R help - Nov 2010 - [klaR package] [NaiveBayes] warning message numerical 0 probability

Hi,

I run R 2.10.1 under ubuntu 10.04 LTS (Lucid Lynx) and klaR version 0.6-4.

I compute a model over a 2 classes dataset (composed of 700 examples).
To that aim, I use the function NaiveBayes provided in the package
klaR.
When I then use the prediction function : predict(my_model, new_data).
I get the following warning :

"In FUN(1:747[[747L]], ...) : Numerical 0 probability with observation
458"

As I did not find any documentation or any discussion concerning this
warning message, I looked in the klaR source code and found the
following line in predict.NaiveBayes.R :

"warning("Numerical 0 probability with observation ", i)"

Unfortunately, it is hard to get a clear picture of the whole process
reading the code. I wonder if someone could help me with the meaning
of this warning message.

Sorry I did not provide an example, but I could not simulate the same
message over a small toy example.

Thank you,

Fabon Dzogang.

On 03.11.2010 16:26, Fabon Dzogang wrote:
> Hi,
>
> I run R 2.10.1 under ubuntu 10.04 LTS (Lucid Lynx) and klaR version 0.6-4.
>
> I compute a model over a 2 classes dataset (composed of 700 examples).
> To that aim, I use the function NaiveBayes provided in the package
> klaR.
> When I then use the prediction function : predict(my_model, new_data).
> I get the following warning :
>
> "In FUN(1:747[[747L]], ...) : Numerical 0 probability with observation
458"
>
> As I did not find any documentation or any discussion concerning this
> warning message, I looked in the klaR source code and found the
> following line in predict.NaiveBayes.R :
>
> "warning("Numerical 0 probability with observation ",
i)"

Within Naive Bayes in order to calculate the posteriori probabilities of
the classes it is necessary to calculate the probabilities of the
observations given the classes. The function NaiveBayes prints a warning
if all these probabilities are numerical 0, i.e. that the observation
has a numerical probability of 0 for *all* classes. Usually this is only
the case when the obs. is an extreme outlier.

I will change the warning to say "all classes" in further releases of
klaR.

Best wishes,
Uwe Ligges


> Unfortunately, it is hard to get a clear picture of the whole process
> reading the code. I wonder if someone could help me with the meaning
> of this warning message.
>
> Sorry I did not provide an example, but I could not simulate the same
> message over a small toy example.
>
> Thank you,
>
> Fabon Dzogang.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Thank you very much for this clarification,

Sincerely,
Fabon Dzogang.

2010/11/15 Uwe Ligges <ligges at
statistik.tu-dortmund.de>:
>
>
> On 03.11.2010 16:26, Fabon Dzogang wrote:
>>
>> Hi,
>>
>> I run R 2.10.1 under ubuntu 10.04 LTS (Lucid Lynx) and klaR version
0.6-4.
>>
>> I compute a model over a 2 classes dataset (composed of 700 examples).
>> To that aim, I use the function NaiveBayes provided in the package
>> klaR.
>> When I then use the prediction function : predict(my_model, new_data).
>> I get the following warning :
>>
>> "In FUN(1:747[[747L]], ...) : Numerical 0 probability with
observation
>> 458"
>>
>> As I did not find any documentation or any discussion concerning this
>> warning message, I looked in the klaR source code and found the
>> following line in predict.NaiveBayes.R :
>>
>> "warning("Numerical 0 probability with observation ",
i)"
>
>
> Within Naive Bayes in order to calculate the posteriori probabilities of
> the classes it is necessary to calculate the probabilities of the
> observations given the classes. The function NaiveBayes prints a warning
> if all these probabilities are numerical 0, i.e. that the observation
> has a numerical probability of 0 for *all* classes. Usually this is only
> the case when the obs. is an extreme outlier.
>
> I will change the warning to say "all classes" in further
releases of klaR.
>
> Best wishes,
> Uwe Ligges
>
>
>
>> Unfortunately, it is hard to get a clear picture of the whole process
>> reading the code. I wonder if someone could help me with the meaning
>> of this warning message.
>>
>> Sorry I did not provide an example, but I could not simulate the same
>> message over a small toy example.
>>
>> Thank you,
>>
>> Fabon Dzogang.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Fabon Dzogang