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bio website fromthebottomoftheheap.net
location Regina, Canada
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visits member for 4 years, 3 months
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I'm Quantitative Environmental Scientist in the Institute of Environmental Change & Society, at the University of Regina, Canada. I undertake research on environmental problems, including climate change and atmospheric pollution, affecting lakes. I use lake sediments to look back in time at the history of lakes to look at what organisms are present and how the species in the lake have changed through time and how lakes evolve and respond to pollution and perturbations.

I'm also an Adjunct Professor in the Department of Biology at the University of Regina.


Dec
10
comment What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
The origin of RDA is due to Rao (1964) which is a statistical paper so should be appropriate.
Dec
10
comment What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
@amoeba We do do SVD of $\mathbf{X}\beta$ (fitted values) not of the coefficients $\beta$, at least that's what fitted() gives: $\mathbf{X}\beta$. Hence RDA is often called reduced-rank regression.
Dec
10
comment What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
@amoeba Sorry for the delay but I've added a section to my answer to try to show the link with regression and how RDA can be viewed as a PCA of fitted values from a series of linear regressions, one per response variable.
Dec
10
revised What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
Add a section on relationship with regression
Dec
9
awarded  Enlightened
Dec
9
awarded  Nice Answer
Dec
8
revised What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
made a dumb mistake in the CCA example; fixed now.
Dec
7
comment What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
Thanks for the suggestion and follow up - it didn't occur to me to make the linear combination examples orthogonal but I have updated them. Re 2), I made a presumption, but given that there are c. 12,000 species of millipedes, I suspect the response here is observations of the abundance of $m$ species at each of $n$ sampling locations. In that sense, the RDA or CCA would model a multivariate response matrix of dimension $n \times m$. I'll try to deal with 4 later after I put the kids to bed.
Dec
7
revised What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
added 6238 characters in body
Dec
7
answered What criteria to use for separating variables into explanatory variables and responses for ordination methods in ecology?
Nov
27
comment How to implement reduced-rank regression in R?
@amoeba we may be talking about slightly different methods - RDA gets called a lot of things. We implement it in rda() via QR decomposition and SVD for efficiency, but that method gets the same result as the R code I showed in the comment earlier. Which makes me think what we do, which has been called reduced rank regression, is not the reduced rank regression the OP is looking for :-)
Nov
27
comment How to implement reduced-rank regression in R?
I'd be surprised is VGAM didn't do this; it has plenty of continuous distribution family functions (though note I haven't looked in detail at the RRR function in VGAM recently). You can also do something that is known as reduced rank regression with the vegan package. We call this Redundancy Analysis (RDA) but it also goes by the name reduced rank regression. And as @amoeba says, RDA can be computed by doing fit <- fitted(lm(Y ~ X, data = foo)) then prcomp(fit). If this is what you want, then rda() in vegan would be a good start.
Nov
18
comment impose an intercept on lm in r
You can add offset in lm() too. Was there a reason to switch to glm() here?
Nov
18
comment impose an intercept on lm in r
Does it matter if the intercept moves around a bit? I presume that the estimate of this constant term is so uncertain as to have a confidence interval on its estimate that includes 0? Just because physics dictates that the intercept be a certain value, doesn't mean you have to force exactly that value. By forcing that value exactly, you may induce bias in the estimation of other parameters of the model. The point is that you have noise in your measurements and you can account for that or at least look at the effect of that on the estimates of the constant term.
Nov
17
comment Can mean plus one standard deviation exceed maximum value?
Why do you want to add (or subtract) one standard deviation from the mean? The SD is a measure of the spread of the data. Did you want the standard error of the mean instead perhaps?
Nov
10
comment weighted disease prevalence in logistic GAM
@John could you use an offset() term to include the population? That's what I might do with a Poisson model for example if I wanted to standardise for effort or sample area etc.
Nov
10
answered weighted disease prevalence in logistic GAM
Nov
7
comment Calculate PCoA scores for dataframe “x”, based on the distance matrix of dataframe “y”
I think I understand conceptually what you want to do, at a higher level, but you can't really do anything to a dataset with the dissimilarities from the first data set. I explain a directly analogue of what you want to do using a constrained PCoA in my answer and suggest an alternative which avoids even doing the embedding in principal coordinates.
Nov
7
answered Calculate PCoA scores for dataframe “x”, based on the distance matrix of dataframe “y”
Nov
4
comment backward selection but regression coefficients not significative?
Depends what you by "in R"? The default step() function doesn't explicitly use the $p$ value at all. Instead it uses AIC to do selection. That may well explain what the OP is seeing, as may other things. We need more details to answer this.