Thanks for the explanation !
Happy to know there is no problem with my models.

Have a good day,

Arnaud

2012/2/3 Simon Wood <s.wood@bath.ac.uk>

> It is completely safe to ignore this. Here is what is going on...
>
> mgcv routine 'mroot' is calling R routine 'chol' to find the *pivoted*
> Choleski factor of a positive semi definite matrix. This is deliberate, and
> completely ok to do, but 'chol' issues a warning when a matrix is only
> positive semi-definite (as opposed to strictly +ve def), even if pivoting
> has been requested. 'mroot' therefore suppresses the warning.
>
> best,
> Simon
>
>
> On 03/02/12 20:38, Arnaud Mosnier wrote:
>
>> Dear list,
>>
>>
>> I fitted the same GAM model using directly the function gam(mgcv) ...
>> then as a parameter of another function that capture the warnings
>> messages (see below).
>> In the first case, there is no warning message printed, but in the last
>> one, the function find two warning messages stating "matrix not positive
>> definite"
>>
>> So my question is: Do I have to worry about those warnings and then why
>> are they not printed in the simple use of the gam function.
>>
>> ##############################**#######################
>>
>> Here is some further description:
>>
>> ## Simple use of gam
>>
>> gam(USE ~ X1 + s(X2) + s(X3), family = binomial, data = data,
>> method="REML") # print no warning message.
>>
>> ## Using a function that capture warnings
>>
>> Model_n_Warnings <- function(expr) {
>>             localWarnings <- list()
>>             outModel <- withCallingHandlers(expr,
>>             warning = function(w) {
>>             localWarnings[[length(**localWarnings)+1]] <<- w$message  #
>> store warning message
>>             invokeRestart("muffleWarning") # avoid printing warning
>> message to console
>>             })
>>             list(outModel=outModel, warnings=localWarnings)
>>   }
>>
>> out <- Model_n_Warnings (gam(USE ~ X1 + s(X2) + s(X3), family =
>> binomial, data = data, method="REML"))
>>
>> out$warnings
>>
>> [[1]]
>> [1] "matrix not positive definite"
>>
>> [[2]]
>> [1] "matrix not positive definite"
>>
>>
>> Thanks,
>>
>> Arnaud
>>
>
>
> --
> Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
> +44 (0)1225 386603               http://people.bath.ac.uk/sw283
>

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