{"action":"created","issue":{"url":"https://api.github.com/repos/vegandevs/vegan/issues/207","repository_url":"https://api.github.com/repos/vegandevs/vegan","labels_url":"https://api.github.com/repos/vegandevs/vegan/issues/207/labels{/name}","comments_url":"https://api.github.com/repos/vegandevs/vegan/issues/207/comments","events_url":"https://api.github.com/repos/vegandevs/vegan/issues/207/events","html_url":"https://github.com/vegandevs/vegan/issues/207","id":182579830,"number":207,"title":"Allow finer control of which eigenvalues (constrained or unconstrained) are returned by 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varechem)\r\nvare.cca <- cca(varespec ~ Al + P*(K + Baresoil), data=varechem)\r\n```\r\n\r\nHow do I extract only the *unconstrained* eigenvalues? With `eigenvals()`, as currently implemented, this is not possible:\r\n\r\n```r\r\n> eigenvals(vare.cca, constrained = TRUE)\r\n     CCA1      CCA2      CCA3      CCA4      CCA5      CCA6 \r\n0.3756307 0.2341897 0.1406696 0.1322908 0.1067518 0.0561409 \r\n> eigenvals(vare.cca, constrained = FALSE)\r\n     CCA1      CCA2      CCA3      CCA4      CCA5      CCA6       CA1       CA2 \r\n0.3756307 0.2341897 0.1406696 0.1322908 0.1067518 0.0561409 0.2757692 0.1541055 \r\n      CA3       CA4       CA5       CA6       CA7       CA8       CA9      CA10 \r\n0.1353625 0.1180342 0.0888713 0.0551092 0.0491937 0.0378095 0.0357212 0.0277773 \r\n     CA11      CA12      CA13      CA14      CA15      CA16      CA17 \r\n0.0212446 0.0136233 0.0092818 0.0059037 0.0045662 0.0030977 0.0020541\r\n```\r\n\r\nI propose modifying the current behaviour of `eigenvals()` such that\r\n\r\n* `constrained` only controls whether or not constrained eigenvalues are returned\r\n* new argument `unconstrained` controls whether or not the unconstrained eigenvalues are returned.\r\n\r\nThoughts?"},"comment":{"url":"https://api.github.com/repos/vegandevs/vegan/issues/comments/253428312","html_url":"https://github.com/vegandevs/vegan/issues/207#issuecomment-253428312","issue_url":"https://api.github.com/repos/vegandevs/vegan/issues/207","id":253428312,"user":{"login":"jarioksa","id":1432933,"avatar_url":"https://avatars.githubusercontent.com/u/1432933?v=3","gravatar_id":"","url":"https://api.github.com/users/jarioksa","html_url":"https://github.com/jarioksa","followers_url":"https://api.github.com/users/jarioksa/followers","following_url":"https://api.github.com/users/jarioksa/following{/other_user}","gists_url":"https://api.github.com/users/jarioksa/gists{/gist_id}","starred_url":"https://api.github.com/users/jarioksa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jarioksa/subscriptions","organizations_url":"https://api.github.com/users/jarioksa/orgs","repos_url":"https://api.github.com/users/jarioksa/repos","events_url":"https://api.github.com/users/jarioksa/events{/privacy}","received_events_url":"https://api.github.com/users/jarioksa/received_events","type":"User","site_admin":false},"created_at":"2016-10-13T06:46:38Z","updated_at":"2016-10-13T06:46:38Z","body":"@gavinsimpson , about `model = c(\"constrained\", \"unconstrained\")` -- that depends how much you want to break things. Now it would be about breaking the user interface. The reason why I used `model = c(\"pCCA\", \"CCA\", \"CA\")` is that I can use `object[[model]]$item` within the code (and indeed, you cannot have `\"all\"` or more than one model with this idiom). You can call this elegant or lazy depending on your point of view. The reason for the models being called `pCCA`, `CCA` and `CA` is that this is how they were called in 2002 when I had no intention to ever implement RDA that I regarded as useless weaker alternative to CCA (but I have become softer with age and now I tolerate RDA, and I think the difference is much smaller than I used to think earlier, and smaller than between CA and the abominable PCA).  "}}
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