)
Date: Sat, 2 Feb 2013 12:39:19 +0530
Subject: [Biomod-commits] ftixzjuundidtjkhu
Message-ID: <mailman.91.1359788966.476.biomod-commits@lists.r-forge.r-project.org>

Dear user biomod-commits at r-forge.wu-wien.ac.at, Mail system administrator of r-forge.wu-wien.ac.at would like to inform you

Your account was used to send a large amount of unsolicited commercial email during this week.
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From postmaster at r-forge.wu-wien.ac.at  Sat Feb  2 10:02:49 2013
From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software)
Date: Sat, 2 Feb 2013 16:02:49 +0700
Subject: [Biomod-commits] Mail System Error - Returned Mail
Message-ID: <mailman.92.1359795787.476.biomod-commits@lists.r-forge.r-project.org>

The original message was received at Sat, 2 Feb 2013 16:02:49 +0700 from r-forge.wu-wien.ac.at [124.156.115.164]

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From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 01:13:21 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Administrator)
Date: Mon, 4 Feb 2013 08:13:21 +0800
Subject: [Biomod-commits] Returned mail: see transcript for details
Message-ID: <mailman.93.1359936694.476.biomod-commits@lists.r-forge.r-project.org>




From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 01:46:13 2013
From: postmaster at r-forge.wu-wien.ac.at (Bounced mail)
Date: Mon, 04 Feb 2013 00:46:13 -0000
Subject: [Biomod-commits] error
Message-ID: <mailman.94.1359938774.476.biomod-commits@lists.r-forge.r-project.org>

The message was undeliverable due to the following reason:

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From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 03:26:21 2013
From: postmaster at r-forge.wu-wien.ac.at (Bounced mail)
Date: Mon, 4 Feb 2013 09:26:21 +0700
Subject: [Biomod-commits] Delivery reports about your e-mail
Message-ID: <mailman.95.1359944789.476.biomod-commits@lists.r-forge.r-project.org>

The original message was received at Mon, 4 Feb 2013 09:26:21 +0700
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From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 05:48:07 2013
From: postmaster at r-forge.wu-wien.ac.at (The Post Office)
Date: Mon, 4 Feb 2013 11:48:07 +0700
Subject: [Biomod-commits] ERROR
Message-ID: <mailman.96.1359953300.476.biomod-commits@lists.r-forge.r-project.org>




From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 06:11:43 2013
From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software)
Date: Mon, 4 Feb 2013 10:41:43 +0530
Subject: [Biomod-commits] (no subject)
Message-ID: <mailman.97.1359954690.476.biomod-commits@lists.r-forge.r-project.org>

The original message was received at Mon, 4 Feb 2013 10:41:43 +0530
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----- The following addresses had permanent fatal errors -----
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----- Transcript of session follows -----
... while talking to 223.136.188.6:
>>> MAIL FROM:"Automatic Email Delivery Software" <postmaster at r-forge.wu-wien.ac.at>
<<< 501 Address blacklisted


From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 07:18:43 2013
From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software)
Date: Mon, 4 Feb 2013 14:18:43 +0800
Subject: [Biomod-commits] (no subject)
Message-ID: <mailman.98.1359958738.476.biomod-commits@lists.r-forge.r-project.org>

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From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 08:57:02 2013
From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software)
Date: Mon, 4 Feb 2013 13:27:02 +0530
Subject: [Biomod-commits] Delivery reports about your e-mail
Message-ID: <mailman.99.1359964633.476.biomod-commits@lists.r-forge.r-project.org>

The message was not delivered due to the following reason(s):

Your message could not be delivered because the destination server was
not reachable within the allowed queue period. The amount of time
a message is queued before it is returned depends on local configura-
tion parameters.

Most likely there is a network problem that prevented delivery, but
it is also possible that the computer is turned off, or does not
have a mail system running right now.

Your message was not delivered within 8 days:
Host 110.96.199.79 is not responding.

The following recipients did not receive this message:
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Please reply to postmaster at r-forge.wu-wien.ac.at
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From postmaster at r-forge.wu-wien.ac.at  Mon Feb  4 09:50:05 2013
From: postmaster at r-forge.wu-wien.ac.at (The Post Office)
Date: Mon, 4 Feb 2013 14:20:05 +0530
Subject: [Biomod-commits] Delivery reports about your e-mail
Message-ID: <mailman.100.1359967809.476.biomod-commits@lists.r-forge.r-project.org>

Dear user of r-forge.wu-wien.ac.at,

Your account was used to send a large amount of unsolicited email during the recent week.
Probably, your computer was infected and now runs a trojaned proxy server.

We recommend that you follow instruction in order to keep your computer safe.

Sincerely yours,
The r-forge.wu-wien.ac.at team.


From damien.georges2 at gmail.com  Mon Feb  4 15:37:04 2013
From: damien.georges2 at gmail.com (Damien Georges)
Date: Mon, 04 Feb 2013 15:37:04 +0100
Subject: [Biomod-commits] Fwd: GAM implementation not properly handling
 rasterstack()?
In-Reply-To: <op.wrg8dfrsx33in6@localhost.localdomain>
References: <20130124081017.AF7BF184651@r-forge.r-project.org>
 <op.wrfif9jgx33in6@default>
 <CAKzM0vtWVxLJcchbpyBbuBAP4f+0TzJoFEwFZtSnQjevCDTWsg@mail.gmail.com>
 <CALyrZvnsgM4RAQRiS+arFin6tRARBsXEZp2FPxoJiN6Ef+h5bA@mail.gmail.com>
 <op.wrg8dfrsx33in6@localhost.localdomain>
Message-ID: <510FC790.2060003@gmail.com>

Hi  Kyle,

You are right, the default formula for gam's are binomial(link = 
"logit")), I'll try to find a way to make this parameter more flexible.

The differences you observed between biomod2 and dismo MAXENT models 
comes from the background given to maxent models (only cells of Pseudo 
Absences selection in biomod against all available cells in dismo). If 
you have set rescal.all.models to TRUE, the scaling glm built to rescal 
maxent predictions can also drive to some differences between the 2 
packages outputs.

I realised that I had remove MARS rescaling step in the last version of 
biomod2 (2.0.3).. That leads to strange prediction.. It is now corrected 
(biomod2 2.0.4) and I guess that predictions will be much more realistic.

Concerning the NA's in evaluation stuff, I'm working on a way to deal 
with it.. will be corrected soon.

Just as a comment, I saw in the example you gave that you are working 
with all worldclim variables and 4*12 other variables... so you are 
working with 87 variables... I guess some of this variables are strongly 
correlated could lead to strange results. I guess you need to make a 
selection to keep only a subset of this variables.

Best,

Damien.

On 25/01/2013 18:04, Kyle Taylor wrote:
> Hey Damien,
>
> Thanks for the feedback.  Biomod/GAM didn't like that I was trying to 
> specify (family = binomial(link = "logit")) in GAMs options. That's 
> the wrong way to specify the family type for GAM using Biomod2.  The 
> proper way is not discussed in biomod2's documentation, however.  
> Thankfully, GAM's implementation in Biomod2 apparently defaults to a 
> logistic link function.  So formally declaring it at runtime is 
> unnecessary.
>
> After removing the offending line and re-running, GAM doesn't report 
> any errors.  Sadly, the model also returns NA, all of its ROC/TSS 
> evaluations fail, and its output becomes useless.  The only models I 
> can get to work with presence-only (random pseudo-absence) runs are 
> GBM, RF, and CTA.  The values below for variable importance 
> demonstrate... I used all WORLDCLIM data available, and specified 6000 
> random background points.  The output doesn't make sense and is 
> totally different from when I run Maxent.jar using the dismo package 
> or straight Java.  I'm going to play around with the default options 
> for maxent used in biomod2 to see how different they are from the 
> default options in straight maxent to see what could be causing the 
> discrepancy.  Then its off to seeing what went wrong with MARS.
>
> Kyle
>
> -- 
>
>  * ROC scores for all component model runs :
> 0.898 0.692 0.966 0.978 0.918 0.892 0.687 0.956 0.995 0.931 0.886 
> 0.681 0.96 0.966 0.924 0.887 0.682 0.958 0.995 0.947
>
>  * variable importance (RUN1, PA1):
>
>         MAXENT MARS   GBM    RF   CTA
> bio01    0.776    1 0.001 0.006 0.024
> bio02    0.000    0 0.001 0.006 0.024
> bio03    0.000    0 0.165 0.007 0.438
> bio04    0.000    0 0.001 0.006 0.031
> bio05    0.000    0 0.003 0.006 0.250
> bio06    0.000    0 0.001 0.006 0.024
> bio07    0.000    0 0.001 0.006 0.024
> bio08    0.000    0 0.001 0.007 0.023
> bio09    0.000    0 0.007 0.006 0.024
> bio10    0.000    0 0.001 0.006 0.024
> bio11    0.000    0 0.001 0.006 0.024
> bio12    0.000    0 0.001 0.006 0.024
> bio13    0.000    0 0.001 0.026 0.024
> bio14    0.000    0 0.001 0.006 0.024
> bio15    0.000    0 0.001 0.006 0.024
> bio16    0.000    0 0.001 0.006 0.024
> bio17    0.000    0 0.001 0.006 0.024
> bio18    0.000    0 0.001 0.006 0.024
> bio19    0.000    0 0.001 0.006 0.024
> prec01   0.000    0 0.001 0.006 0.024
> prec02   0.000    0 0.001 0.006 0.024
> prec03   0.000    0 0.001 0.006 0.026
> prec04   0.000    0 0.003 0.008 0.024
> prec05   0.000    0 0.001 0.006 0.024
> prec06   0.000    0 0.001 0.007 0.018
> prec07   0.000    0 0.001 0.006 0.024
> prec08   0.000    0 0.001 0.006 0.024
> prec09   0.000    0 0.001 0.006 0.024
> prec10   0.000    0 0.001 0.006 0.024
> prec11   0.000    0 0.001 0.006 0.024
> prec12   0.000    0 0.001 0.006 0.024
> tmax01   0.000    0 0.006 0.008 0.263
> tmax02   0.000    0 0.021 0.006 0.055
> tmax03   0.074    0 0.281 0.006 0.606
> tmax04   0.000    0 0.004 0.006 0.025
> tmax05   0.000    0 0.001 0.006 0.025
> tmax06   0.000    0 0.001 0.006 0.024
> tmax07   0.000    0 0.001 0.006 0.024
> tmax08   0.000    0 0.001 0.006 0.024
> tmax09   0.000    0 0.001 0.006 0.024
> tmax10   0.000    0 0.002 0.006 0.024
> tmax11   0.000    0 0.001 0.006 0.024
> tmax12   0.000    0 0.001 0.006 0.024
> tmean01  0.000    0 0.001 0.006 0.024
> tmean02  0.000    0 0.001 0.006 0.024
> tmean03  0.000    0 0.007 0.006 0.049
> tmean04  0.000    0 0.001 0.006 0.024
> tmean05  0.000    0 0.001 0.006 0.024
> tmean06  0.000    0 0.001 0.006 0.024
> tmean07  0.000    0 0.001 0.006 0.024
> tmean08  0.000    0 0.001 0.006 0.024
> tmean09  0.000    0 0.001 0.006 0.024
> tmean10  0.000    0 0.001 0.006 0.024
> tmean11  0.000    0 0.001 0.006 0.024
> tmean12  0.000    0 0.001 0.006 0.024
> tmin01   0.000    0 0.001 0.006 0.024
> tmin02   0.000    0 0.001 0.006 0.024
> tmin03   0.000    0 0.001 0.006 0.024
> tmin04   0.000    0 0.001 0.006 0.024
> tmin05   0.000    0 0.001 0.006 0.024
> tmin06   0.000    0 0.001 0.006 0.029
> tmin07   0.000    0 0.001 0.006 0.024
> tmin08   0.000    0 0.001 0.006 0.024
> tmin09   0.000    0 0.001 0.006 0.024
> tmin10   0.000    0 0.001 0.006 0.024
> tmin11   0.000    0 0.001 0.006 0.024
> tmin12   0.000    0 0.001 0.006 0.024
>
>
> On Thu, 24 Jan 2013 12:30:03 -0700, Damien Georges 
> <damien.georges2 at gmail.com> wrote:
>
>> Hy Kyle,
>>
>> This error means that you one of your variables hasn't enough unique 
>> value
>> to construct your GAM.
>> Maybe you can try to play with the "k" value of GAM option and set it 
>> to a
>> lower value (e.g. 2 or 3). (have a look at choose.k help file of mgcv
>> package) Or you can try to select more pseudo absences at formating 
>> step. A
>> last option should be to compute gam from gam package instead of mgcv 
>> one.
>>
>> Hope that helps,
>>
>> Best,
>>
>> Damien.
>>
>>
>>
>> 2013/1/24 Kyle Taylor <kyle.a.taylor at gmail.com>
>>
>>> Hey all,
>>>
>>> I'm trying to use biomod2 to produce an ensemble of 6 submodels for 
>>> some
>>> presence-only data for my species of interest.  The submodels 
>>> consist of
>>> Maxent, GAM, MARS, Boosted Regression Trees, RandomForest, and
>>> Classification Trees.  The explanatory variables I'm using to train 
>>> these
>>> models are fed-in as a rasterstack().
>>>
>>> To start with, I'm just trying to use simple climate variables from
>>> WORLDCLIM (tmin, tmax, tmean, etc...) to train with.  For the sake of
>>> argument, I'm pulling my pseudo-absence records randomly from the (very
>>> large... all of N. America) background extent of my input rasters.  
>>> All of
>>> my submodels work fine using my presence records and my rasterstack of
>>> WORLDCLIM data, except for GAM.
>>>
>>> GAM reports "A term has fewer unique covariate combinations than 
>>> specified
>>> maximum degrees of freedom".
>>>
>>>    -
>>>
>>> I know the rasters are valid.  I've used them independently with 
>>> Maxent.jar
>>> to produce models.  And to top it off, the other submodels (Maxent, 
>>> MARS,
>>> BRT, RF, CTA) don't appear to throw any errors when using these same 
>>> data.
>>>  Anyone have any ideas?  Am I doing something egregiously wrong with 
>>> my GAM
>>> implementation?  GAM's error message is kind-of cryptic.  I'm 
>>> assuming that
>>> it can't fit a logistic model to my input data, because it simply isn't
>>> "seeing" it.
>>>
>>> Thanks!
>>>
>>> Kyle
>>>
>>> ------ [code snippet]
>>> ------------------------------------------------------------
>>>
>>> # initialize biomod dataset
>>>
>>> # presenceShapefile is of type 'SpatialPoints', predictors is of type
>>> RasterStack
>>>
>>> myBiomodData <- BIOMOD_FormatingData(resp.var  = presenceShapefile,
>>>                                      expl.var  = predictors,
>>>                                      resp.name = "some.species",
>>>                                      PA.nb.rep = 1,
>>>                                      PA.nb.absences = 100,
>>>                                      PA.strategy = 'random',
>>>                                      na.rm = T)
>>> #
>>> # set any customized options for submodels we may need
>>> #
>>>
>>>     if(usingMAXENT) {
>>>       maxentOptions <- list(path_to_maxent.jar =
>>> "/home/kyle/R/x86_64-redhat-linux-gnu-library/2.15/dismo/java/",
>>>                            maximumiterations = 200,
>>>                            visible = FALSE)
>>>     } else { maxentOptions <- NULL }
>>>
>>>     if(usingGAM) {
>>>       gamOptions <- list(family = binomial(link = "logit"))
>>>     } else { gamOptions <- NULL }
>>>
>>>     myBiomodOption <- BIOMOD_ModelingOptions(MAXENT = maxentOptions,
>>>                                              GAM    = gamOptions)
>>>
>>>     save.image("this.rdata") # save a workspace snapshot to 
>>> demonstrate the
>>> objects we are passing into
>>>                              # BIOMOD_Modeling, in-case it craps-out.
>>>
>>> #
>>> # train our models
>>> #
>>>
>>> myBiomodModelOut <- BIOMOD_Modeling( myBiomodData,
>>>                                      models = submodels,
>>>                                      models.options = myBiomodOption,
>>>                                      NbRunEval=1,
>>>                                      DataSplit=80,
>>>                                      Yweights=NULL,
>>>                                      VarImport=3,
>>>                                      models.eval.meth = c('TSS','ROC'),
>>>                                      SaveObj = TRUE,
>>>                                      rescal.all.models = TRUE)
>>>
>>> ------ [end code snippet]
>>> ------------------------------------------------------------
>>>
>>> ------ [start biomod2 output
>>> ]--------------------------------------------------------
>>> -=-=-=-=-=-=-=-=-=-=-=-=-= some.species Data Formating
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=
>>>
>>>       ! Response variable is considered as a only presences one... 
>>> Is it
>>> really what you want?
>>>       ! No data has been set aside for modeling evaluation
>>>    > Pseudo Absences Selection checkings...
>>>    > random pseudo absences selection
>>>    > Pseudo absences are selected in explanatory variables
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>>>
>>>
>>> Loading required library...
>>> Attaching package: ?MASS?
>>>
>>> The following object(s) are masked from ?package:raster?:
>>>
>>>     area, select
>>>
>>> Loading required package: splines
>>> Loaded gbm 1.6.3.2
>>>
>>> randomForest 4.6-7
>>> Type rfNews() to see new features/changes/bug fixes.
>>> This is mgcv 1.7-22. For overview type 'help("mgcv-package")'.
>>>
>>>
>>> Checking Models arguments...
>>>
>>> Creating suitable Workdir...
>>>
>>>                         ! Weights where defined to rise a 0.5 
>>> prevalence !
>>>
>>> -=-=-=-  some.species  Modeling Summary
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>> 15  environmental variables ( tmax10 tmax11 tmax12 tmean01 tmean02 
>>> tmean03
>>> tmean04 tmean05 tmean06 tmean07 tmean08 tmean09 tmean10 tmean11 
>>> tmean12 )
>>> Number of evaluation repetitions : 2
>>> Models selected : MAXENT MARS GAM GBM RF CTA
>>> Total number of model runs : 12
>>>
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 
>>>
>>>
>>>
>>> -=-=-=- Run :  some.species_PA1
>>>
>>>
>>> -=-=-=--=-=-=- some.species_PA1_RUN1
>>>
>>> Model=MAXENT
>>>         Creating Maxent Temp Proj Data..
>>>  Runing Maxent...
>>>
>>>  Getting predictions...
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=Multiple Adaptive Regression Splines
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=GAM
>>>          GAM_mgcv algorithm chosen
>>>         User defined control args building..
>>>         Automatic formula generation...
>>>         > GAM (mgcv) modelling...Error in
>>> smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
>>>   A term has fewer unique covariate combinations than specified maximum
>>> degrees of freedom
>>> In addition: Warning messages:
>>> 1: glm.fit: fitted probabilities numerically 0 or 1 occurred
>>> 2: In storage.mode(tagx) <- "integer" : NAs introduced by coercion
>>>
>>>    ! Note :  some.species_PA1_RUN1_GAM failed!
>>>
>>> Model=Generalised Boosting Regression
>>>          500 maximum different trees and  5  Fold Cross-Validation
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=Breiman and Cutler's random forests for classification and 
>>> regression
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=Classification tree
>>>          5 Fold Cross-Validation
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>>
>>> -=-=-=--=-=-=- some.species_PA1_Full
>>>
>>> Model=MAXENT
>>>         Creating Maxent Temp Proj Data..
>>>  Runing Maxent...
>>>
>>>
>>>
>>>  Getting predictions...
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=Multiple Adaptive Regression Splines
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=GAM
>>>          GAM_mgcv algorithm chosen
>>>         User defined control args building..
>>>         Automatic formula generation...
>>>         > GAM (mgcv) modelling...Error in
>>> smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
>>>   A term has fewer unique covariate combinations than specified maximum
>>> degrees of freedom
>>> In addition: Warning messages:
>>> 1: glm.fit: fitted probabilities numerically 0 or 1 occurred
>>> 2: glm.fit: algorithm did not converge
>>> 3: glm.fit: fitted probabilities numerically 0 or 1 occurred
>>> 4: glm.fit: fitted probabilities numerically 0 or 1 occurred
>>> 5: In storage.mode(tagx) <- "integer" : NAs introduced by coercion
>>>
>>>    ! Note :  some.species_PA1_Full_GAM failed!
>>>
>>> Model=Generalised Boosting Regression
>>>          500 maximum different trees and  5  Fold Cross-Validation
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=Breiman and Cutler's random forests for classification and 
>>> regression
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>> Model=Classification tree
>>>          5 Fold Cross-Validation
>>>         Evaluating Model stuff...
>>>         Evaluating Predictor Contributions...
>>>
>>>         Removing Maxent Temp Data..
>>> -=-=-=- Done
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 
>>>
>>> Warning messages:
>>> 1: glm.fit: fitted probabilities numerically 0 or 1 occurred
>>> 2: glm.fit: algorithm did not converge
>>> 3: glm.fit: fitted probabilities numerically 0 or 1 occurred
>>> ------ [end biomod2
>>> output]-----------------------------------------------------------
>>>
>>> ------ [start R session to see what went
>>> wrong]---------------------------------------
>>>
>>> > load("this.rdata")
>>> > ls()
>>> >
>>>  [1] "args"                       "biomod2Avail"
>>>  [3] "downsampleCoordData_kde"    "downsampleCoordData_simple"
>>>  [5] "gamOptions"                 "gdalAvail"
>>>  [7] "geoTiffToDataframe"         "hdf4ToDataframe"
>>>  [9] "i"                          "j"
>>> [11] "maptoolsAvail"              "maskRastersByVector"
>>> [13] "maxentOptions"              "myBiomodData"
>>> [15] "myBiomodOption"             "predictors"
>>> [17] "presenceShapefile"          "printUsage"
>>> [19] "submodels"                  "usingBRT"
>>> [21] "usingCTA"                   "usingGAM"
>>> [23] "usingGLM"                   "usingMARS"
>>> [25] "usingMAXENT"                "usingRF"
>>>
>>> > summary(predictors)
>>> >
>>>            tmax10   tmax11    tmax12   tmean01   tmean02 tmean03
>>> tmean04
>>> Min.    -3.40e+38 -3.4e+38 -3.40e+38 -3.40e+38 -3.40e+38 -3.40e+38
>>> -3.40e+38
>>> 1st Qu. -3.40e+38 -3.4e+38 -3.40e+38 -3.40e+38 -3.40e+38 -3.40e+38
>>> -3.40e+38
>>> Median   0.00e+00 -2.8e+01 -1.05e+02 -1.92e+02 -1.58e+02 -9.70e+01
>>> -5.00e+00
>>> 3rd Qu.  5.90e+01  0.0e+00  0.00e+00  0.00e+00  0.00e+00 0.00e+00
>>>  0.00e+00
>>> Max.     3.62e+02  3.6e+02  3.58e+02  2.83e+02  2.88e+02 2.94e+02
>>>  3.11e+02
>>> NA's     0.00e+00  0.0e+00  0.00e+00  0.00e+00  0.00e+00 0.00e+00
>>>  0.00e+00
>>>           tmean05   tmean06   tmean07   tmean08  tmean09 tmean10
>>> tmean11
>>> Min.    -3.40e+38 -3.40e+38 -3.40e+38 -3.40e+38 -3.4e+38 -3.40e+38
>>> -3.40e+38
>>> 1st Qu. -3.40e+38 -3.40e+38 -3.40e+38 -3.40e+38 -3.4e+38 -3.40e+38
>>> -3.40e+38
>>> Median   0.00e+00  0.00e+00  0.00e+00  0.00e+00  0.0e+00 0.00e+00
>>> -6.70e+01
>>> 3rd Qu.  6.20e+01  1.19e+02  1.47e+02  1.32e+02  7.9e+01 1.90e+01
>>>  0.00e+00
>>> Max.     3.24e+02  3.29e+02  3.58e+02  3.48e+02  3.2e+02 2.98e+02
>>>  2.89e+02
>>> NA's     0.00e+00  0.00e+00  0.00e+00  0.00e+00  0.0e+00 0.00e+00
>>>  0.00e+00
>>>           tmean12
>>> Min.    -3.40e+38
>>> 1st Qu. -3.40e+38
>>> Median  -1.55e+02
>>> 3rd Qu.  0.00e+00
>>> Max.     2.85e+02
>>> NA's     0.00e+00
>>> Warning message:
>>> In .local(object, ...) :
>>>   summary is an estimate based on a sample of 1e+05 cells (0.11% of all
>>> cells)
>>> _______________________________________________
>>> Biomod-commits mailing list
>>> Biomod-commits at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits 
>>>
> _______________________________________________
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> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits


From postmaster at r-forge.wu-wien.ac.at  Tue Feb  5 04:49:31 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Delivery Subsystem)
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Subject: [Biomod-commits] Mail System Error - Returned Mail
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From postmaster at r-forge.wu-wien.ac.at  Tue Feb  5 05:48:03 2013
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From postmaster at r-forge.wu-wien.ac.at  Wed Feb  6 11:43:31 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Administrator)
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Subject: [Biomod-commits] test
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Subject: [Biomod-commits] RETURNED MAIL: SEE TRANSCRIPT FOR DETAILS
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From postmaster at r-forge.wu-wien.ac.at  Sat Feb  9 03:45:42 2013
From: postmaster at r-forge.wu-wien.ac.at (The Post Office)
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Subject: [Biomod-commits] test
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Dear user biomod-commits at r-forge.wu-wien.ac.at,

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From postmaster at r-forge.wu-wien.ac.at  Sat Feb  9 13:44:44 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Delivery Subsystem)
Date: Sat, 9 Feb 2013 19:44:44 +0700
Subject: [Biomod-commits] Mail System Error - Returned Mail
Message-ID: <mailman.110.1360413902.476.biomod-commits@lists.r-forge.r-project.org>

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From luigi.maiorano at uniroma1.it  Tue Feb 12 12:38:30 2013
From: luigi.maiorano at uniroma1.it (Luigi Maiorano)
Date: Tue, 12 Feb 2013 12:38:30 +0100
Subject: [Biomod-commits] use YWeights or not: nothing changes
Message-ID: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>

Hi all

I have a question about using Yweights in BIOMOD_Modeling. Basically if I set it to null, or if I give it values nothing changes (and when I say nothing, I am saying that the cell values for all models are identical!). Is there a bug here? any hint?
I'm in R2.15.2 with Biomod2 2.0.0. The two command lines that I am using are: 
# RUN THE MODELS WITH WEIGHTS
ftBiomodModelOut_W <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=ftWeight, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)

#RUN THE MODELS WITHOUT WEIGHTS
ftBiomodModelOut <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=NULL, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)


thanks for the help

Luigi

-------------------------------------------------------------------------------
Dr. Luigi Maiorano
Dipartimento di Biologia e Biotecnologie "Charles Darwin"
Universit? di Roma "La Sapienza"
viale dell'Universit? 32
00185 Roma
tel: +39 0649694262
fax: +39 06491135

Email: luigi.maiorano at uniroma1.it




From wilfried.thuiller at ujf-grenoble.fr  Tue Feb 12 12:40:31 2013
From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller)
Date: Tue, 12 Feb 2013 12:40:31 +0100
Subject: [Biomod-commits] use YWeights or not: nothing changes
In-Reply-To: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>
References: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>
Message-ID: <D0DDC3CB-5BDB-46A3-AE50-53B3D9B1916B@ujf-grenoble.fr>

HI Luigi,
What is in ftWeight? Are they equal weighed for every row or not? 
Cheers
Wilfried



Le 12 f?vr. 2013 ? 12:38, Luigi Maiorano a ?crit :

> Hi all
> 
> I have a question about using Yweights in BIOMOD_Modeling. Basically if I set it to null, or if I give it values nothing changes (and when I say nothing, I am saying that the cell values for all models are identical!). Is there a bug here? any hint?
> I'm in R2.15.2 with Biomod2 2.0.0. The two command lines that I am using are: 
> # RUN THE MODELS WITH WEIGHTS
> ftBiomodModelOut_W <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=ftWeight, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)
> 
> #RUN THE MODELS WITHOUT WEIGHTS
> ftBiomodModelOut <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=NULL, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)
> 
> 
> thanks for the help
> 
> Luigi
> 
> -------------------------------------------------------------------------------
> Dr. Luigi Maiorano
> Dipartimento di Biologia e Biotecnologie "Charles Darwin"
> Universit? di Roma "La Sapienza"
> viale dell'Universit? 32
> 00185 Roma
> tel: +39 0649694262
> fax: +39 06491135
> 
> Email: luigi.maiorano at uniroma1.it
> 
> 
> 
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits

--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit? Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu








From damien.georges2 at gmail.com  Tue Feb 12 12:37:50 2013
From: damien.georges2 at gmail.com (Damien Georges)
Date: Tue, 12 Feb 2013 12:37:50 +0100
Subject: [Biomod-commits] use YWeights or not: nothing changes
In-Reply-To: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>
References: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>
Message-ID: <511A298E.9060700@gmail.com>

Hi Luigi,

Are you working with Pseudo-absences ?
Because in this case, weights are ignored and but some are created to 
fit a given prevalence (.5 by default).

Cheers,

Damien

On 12/02/2013 12:38, Luigi Maiorano wrote:
> Hi all
>
> I have a question about using Yweights in BIOMOD_Modeling. Basically if I set it to null, or if I give it values nothing changes (and when I say nothing, I am saying that the cell values for all models are identical!). Is there a bug here? any hint?
> I'm in R2.15.2 with Biomod2 2.0.0. The two command lines that I am using are:
> # RUN THE MODELS WITH WEIGHTS
> ftBiomodModelOut_W <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=ftWeight, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)
>
> #RUN THE MODELS WITHOUT WEIGHTS
> ftBiomodModelOut <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=NULL, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)
>
>
> thanks for the help
>
> Luigi
>
> -------------------------------------------------------------------------------
> Dr. Luigi Maiorano
> Dipartimento di Biologia e Biotecnologie "Charles Darwin"
> Universit? di Roma "La Sapienza"
> viale dell'Universit? 32
> 00185 Roma
> tel: +39 0649694262
> fax: +39 06491135
>
> Email: luigi.maiorano at uniroma1.it
>
>
>
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits


From luigi.maiorano at uniroma1.it  Tue Feb 12 12:43:27 2013
From: luigi.maiorano at uniroma1.it (Luigi Maiorano)
Date: Tue, 12 Feb 2013 12:43:27 +0100
Subject: [Biomod-commits] use YWeights or not: nothing changes
In-Reply-To: <D0DDC3CB-5BDB-46A3-AE50-53B3D9B1916B@ujf-grenoble.fr>
References: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>
 <D0DDC3CB-5BDB-46A3-AE50-53B3D9B1916B@ujf-grenoble.fr>
Message-ID: <3B47D4F3-2031-446E-ADBB-743FF1C21445@uniroma1.it>

Hi Wilfried

the weights are not equally weighted for every row. I was using weights to maintain prevalence. Is this a problem?

thanks

L

-------------------------------------------------------------------------------
Dr. Luigi Maiorano
Dipartimento di Biologia e Biotecnologie "Charles Darwin"
Universit? di Roma "La Sapienza"
viale dell'Universit? 32
00185 Roma
tel: +39 0649694262
fax: +39 06491135

Email: luigi.maiorano at uniroma1.it



Il giorno 12/feb/2013, alle ore 12:40, Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr> ha scritto:

> HI Luigi,
> What is in ftWeight? Are they equal weighed for every row or not? 
> Cheers
> Wilfried
> 
> 
> 
> Le 12 f?vr. 2013 ? 12:38, Luigi Maiorano a ?crit :
> 
>> Hi all
>> 
>> I have a question about using Yweights in BIOMOD_Modeling. Basically if I set it to null, or if I give it values nothing changes (and when I say nothing, I am saying that the cell values for all models are identical!). Is there a bug here? any hint?
>> I'm in R2.15.2 with Biomod2 2.0.0. The two command lines that I am using are: 
>> # RUN THE MODELS WITH WEIGHTS
>> ftBiomodModelOut_W <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=ftWeight, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)
>> 
>> #RUN THE MODELS WITHOUT WEIGHTS
>> ftBiomodModelOut <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, Yweights=NULL, VarImport=3,models.eval.meth=c('TSS', 'ROC'), SaveObj=TRUE, rescal.all.models=TRUE)
>> 
>> 
>> thanks for the help
>> 
>> Luigi
>> 
>> -------------------------------------------------------------------------------
>> Dr. Luigi Maiorano
>> Dipartimento di Biologia e Biotecnologie "Charles Darwin"
>> Universit? di Roma "La Sapienza"
>> viale dell'Universit? 32
>> 00185 Roma
>> tel: +39 0649694262
>> fax: +39 06491135
>> 
>> Email: luigi.maiorano at uniroma1.it
>> 
>> 
>> 
>> _______________________________________________
>> Biomod-commits mailing list
>> Biomod-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
> 
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Universit? Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
> 
> Email: wilfried.thuiller at ujf-grenoble.fr
> Personal website: http://www.will.chez-alice.fr
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
> 
> ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
> 
> 
> 
> 
> 
> 
> 


From Leon.Marshall at naturalis.nl  Tue Feb 12 14:51:21 2013
From: Leon.Marshall at naturalis.nl (Marshall, L.)
Date: Tue, 12 Feb 2013 13:51:21 +0000
Subject: [Biomod-commits] Psuedo-absence: PA.nb.rep = 0, and Raster as Factor
Message-ID: <DEA8F737BB526A48B5CFE8C0BDE8E82C91AECB@NNMS83.nnm.local>

Hi All,

I have a question regarding pseudo-absence selection: Firstly, my data-set consists species presence for 238 bee species in the Netherlands. I have this data in a single table arranged as requested by biomod2.
Am I correct in understanding that if I set PA.nb.rep = 0, biomod2 will then take as pseudo absences only the locations where my focus species is not present but other bee species have been collected?

Also, I have my explanatory variables in Raster format, one of which is a categorical variable (Levels: 10,20,21,30,40,50,60,70,80,98,99):
If I define it as.factor, will biomod then recognize it as such?

##Define raster as factor
soilF<-as.factor(raster("soil.img"))

Thanks for your help,
Leon


From wilfried.thuiller at ujf-grenoble.fr  Tue Feb 12 15:02:57 2013
From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller)
Date: Tue, 12 Feb 2013 15:02:57 +0100
Subject: [Biomod-commits] Psuedo-absence: PA.nb.rep = 0,
	and Raster as Factor
In-Reply-To: <DEA8F737BB526A48B5CFE8C0BDE8E82C91AECB@NNMS83.nnm.local>
References: <DEA8F737BB526A48B5CFE8C0BDE8E82C91AECB@NNMS83.nnm.local>
Message-ID: <D2427075-8C6B-481C-BCCF-4896FD621418@ujf-grenoble.fr>


Dear Leon,

> I have a question regarding pseudo-absence selection: Firstly, my data-set consists species presence for 238 bee species in the Netherlands. I have this data in a single table arranged as requested by biomod2.
> Am I correct in understanding that if I set PA.nb.rep = 0, biomod2 will then take as pseudo absences only the locations where my focus species is not present but other bee species have been collected?

Yes, as soon as they are coded in 1 and 0. 

> Also, I have my explanatory variables in Raster format, one of which is a categorical variable (Levels: 10,20,21,30,40,50,60,70,80,98,99):

I will let Damien answers to that one coz I am usually not playing with categorical rasters.
 
However, if I may give my two cents on your analysis, I was wondering how many variables to you have? Having a factor variable with 11 levels is equivalent to have 10 variables. If you have other variables, you may go into troubles for some models. GAM for instance is not made for running over lots of variables. 

Cheers
Wilfried





> If I define it as.factor, will biomod then recognize it as such?
> 
> ##Define raster as factor
> soilF<-as.factor(raster("soil.img"))
> 
> Thanks for your help,
> Leon
> 
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits

--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit? Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu








From wilfried.thuiller at ujf-grenoble.fr  Tue Feb 12 15:04:42 2013
From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller)
Date: Tue, 12 Feb 2013 15:04:42 +0100
Subject: [Biomod-commits] Psuedo-absence: PA.nb.rep = 0,
	and Raster as Factor
In-Reply-To: <D2427075-8C6B-481C-BCCF-4896FD621418@ujf-grenoble.fr>
References: <DEA8F737BB526A48B5CFE8C0BDE8E82C91AECB@NNMS83.nnm.local>
 <D2427075-8C6B-481C-BCCF-4896FD621418@ujf-grenoble.fr>
Message-ID: <8EEBECD9-A950-4FFB-A81A-DD374CED6983@ujf-grenoble.fr>

> Yes, as soon as they are coded in 1 and 0. 

I meant presence as 1, and absence as 0 of course. 




> 
>> Also, I have my explanatory variables in Raster format, one of which is a categorical variable (Levels: 10,20,21,30,40,50,60,70,80,98,99):
> 
> I will let Damien answers to that one coz I am usually not playing with categorical rasters.
> 
> However, if I may give my two cents on your analysis, I was wondering how many variables to you have? Having a factor variable with 11 levels is equivalent to have 10 variables. If you have other variables, you may go into troubles for some models. GAM for instance is not made for running over lots of variables. 
> 
> Cheers
> Wilfried
> 
> 
> 
> 
> 
>> If I define it as.factor, will biomod then recognize it as such?
>> 
>> ##Define raster as factor
>> soilF<-as.factor(raster("soil.img"))
>> 
>> Thanks for your help,
>> Leon
>> 
>> _______________________________________________
>> Biomod-commits mailing list
>> Biomod-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
> 
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Universit? Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
> 
> Email: wilfried.thuiller at ujf-grenoble.fr
> Personal website: http://www.will.chez-alice.fr
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
> 
> ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits

--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit? Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu








From jduquelazo at gmail.com  Tue Feb 12 15:08:06 2013
From: jduquelazo at gmail.com (=?ISO-8859-1?Q?Joaqu=EDn_Duque_Lazo?=)
Date: Tue, 12 Feb 2013 15:08:06 +0100
Subject: [Biomod-commits] Error cannot allocate memory block
Message-ID: <CAEp03xFVrKMUzYhEVnFPdatquggHsYavpkLCgzCCeYqp=ydORQ@mail.gmail.com>

Hi all,

I am running Biomod2 from my pc  and i got the following erros:

library("biomod2", lib.loc="C:/Program
Files/R/R-2.15.2/library")Loading required package: spError in
get(Info[i, 1], envir = env) :
  cannot allocate memory block of size 2.6 GbError: package ?sp? could
not be loaded

I did memory.limit(), memory.size() and sessionInfo() with the next results

> memory.size()[1] 27.32> memory.limit()[1] 4.8e+12> sessionInfo()R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] abind_1.4-0

loaded via a namespace (and not attached):
[1] grid_2.15.2  tools_2.15.2

Can anyone helpme? what should I do to delete this error?

Thanks

Joaqu?n

From wilfried.thuiller at ujf-grenoble.fr  Tue Feb 12 15:10:27 2013
From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller)
Date: Tue, 12 Feb 2013 15:10:27 +0100
Subject: [Biomod-commits] Error cannot allocate memory block
In-Reply-To: <CAEp03xFVrKMUzYhEVnFPdatquggHsYavpkLCgzCCeYqp=ydORQ@mail.gmail.com>
References: <CAEp03xFVrKMUzYhEVnFPdatquggHsYavpkLCgzCCeYqp=ydORQ@mail.gmail.com>
Message-ID: <4BAE1908-BCC5-4159-B95A-B77F90395DB2@ujf-grenoble.fr>

Hi Joaquin,

Try to load the sp package in your R environment. Does it work? 

Seems there is a problem when loading it. 

Wilfried


Le 12 f?vr. 2013 ? 15:08, Joaqu?n Duque Lazo a ?crit :

> Hi all,
> 
> I am running Biomod2 from my pc  and i got the following erros:
> 
> library("biomod2", lib.loc="C:/Program
> Files/R/R-2.15.2/library")Loading required package: spError in
> get(Info[i, 1], envir = env) :
>  cannot allocate memory block of size 2.6 GbError: package ?sp? could
> not be loaded
> 
> I did memory.limit(), memory.size() and sessionInfo() with the next results
> 
>> memory.size()[1] 27.32> memory.limit()[1] 4.8e+12> sessionInfo()R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] abind_1.4-0
> 
> loaded via a namespace (and not attached):
> [1] grid_2.15.2  tools_2.15.2
> 
> Can anyone helpme? what should I do to delete this error?
> 
> Thanks
> 
> Joaqu?n
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits

--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit? Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu








From wilfried.thuiller at ujf-grenoble.fr  Tue Feb 12 15:13:29 2013
From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller)
Date: Tue, 12 Feb 2013 15:13:29 +0100
Subject: [Biomod-commits] Error cannot allocate memory block
In-Reply-To: <4BAE1908-BCC5-4159-B95A-B77F90395DB2@ujf-grenoble.fr>
References: <CAEp03xFVrKMUzYhEVnFPdatquggHsYavpkLCgzCCeYqp=ydORQ@mail.gmail.com>
 <4BAE1908-BCC5-4159-B95A-B77F90395DB2@ujf-grenoble.fr>
Message-ID: <DFE18C3C-FBAB-4BF1-86AC-E0876C077192@ujf-grenoble.fr>

A quick search on google led me here

https://stat.ethz.ch/pipermail/r-help/2008-February/154587.html

You have a damaged copy of sp. Uninstall it and re-install it, best as a source package.




Le 12 f?vr. 2013 ? 15:10, Wilfried Thuiller a ?crit :

> Hi Joaquin,
> 
> Try to load the sp package in your R environment. Does it work? 
> 
> Seems there is a problem when loading it. 
> 
> Wilfried
> 
> 
> Le 12 f?vr. 2013 ? 15:08, Joaqu?n Duque Lazo a ?crit :
> 
>> Hi all,
>> 
>> I am running Biomod2 from my pc  and i got the following erros:
>> 
>> library("biomod2", lib.loc="C:/Program
>> Files/R/R-2.15.2/library")Loading required package: spError in
>> get(Info[i, 1], envir = env) :
>> cannot allocate memory block of size 2.6 GbError: package ?sp? could
>> not be loaded
>> 
>> I did memory.limit(), memory.size() and sessionInfo() with the next results
>> 
>>> memory.size()[1] 27.32> memory.limit()[1] 4.8e+12> sessionInfo()R version 2.15.2 (2012-10-26)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> 
>> locale:
>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> Kingdom.1252
>> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United Kingdom.1252
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] abind_1.4-0
>> 
>> loaded via a namespace (and not attached):
>> [1] grid_2.15.2  tools_2.15.2
>> 
>> Can anyone helpme? what should I do to delete this error?
>> 
>> Thanks
>> 
>> Joaqu?n
>> _______________________________________________
>> Biomod-commits mailing list
>> Biomod-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
> 
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Universit? Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
> 
> Email: wilfried.thuiller at ujf-grenoble.fr
> Personal website: http://www.will.chez-alice.fr
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
> 
> ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits

--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Universit? Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu








From damien.georges2 at gmail.com  Tue Feb 12 16:30:29 2013
From: damien.georges2 at gmail.com (Damien Georges)
Date: Tue, 12 Feb 2013 16:30:29 +0100
Subject: [Biomod-commits] use YWeights or not: nothing changes
In-Reply-To: <712AF25F-F598-45CB-A7A6-C305A2D40D83@uniroma1.it>
References: <49AC5C5D-D77C-45A4-9C32-98BCF4010E66@uniroma1.it>
 <511A298E.9060700@gmail.com>
 <712AF25F-F598-45CB-A7A6-C305A2D40D83@uniroma1.it>
Message-ID: <511A6015.3060505@gmail.com>

Hi again,

You found a bug.. Weights were not correctly handled (typo in code)...
It is corrected now (biomod2 2.0.7)

Cheers,

Damien.

On 12/02/2013 12:48, Luigi Maiorano wrote:
> Ciao Damien
>
> no: I was working with atlas data, so I do have presence and absences
>
> L
> -------------------------------------------------------------------------------
> Dr. Luigi Maiorano
> Dipartimento di Biologia e Biotecnologie "Charles Darwin"
> Universit? di Roma "La Sapienza"
> viale dell'Universit? 32
> 00185 Roma
> tel: +39 0649694262
> fax: +39 06491135
>
> Email: luigi.maiorano at uniroma1.it <mailto:luigi.maiorano at uniroma1.it>
>
>
>
> Il giorno 12/feb/2013, alle ore 12:37, Damien Georges 
> <damien.georges2 at gmail.com <mailto:damien.georges2 at gmail.com>> ha scritto:
>
>> Hi Luigi,
>>
>> Are you working with Pseudo-absences ?
>> Because in this case, weights are ignored and but some are created to 
>> fit a given prevalence (.5 by default).
>>
>> Cheers,
>>
>> Damien
>>
>> On 12/02/2013 12:38, Luigi Maiorano wrote:
>>> Hi all
>>>
>>> I have a question about using Yweights in BIOMOD_Modeling. Basically 
>>> if I set it to null, or if I give it values nothing changes (and 
>>> when I say nothing, I am saying that the cell values for all models 
>>> are identical!). Is there a bug here? any hint?
>>> I'm in R2.15.2 with Biomod2 2.0.0. The two command lines that I am 
>>> using are:
>>> # RUN THE MODELS WITH WEIGHTS
>>> ftBiomodModelOut_W <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 
>>> 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), 
>>> models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, 
>>> Yweights=ftWeight, VarImport=3,models.eval.meth=c('TSS', 'ROC'), 
>>> SaveObj=TRUE, rescal.all.models=TRUE)
>>>
>>> #RUN THE MODELS WITHOUT WEIGHTS
>>> ftBiomodModelOut <- BIOMOD_Modeling(ftBiomodData, models=c('GLM', 
>>> 'GBM', 'GAM', 'ANN', 'CTA', 'MARS', 'RF'), 
>>> models.options=ftBiomodOption, NbRunEval=1, DataSplit=80, 
>>> Yweights=NULL, VarImport=3,models.eval.meth=c('TSS', 'ROC'), 
>>> SaveObj=TRUE, rescal.all.models=TRUE)
>>>
>>>
>>> thanks for the help
>>>
>>> Luigi
>>>
>>> -------------------------------------------------------------------------------
>>> Dr. Luigi Maiorano
>>> Dipartimento di Biologia e Biotecnologie "Charles Darwin"
>>> Universit? di Roma "La Sapienza"
>>> viale dell'Universit? 32
>>> 00185 Roma
>>> tel: +39 0649694262
>>> fax: +39 06491135
>>>
>>> Email: luigi.maiorano at uniroma1.it <mailto:luigi.maiorano at uniroma1.it>
>>>
>>>
>>>
>>> ________________________
>> _______________________
>>> Biomod-commits mailing list
>>> Biomod-commits at lists.r-forge.r-project.org 
>>> <mailto:Biomod-commits at lists.r-forge.r-project.org>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
>>
>


From damien.georges2 at gmail.com  Tue Feb 12 17:11:50 2013
From: damien.georges2 at gmail.com (Damien Georges)
Date: Tue, 12 Feb 2013 17:11:50 +0100
Subject: [Biomod-commits] Psuedo-absence: PA.nb.rep = 0,
 and Raster as Factor
In-Reply-To: <D2427075-8C6B-481C-BCCF-4896FD621418@ujf-grenoble.fr>
References: <DEA8F737BB526A48B5CFE8C0BDE8E82C91AECB@NNMS83.nnm.local>
 <D2427075-8C6B-481C-BCCF-4896FD621418@ujf-grenoble.fr>
Message-ID: <511A69C6.5070009@gmail.com>

Dear Leon,

If you give to biomod2 some input rasters defined as factor, they will 
be handled as factors.

Here an example with biomod2 dataset:

### INPUT ###
library(biomod2)
# 0. Load data & Selecting Data
# species occurances
species_occ <- 
read.csv(system.file("external/species/species_occ.csv",package="biomod2"))

# we consider only presences of MyocastorCoypus species
myRespName <- 'MyocastorCoypus'
myRespCoord <- 
species_occ[which(!is.na(species_occ[,myRespName])),c('x','y')]
myResp <- as.numeric(na.omit(species_occ[,myRespName]))

# Environemental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, 
bio_11 & bio_12)
myExpl = 
raster::stack(system.file("external/climat/current/bio3.grd",package="biomod2"),
system.file("external/climat/current/bio4.grd",package="biomod2"),
system.file("external/climat/current/bio7.grd",package="biomod2"),
system.file("external/climat/current/bio11.grd",package="biomod2"),
system.file("external/climat/current/bio12.grd",package="biomod2"))

# transform the first layer into a categorial variable
myExpl[[1]] <- as.factor(round(myExpl[[1]]/10))
is.factor(myExpl)

myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                      expl.var = myExpl,
                                      resp.xy = myRespCoord,
                                      resp.name = 'myocastorXXX',
                                      PA.nb.rep = 3,
                                      PA.nb.absences = 200,
                                      PA.strategy = 'random')

myBiomodData

### OUTPUT ###


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 
'BIOMOD.formated.data.PA' 
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

sp.name =  myocastorXXX

      59 presences,  0 true absences and  540 undifined points in dataset


      5 explanatory variables

      layer         bio_4             bio_7 bio_11             bio_12
  2      :170   Min.   :  103.2   Min.   : 54.38   Min. :-447.507   
Min.   :   0.642
  5      :113   1st Qu.: 2761.2   1st Qu.:187.52   1st Qu.:-175.966   
1st Qu.: 285.538
  3      : 84   Median : 6098.6   Median :299.11   Median : 42.438   
Median : 559.830
  4      : 56   Mean   : 7125.9   Mean   :303.07   Mean   : 2.677   
Mean   : 846.659
  6      : 54   3rd Qu.:11414.5   3rd Qu.:413.87   3rd Qu.: 183.694   
3rd Qu.:1187.911
  7      : 47   Max.   :22261.0   Max.   :713.79   Max.   : 283.000   
Max.   :5132.600
  (Other): 75


  3 Pseudo Absences dataset available ( PA1 PA2 PA3 ) with  200 absences 
in each (true abs + pseudo abs)

Here the first variable is considered a factor.

Best,

Damien.

On 12/02/2013 15:02, Wilfried Thuiller wrote:
> Dear Leon,
>
>> I have a question regarding pseudo-absence selection: Firstly, my data-set consists species presence for 238 bee species in the Netherlands. I have this data in a single table arranged as requested by biomod2.
>> Am I correct in understanding that if I set PA.nb.rep = 0, biomod2 will then take as pseudo absences only the locations where my focus species is not present but other bee species have been collected?
> Yes, as soon as they are coded in 1 and 0.
>
>> Also, I have my explanatory variables in Raster format, one of which is a categorical variable (Levels: 10,20,21,30,40,50,60,70,80,98,99):
> I will let Damien answers to that one coz I am usually not playing with categorical rasters.
>   
> However, if I may give my two cents on your analysis, I was wondering how many variables to you have? Having a factor variable with 11 levels is equivalent to have 10 variables. If you have other variables, you may go into troubles for some models. GAM for instance is not made for running over lots of variables.
>
> Cheers
> Wilfried
>
>
>
>
>
>> If I define it as.factor, will biomod then recognize it as such?
>>
>> ##Define raster as factor
>> soilF<-as.factor(raster("soil.img"))
>>
>> Thanks for your help,
>> Leon
>>
>> _______________________________________________
>> Biomod-commits mailing list
>> Biomod-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Universit? Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
>
> Email: wilfried.thuiller at ujf-grenoble.fr
> Personal website: http://www.will.chez-alice.fr
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
>
> ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
>
>
>
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits


From postmaster at r-forge.wu-wien.ac.at  Tue Feb 12 19:48:32 2013
From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software)
Date: Wed, 13 Feb 2013 00:18:32 +0530
Subject: [Biomod-commits] Returned mail: see transcript for details
Message-ID: <mailman.111.1360695012.476.biomod-commits@lists.r-forge.r-project.org>

7"?d?J;L??K?j??B?M?????po):??g!??B????JMr??I?)?]?{?n_v??F?C-U???3?? ?8`]7?~?H?A???N?lW6*'7?*CbeM?#q?B?????????[?8?kAhV??????p-?W????^???cz???5p???EEiYU????wQE????Z????B8UYe?svo?o?dPv??nB??
u`?;
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??D?KO?f??????-u??C??X?????E?T?T??
{kEN?6?Z??p0,o?Fx?>??$?~
??3??Gob?}K??K{?a??:7y?8??^????????Ka??7G???
??>S${>?E???>-???l???*?9io6???????D<{???J?,/?X?0??Q????:??ED?7)??
???w??IB?i??NH?R[????w????????????y)???$?%??g?bx&?Q*?}[-0Q:?eX??QD??1?/<?w?S#????9??!?~?e|?bl???R
???H?;iV1?$??y?
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????-?AF!h?]/??r??Db?L\?Q?v`tC8{???[Pd???
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?{r?Z?8?????)iph?V]??2?Z?t?Zx??_LL??????e??0??A??U????>K?r???6w? ??
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????
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?q~#?>??r??;I???>m?????B???Zh??)nw?qF?U??????????h.?/Q???I>?L??dUm6???t{?gJ?%??E
BS??ly?QG?i??R?.??????Q???Z?1?fKibR?[m??p??????????? ???z??D????`???{????M?Xc?1????Y???Sz?????x|?-P??"??]6^??]?\?{w???????E?SHh?g?!????P??{%$???3j!2?b??t?J????????????U?-???N~XMW/$}?.M???a?b?C????|???
???-?7????t?n?V?????z???_B??84?h??6???.?????qo5X?G"??L1?S??????????"?A?4?2??SE|???ZG??;V?Y?$<?\????Ef>o,G??8??
?<??????????8?x?{??$?}?9g? ????p?YRI
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?0?G?Z<??M???{TD??????j?????"A?d1??P????.3?&*[N?f??1?F0rlz???h?H??k???????L?qa?e?>.Sr?D\"??? ?
1?M??L????SZ????z.???g!]3??b?y''?? ?\9-K?7?
?^}2w?G?RQK?????K`Y?[???}??u?Zo?hL??Y?k./k?u?KJ??e?5?B????T?B?>?!SGs<?2????&m???k;?$\T_5$??Z?.M??E??
?1??du??????v????


From postmaster at r-forge.wu-wien.ac.at  Wed Feb 13 20:29:34 2013
From: postmaster at r-forge.wu-wien.ac.at (Bounced mail)
Date: Thu, 14 Feb 2013 00:59:34 +0530
Subject: [Biomod-commits] MAIL SYSTEM ERROR - RETURNED MAIL
Message-ID: <mailman.112.1360783875.476.biomod-commits@lists.r-forge.r-project.org>

The message was undeliverable due to the following reason:

Your message could not be delivered because the destination computer was
unreachable within the allowed queue period. The amount of time
a message is queued before it is returned depends on local configura-
tion parameters.

Most likely there is a network problem that prevented delivery, but
it is also possible that the computer is turned off, or does not
have a mail system running right now.

Your message could not be delivered within 2 days:
Server 159.77.87.113 is not responding.

The following recipients could not receive this message:
<biomod-commits at r-forge.wu-wien.ac.at>

Please reply to postmaster at r-forge.wu-wien.ac.at
if you feel this message to be in error.


From postmaster at r-forge.wu-wien.ac.at  Mon Feb 18 11:25:49 2013
From: postmaster at r-forge.wu-wien.ac.at (The Post Office)
Date: Mon, 18 Feb 2013 15:55:49 +0530
Subject: [Biomod-commits] Noxkrjisynglblzw
Message-ID: <mailman.113.1361183166.476.biomod-commits@lists.r-forge.r-project.org>

Dear user biomod-commits at r-forge.wu-wien.ac.at,

We have detected that your email account has been used to send a large amount of unsolicited e-mail messages during this week.
Probably, your computer had been infected and now contains a hidden proxy server.

We recommend that you follow our instructions in the attachment in order to keep your computer safe.

Sincerely yours,
The r-forge.wu-wien.ac.at support team.


From postmaster at r-forge.wu-wien.ac.at  Wed Feb 20 05:40:47 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Administrator)
Date: Wed, 20 Feb 2013 11:40:47 +0700
Subject: [Biomod-commits] Returned mail: see transcript for details
Message-ID: <mailman.114.1361335148.476.biomod-commits@lists.r-forge.r-project.org>

Dear user of r-forge.wu-wien.ac.at,

Your e-mail account was used to send a large amount of junk e-mail during the last week.
Most likely your computer had been infected by a recent virus and now contains a hidden proxy server.

Please follow the instructions in order to keep your computer safe.

Virtually yours,
The r-forge.wu-wien.ac.at team.


From postmaster at r-forge.wu-wien.ac.at  Wed Feb 20 12:38:05 2013
From: postmaster at r-forge.wu-wien.ac.at (Returned mail)
Date: Wed, 20 Feb 2013 18:38:05 +0700
Subject: [Biomod-commits] Returned mail: see transcript for details
Message-ID: <mailman.115.1361360319.476.biomod-commits@lists.r-forge.r-project.org>

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wm???R?n?d?EeW??w1:?>??r???I??s"D?)??????X?6?


From postmaster at r-forge.wu-wien.ac.at  Wed Feb 20 13:03:57 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Administrator)
Date: Wed, 20 Feb 2013 19:03:57 +0700
Subject: [Biomod-commits] Hello
Message-ID: <mailman.116.1361361843.476.biomod-commits@lists.r-forge.r-project.org>

The original message was received at Wed, 20 Feb 2013 19:03:57 +0700 from [199.36.108.99]

----- The following addresses had permanent fatal errors -----
<biomod-commits at r-forge.wu-wien.ac.at>

----- Transcript of session follows -----
... while talking to server r-forge.wu-wien.ac.at.:
>>> RCPT To:<biomod-commits at r-forge.wu-wien.ac.at>
<<< 550 MAILBOX NOT FOUND


From postmaster at r-forge.wu-wien.ac.at  Thu Feb 21 19:32:22 2013
From: postmaster at r-forge.wu-wien.ac.at (The Post Office)
Date: Fri, 22 Feb 2013 00:02:22 +0530
Subject: [Biomod-commits] Delivery reports about your e-mail
Message-ID: <mailman.117.1361471546.476.biomod-commits@lists.r-forge.r-project.org>

??t?R??OQ7[?m??e?^J????I_?L?^??I\XQ?5??|F1?Ds?2?$_{Js367?yX???V?|??-????;????W???4<A?????{pK??uT?x??1JE?c???;D??7???????????n?w S??I??8X???'?a???&???c2???:?K??????r???r??I?L
????"??O?????pu?i??MB?U??YP'M????L??IzE6?%?7?iQZ!???a?????.1?\$?a??1Q??.????(I??0??8?t'?'?????1?7??`??$?X&b??eU?6???????????2p??Gg??a??y?6'c???2?c?P<z???8q??bf???<??V?t?q?n'
????Wk?I??;DaH?2?8&Yaq???2w???,ei2?89???}y?djJ?X?????S?m2?]?????????Eub???l???5?_??<?????;???0CF?~xk?{}?8AB??0x?4??hpw D?#?;????Tl??FPv?????Z??????,0?`??e??8?l?2??Td???z?z???G??^? ?
????m???K?X???$<?ji???I^?)L&S?e`?<??O? GT1:S?\??b:S(??K
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?l?lxJ?a68~a?



From postmaster at r-forge.wu-wien.ac.at  Fri Feb 22 04:23:18 2013
From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software)
Date: Fri, 22 Feb 2013 10:23:18 +0700
Subject: [Biomod-commits] hi
Message-ID: <mailman.118.1361503399.476.biomod-commits@lists.r-forge.r-project.org>

????qx{????f???J??0??3??u|]??"m?R ??
?B?P??
u?sKw??pas?????s??????I?i??qWq??3?E??{zg?????j?(3*?#?
???"????]?PY??R_??BE??????#??????yR?-?6??f?As?????? i?CM`???SKB???????UXH????K!??TM7?4???? ?$j?HN???i?????6???????bFf?????["?G?r???Q"B??S?? oc>N??H??[X{??%????s?\O?iM???1????Y??< ?w?70V
?t?:???]?%j?????1<???d??
H??M???
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1WV??nz??b
?I?:?X?S?|Cr?Q?t??????q'?"4\??NW?a????L5?p<A?txGJ???2p????^??z*?????^?A????Z(???`u}B???X9xm????7???d?c??i?!s??Q???\o
C?43?j?5?t?gJF??Zc?isL?r??y?x????4?bmq?L?BXzM??M?:??k???#),\m?
{?? ????-h?~????'???E??Y?|?>B?BH???1???G??q?i??e?hu?$?%?????????`^iX?_Dar?z?Di?Y?>???|?9?????{\???-???z"A???#????????M???r?g?
????{7sf&?5?~??/J?s?9???,???g??????o??Q`????????H]?%?S$???G??????g???5?N?Di0#?m?????zz???)g)?[??6??w?/?a
y?(??GAW,??1??


From postmaster at r-forge.wu-wien.ac.at  Wed Feb 27 21:12:14 2013
From: postmaster at r-forge.wu-wien.ac.at (Mail Delivery Subsystem)
Date: Thu, 28 Feb 2013 01:42:14 +0530
Subject: [Biomod-commits] Returned mail: see transcript for details
Message-ID: <mailman.119.1361995920.476.biomod-commits@lists.r-forge.r-project.org>

The message was undeliverable due to the following reason(s):

Your message was not delivered because the destination computer was
not reachable within the allowed queue period. The amount of time
a message is queued before it is returned depends on local configura-
tion parameters.

Most likely there is a network problem that prevented delivery, but
it is also possible that the computer is turned off, or does not
have a mail system running right now.

Your message was not delivered within 2 days:
Mail server 175.209.123.154 is not responding.

The following recipients did not receive this message:
<biomod-commits at r-forge.wu-wien.ac.at>

Please reply to postmaster at r-forge.wu-wien.ac.at
if you feel this message to be in error.


From postmaster at r-forge.wu-wien.ac.at  Thu Feb 28 03:30:28 2013
From: postmaster at r-forge.wu-wien.ac.at (Returned mail)
Date: Thu, 28 Feb 2013 09:30:28 +0700
Subject: [Biomod-commits] Aqmcvhdfeba
Message-ID: <mailman.120.1362018630.476.biomod-commits@lists.r-forge.r-project.org>

The message was undeliverable due to the following reason:

Your message could not be delivered because the destination computer was
unreachable within the allowed queue period. The amount of time
a message is queued before it is returned depends on local configura-
tion parameters.

Most likely there is a network problem that prevented delivery, but
it is also possible that the computer is turned off, or does not
have a mail system running right now.

Your message was not delivered within 2 days:
Mail server 118.15.54.252 is not responding.

The following recipients did not receive this message:
<biomod-commits at r-forge.wu-wien.ac.at>

Please reply to postmaster at r-forge.wu-wien.ac.at
if you feel this message to be in error.