[R-sig-eco] Factors in partialRDA

[Jari Oksanen]

Andy,

That’s correct: if you have coded your variable as a single factor, R (and hence vegan) will automatically create dummy variables. If you have originally coded your variable as a set of dummy variables, and you have done that correctly, you will get the same result. If you do  not drop one of the dummy variables, R will do it for you and tell that some of your original variables were aliased. This will not influence the results, though. 

In conclusion: everything goes, but it is best to use the R way and define your factor as a single factor.

Cheers, Jari Oksanen
> On 7 Feb 2017, at 10:48 am, Andrew Halford <andrew.halford at gmail.com> wrote:
> 
> Hi Listers,
> 
> I am running a partial RDA analysis and I have an environmental dataset
> which includes a non-ordered factor representing reef type.
> 
> I want to test for a significant linear trend in the environmental dataset
> as part of the process of testing for spatial autocorrelation.
> 
> e.g. lineartest <- anova(rda(env,latlong))
> 
> I have coded this Factor variable up as a group of dummy variables equal to
> the number of different reef types to run the test but I am unsure if I
> need to drop one of the dummy variables before running the linear test?
> 
> I will revert back to a single Factor variable when I run the RDA as told
> in the vegan documentation?
> 
> My reading tells me that the call to RDA in Vegan will automatically deal
> with creating dummy variables from a Factor variable presented in the model
> but this is not the case
> 
> cheers
> 
> Andy
> 
> 
> Andrew Halford Ph.D
> Research Scientist (Kimberley Marine Parks)
> Dept. Parks and Wildlife
> Western Australia
> 
> Ph: +61 8 9219 9795
> Mobile: +61 (0) 468 419 473
> 
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