On Fri, 2009-09-04 at 17:15 +0200, Kim Vanselow wrote: > Dear all, > I would like to calculate a cca (package vegan) with species and > environmental data. One of these environmental variables is > cos(EXPOSURE). > The problem: for flat releves there is no exposure. The value is > missing and I can't call it 0 as 0 stands for east and west. > The cca does not run with missing values. What can I do to make vegan > cca ignoring these missing values? > Thanks a lot, > Kim
Hi Kim, This is timely as Jari Oksanen (lead developer on vegan) has been looking into making this happen automatically in vegan ordination functions. The solution for something like cca is very simple but it gets more complicated when you might like to allow features like na.exclude etc and have all the functions that operate on objects of class "cca" work nicely. For the moment, you should just process your data before it goes into cca. Here I assume that you have two data frames; i) Y is the species data, and ii) X the environmental data. Further I assume that only one variable in X has missings, lets call this Exposure: ## dummy data set.seed(1234) ## 20 samples of 10 species Y <- data.frame(matrix(rpois(20*10, 2), ncol = 10)) ## 20 samples and 5 env variables X <- data.frame(matrix(rnorm(20*5), ncol = 5)) names(X) <- c(paste("Var", 1:4, sep = ""), "Exposure") ## simulate some NAs in Exposure X$Exposure[sample(1:20, 3)] <- NA ## show X X ## Now create a new variable indicating which are missing miss <- with(X, is.na(Exposure)) ## now create new X and Y omitting these rows Y2 <- Y[!miss, ] X2 <- X[!miss, ] ## Now submit to CCA mod <- cca(Y2 ~ ., data = X2) mod ## plot it plot(mod, display = c("sites","bp"), scaling = 3) ## It'd be nice to get predictions for the 3 samples we missed out pred <- predict(mod, newdata = Y[miss, ], type = "wa", scaling = 3) ## add these points to the ordination: points(pred[, 1:2], col = "red", cex = 1.5) HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.