The Proportion of trace will only show up if there are two or more linear discriminant functions. With two groups you have only one function, so the Proportion of trace is 1.0 for that function.
group1 <- data.frame(Group="G1", Var1=rnorm(50), Var2=rnorm(50)) group2 <- data.frame(Group="G2", Var1=rnorm(50), Var2=rnorm(50)) Groups <- rbind(group1, group2) lda(Group~Var1+Var2, Groups) # No Proportion of trace group3 <- data.frame(Group="G3", Var1=rnorm(50), Var2=rnorm(50)) Groups <- rbind(group1, group2, group3) lda(Group~Var1+Var2, Groups) # Now it shows up For predicted group membership, look at predict.lda For tests of significance, look at Anova in package car For canonical discriminant analysis, look at package candisc ---------------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77843-4352 -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sarah Goslee Sent: Thursday, December 08, 2011 11:13 AM To: David Lutz Cc: r-help@r-project.org Subject: Re: [R] lda output missing That's odd. You don't provide a reproducible example, but using a built-in dataset (from the help for lda) I get the Proportion of Trace given by the print.lda method. library(MASS) Iris <- data.frame(rbind(iris3[,,1], iris3[,,2], iris3[,,3]), Sp = rep(c("s","c","v"), rep(50,3))) train <- sample(1:150, 75) z <- lda(Sp ~ ., Iris, prior = c(1,1,1)/3, subset = train) print(z) Call: lda(Sp ~ ., data = Iris, prior = c(1, 1, 1)/3, subset = train) Prior probabilities of groups: c s v 0.3333333 0.3333333 0.3333333 Group means: Sepal.L. Sepal.W. Petal.L. Petal.W. c 5.947826 2.786957 4.326087 1.3652174 s 5.050000 3.380769 1.465385 0.2346154 v 6.811538 3.023077 5.700000 2.0653846 Coefficients of linear discriminants: LD1 LD2 Sepal.L. -1.6665885 1.104460 Sepal.W. -0.8681909 1.872188 Petal.L. 2.4670375 -1.499070 Petal.W. 4.2156275 2.948759 Proportion of trace: LD1 LD2 0.9916 0.0084 Here's my sessionInfo(). Are you certain everything is up-to-date? What OS are you running? Do you have other packages loaded that could be interfering? What happens when you run the example I used? > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MASS_7.3-16 loaded via a namespace (and not attached): [1] tools_2.14.0 On Thu, Dec 8, 2011 at 10:29 AM, David Lutz <lut...@wfu.edu> wrote: > Hello everyone, > > I am working on a linear discriminant analysis and am having issues finding > the full output of my lda. Specifically, there is no reporting of the > Proportion of Trace that is a normal output of the procedure. I'm using a > csv file and everything is reading in correctly. I've looked and looked and > can't figure out why my output is not complete. Is it something simple that > I am overlooking? > > I am working in R 2.14.0 with an updated MASS package. Here is my syntax: > > lda(CC ~ sumstem + maxdbh + maxh + cdlai + sumlai + sumbas + > totalbio + ratio, data = practice) > > and the output is: > > Prior probabilities of groups: > normal warm > 0.5 0.5 > > Group means: > sumstem maxdbh maxh cdlai sumlai sumbas totalbio > normal 901.3722 16.66994 15.70927 0.010393258 1.672247 5.471812 27.67875 > warm 972.4916 22.27247 19.64740 0.002429775 3.181994 9.892683 47.68511 > ratio > normal 0.01162921 > warm 0.85721910 > > Coefficients of linear discriminants: > LD1 > sumstem 0.001111176 > maxdbh 0.034299258 > maxh -0.287343783 > cdlai -2.021350057 > sumlai 1.407215702 > sumbas -0.419422181 > totalbio 0.110403369 > ratio 0.001657649 > > > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ 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. ______________________________________________ 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.
