-
Notifications
You must be signed in to change notification settings - Fork 97
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Related to #655 should the wrappers allow partial unconstrained ordination via formula and Condition()
?
#662
Comments
This is allowed and has been allowed always. It can be written as: cca(y ~ Condition(x+z), data=...) The result object will have partial component ( We can do this without explicit term for constraints because ordination models are centred meaning that they have zero-intercept and omitting a term component (like constraints) means just the same as making it return 0-coefficients. Naturally we must take this centring into account in some cases, like you see, for instance, in functions Actually, you can do this also without formula (and this, I think, has always been the case):
|
@jarioksa Yes to all that; but the question at hand was whether to allow the new wrappers to use |
@gavinsimpson Fair enough, but I don't see a need for this feature. The stated purpose of the wrapper was to have an educational simple function for basic PCA, CA & PCO. Having partialized PCA, CA & PCO is not such a simple educational case, but rather a special case of RDA, CCA & dbRDA, and could wait till you have advanced to these methods. BTW, to my surprise, |
|
Right now we have
pca()
,ca()
, andpco()
as wrappers to fitting functionsrda()
,cca()
andpco()
. These unconstrained ordination wrappers allow arguments to be passed to the fitting function, so partial ordination is possible but only via the matrix-element interface.Should we turn the wrappers for unconstrained ordination into S3 generics with the currently-implemented functions becoming the default method and then allowing a formula interface of the form
y ~ 1 + Condition(x + z)
?I know you can you just use
cca()
etc for this, but the same argument as the one given in #655 applies.If we allow this, should we check that the formula only contains
1
(or0
?) andCondition()
? so that it really is an unconstrained model? Or should we allow abuse of the wrappers to pass covariates but check the object returned bycca()
etc for presence of covariates (constraints) and if present return that object unmodified, so that we only return a"ca"
(etc) classed object if the model has no covariates (constraints)?The text was updated successfully, but these errors were encountered: