Subject: Marine Geospatial Ecology Tools (MGET) help
Text archives
| From: | Mara<> |
|---|---|
| To: | |
| Subject: | [mget-help] GAM and GLM |
| Date: | Thu, 16 Apr 2009 13:23:12 -0400 (EDT) |
Hello!
I use mget to predict the occurence of species and Jason already helped me
with
inital problems. I have to admit that I am a beginner in statistic modeling
and
also just started using R. Please forgive me if I thus address minor problems
here (and that I wrote half a novel).
When I want to fit a GAM using the mgcv package I sometimes have problems when
adding splines with "shrinkage". (Models with exactly the same input but
without shrinking run perfectly.) I used variables separately to see if I can
track down the problem but here the models will always run. Depending on the
combination of variables I get one of the following error messages:
RPy_RException: Error: NA/NaN/Inf in foreign function call (arg 3)
or
RPy_RException: Error: no valid set of coefficients has been found:please
supply starting values
As far as I understand this normally means there are missing values or maybe
typing errors but like I said before the input is always the same (and it
works
without shrinkage).
On the other hand, using the same predictors but a difference response will
work perfectly even with shrinkage...
Using the gam package I don't get results at all but Df=1 for all predictor
variables:
Df
(Intercept) 1
Depth 1
...
What does this mean?
Last but not least I have a comment/question regarding GLMs. I used cook's
distance to identify outliers. Row numbers are used to identify samples and
numbers of the first three samples with highest values are plotted. As far as
I
can see it there is no way to identify the other numbers/samples. Only when I
remove the first three outliers (using the "where clause") I can see the row
numbers of the next three samples with highest values. Unfortunately, the row
numbers are now not identically to the input table as three samples were not
considered. Identification of the propper row can be very time consuming. Is
there a way to improve this (other than changing the input table)?!
Thanks already for reading all of this! Am looking forward to help, thanks!
I use mget to predict the occurence of species and Jason already helped me
with
inital problems. I have to admit that I am a beginner in statistic modeling
and
also just started using R. Please forgive me if I thus address minor problems
here (and that I wrote half a novel).
When I want to fit a GAM using the mgcv package I sometimes have problems when
adding splines with "shrinkage". (Models with exactly the same input but
without shrinking run perfectly.) I used variables separately to see if I can
track down the problem but here the models will always run. Depending on the
combination of variables I get one of the following error messages:
RPy_RException: Error: NA/NaN/Inf in foreign function call (arg 3)
or
RPy_RException: Error: no valid set of coefficients has been found:please
supply starting values
As far as I understand this normally means there are missing values or maybe
typing errors but like I said before the input is always the same (and it
works
without shrinkage).
On the other hand, using the same predictors but a difference response will
work perfectly even with shrinkage...
Using the gam package I don't get results at all but Df=1 for all predictor
variables:
Df
(Intercept) 1
Depth 1
...
What does this mean?
Last but not least I have a comment/question regarding GLMs. I used cook's
distance to identify outliers. Row numbers are used to identify samples and
numbers of the first three samples with highest values are plotted. As far as
I
can see it there is no way to identify the other numbers/samples. Only when I
remove the first three outliers (using the "where clause") I can see the row
numbers of the next three samples with highest values. Unfortunately, the row
numbers are now not identically to the input table as three samples were not
considered. Identification of the propper row can be very time consuming. Is
there a way to improve this (other than changing the input table)?!
Thanks already for reading all of this! Am looking forward to help, thanks!
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