Mixing
Model selection for partial RDA
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I performed a partial RDA with the help of the vegan package. I know that I can select the most parsimonious model with the ordiR2step function. OrdiR2step uses the adjusted R2 as goodness of fit measure.
However, apparently this function does not work for partial RDAs. This is stated in the vegan documentary, also I get an error when trying the following code:
> step_both_R2 <- ordiR2step(rda(species_data ~ treatment +
> Condition(stream), data=chemical_data), scope = formula(rda_1),
> direction="both", pstep = 1000 )
Does anyone know of any other way to find the most parsimious model for a partial RDA?
As I have about 10 explanatory variables in my model it would be quite time-intensive to compute every single combination of parameters.
r vegan rda
asked Jan 3 at 14:55
gamelgamel
196
add a comment |
I performed a partial RDA with the help of the vegan package. I know that I can select the most parsimonious model with the ordiR2step function. OrdiR2step uses the adjusted R2 as goodness of fit measure.
However, apparently this function does not work for partial RDAs. This is stated in the vegan documentary, also I get an error when trying the following code:
> step_both_R2 <- ordiR2step(rda(species_data ~ treatment +
> Condition(stream), data=chemical_data), scope = formula(rda_1),
> direction="both", pstep = 1000 )
Does anyone know of any other way to find the most parsimious model for a partial RDA?
As I have about 10 explanatory variables in my model it would be quite time-intensive to compute every single combination of parameters.
r vegan rda
asked Jan 3 at 14:55
gamelgamel
196
1
See github.com/vegandevs/vegan/issues/295 It's been reported and Pierre Legendre indicates there how to do it (not in a practical sense unless you have access to their book). We just haven't had chance to implement this yet.
– Gavin Simpson
Jan 3 at 17:07
add a comment |
I performed a partial RDA with the help of the vegan package. I know that I can select the most parsimonious model with the ordiR2step function. OrdiR2step uses the adjusted R2 as goodness of fit measure.
However, apparently this function does not work for partial RDAs. This is stated in the vegan documentary, also I get an error when trying the following code:
> step_both_R2 <- ordiR2step(rda(species_data ~ treatment +
> Condition(stream), data=chemical_data), scope = formula(rda_1),
> direction="both", pstep = 1000 )
Does anyone know of any other way to find the most parsimious model for a partial RDA?
As I have about 10 explanatory variables in my model it would be quite time-intensive to compute every single combination of parameters.
r vegan rda
asked Jan 3 at 14:55
gamelgamel
196
I performed a partial RDA with the help of the vegan package. I know that I can select the most parsimonious model with the ordiR2step function. OrdiR2step uses the adjusted R2 as goodness of fit measure.
However, apparently this function does not work for partial RDAs. This is stated in the vegan documentary, also I get an error when trying the following code:
> step_both_R2 <- ordiR2step(rda(species_data ~ treatment +
> Condition(stream), data=chemical_data), scope = formula(rda_1),
> direction="both", pstep = 1000 )
Does anyone know of any other way to find the most parsimious model for a partial RDA?
As I have about 10 explanatory variables in my model it would be quite time-intensive to compute every single combination of parameters.
r vegan rda
r vegan rda
asked Jan 3 at 14:55
gamelgamel
196
asked Jan 3 at 14:55
gamelgamel
196
edited Jan 3 at 15:07
gamel
asked Jan 3 at 14:55
gamelgamel
196
asked Jan 3 at 14:55
gamelgamel
196
asked Jan 3 at 14:55
gamelgamel
196
196
1
See github.com/vegandevs/vegan/issues/295 It's been reported and Pierre Legendre indicates there how to do it (not in a practical sense unless you have access to their book). We just haven't had chance to implement this yet.
– Gavin Simpson
Jan 3 at 17:07
add a comment |
1
See github.com/vegandevs/vegan/issues/295 It's been reported and Pierre Legendre indicates there how to do it (not in a practical sense unless you have access to their book). We just haven't had chance to implement this yet.
– Gavin Simpson
Jan 3 at 17:07
1
1
See github.com/vegandevs/vegan/issues/295 It's been reported and Pierre Legendre indicates there how to do it (not in a practical sense unless you have access to their book). We just haven't had chance to implement this yet.
– Gavin Simpson
Jan 3 at 17:07
See github.com/vegandevs/vegan/issues/295 It's been reported and Pierre Legendre indicates there how to do it (not in a practical sense unless you have access to their book). We just haven't had chance to implement this yet.
– Gavin Simpson
Jan 3 at 17:07
add a comment |
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See github.com/vegandevs/vegan/issues/295 It's been reported and Pierre Legendre indicates there how to do it (not in a practical sense unless you have access to their book). We just haven't had chance to implement this yet.
– Gavin Simpson
Jan 3 at 17:07