[R] lda output missing
David L Carlson
dcarlson at tamu.edu
Thu Dec 8 22:16:12 CET 2011
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-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Sarah Goslee
Sent: Thursday, December 08, 2011 11:13 AM
To: David Lutz
Cc: r-help at 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 <lutzda at 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
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