R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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[Previously saved workspace restored]
> data(Cushings)
Warning message:
In data(Cushings) : data set 'Cushings' not found
> plot(Cushings[,1:2], col=unclass(Cushings[,3]),
+ pch=as.character(Cushings[,3]))
Error in plot(Cushings[, 1:2], col = unclass(Cushings[, 3]), pch
= as.character(Cushings[, :
object 'Cushings' not found
> Cushings
Error: object 'Cushings' not found
>
> library(MASS)
> data(Cushings)
> plot(Cushings[,1:2], col=unclass(Cushings[,3]),
+ pch=as.character(Cushings[,3]))
> Cushings
Tetrahydrocortisone Pregnanetriol Type
a1
3.1
11.70
a
a2
3.0
1.30
a
a3
1.9
0.10
a
a4
3.8
0.04
a
a5
4.1
1.10
a
a6
1.9
0.40
a
b1
8.3
1.00
b
b2
3.8
0.20
b
b3
3.9
0.60
b
b4
7.8
1.20
b
b5
9.1
0.60
b
b6
15.4
3.60
b
b7
7.7
1.60
b
b8
6.5
0.40
b
b9
5.7
0.40
b
b10
13.6
1.60
b
c1
10.2
6.40
c
c2
9.2
7.90
c
c3
9.6
3.10
c
c4
53.8
2.50
c
c5
15.8
7.60
c
u1
5.1
0.40
u
u2
12.9
5.00
u
u3
13.0
0.80
u
u4
2.6
0.10
u
u5
30.0
0.10
u
u6
20.5
0.80
u
>
> unk <- (1:27)[Cushings[,3]=="u"]
> cush.ltp <- log(Cushings[-unk,1:2])
> cush.class <- factor(Cushings[-unk,3])
>
> cush.lda <- lda(cush.ltp, cush.class)
> cush.pred.l <- predict(cush.lda, cush.ltp)
> cush.qda <- qda(cush.ltp, cush.class)
> cush.pred.q <- predict(cush.qda, cush.ltp)
>
plot(cush.ltp,pch=unclass(cush.class),col=unclass(cush.pred.q$cl
ass))
> predplot(cush.qda, cush.ltp, cush.class)
Error: could not find function "predplot"
> #decrease len if you have little memory.
> predplot <- function(object, data, class, len = 100, ...)
+ {
+
plot(data,col=unclass(class),pch=unclass(class))
+
xp <- seq(min(data[,1]),max(data[,1]),length=len)
+
yp <- seq(min(data[,2]),max(data[,2]),length=len)
+
grid <- expand.grid(xp,yp)
+
colnames(grid) <- colnames(data)
+
Z <- predict(object, grid, ...);
+
zc <- as.numeric(Z$class)
+ #browser()
+
for (i in unique(zc))
+ {zp <- Z$post[,i] - apply(as.matrix(Z$post[,-i]),1,max)
+
contour(xp, yp, matrix(zp, len),
+
add = T, levels = 0, drawlabels = F)}
+
invisible()
+ }
> predplot(cush.qda, cush.ltp, cush.class)
>
> cush.class
[1] a a a a a a b b b b b b b b b b c c c c c
Levels: a b c
> as.factor(produce$Location)
Error in inherits(x, "factor") : object 'produce' not found
> table(Actual=cush.class, Classified=cush.pred.q$class)
Classified
Actual a b c
a 6 0 0
b 0 9 1
c 0 1 4
> (1+1)/length(cush.class)
[1] 0.0952381
> ?qda
> cush.qda.cv <- qda(cush.ltp, cush.class, CV=T)
> cush.qda.cv
$class
[1] c a a a a a b b a b b c b b b b c c b b c
Levels: a b c
$posterior
a1
a2
a3
a4
a5
a6
b1
b2
b3
b4
b5
b6
b7
b8
b9
b10
c1
c2
c3
c4
c5
a
2.710769e-01
9.995486e-01
7.173135e-01
9.387700e-01
8.075482e-01
9.967018e-01
1.208229e-03
4.941469e-01
8.949635e-01
2.741092e-03
1.326874e-03
1.453647e-06
7.328264e-03
1.637380e-02
3.080219e-02
1.142217e-05
4.771808e-04
1.884260e-03
2.047639e-03
4.568707e-11
2.253315e-06
b
1.063718e-15
4.488013e-04
2.826865e-01
6.122998e-02
1.924446e-01
3.298205e-03
9.987690e-01
5.058531e-01
1.050365e-01
9.971409e-01
9.986728e-01
2.095953e-01
9.896376e-01
9.836262e-01
9.691978e-01
9.684997e-01
1.355948e-02
1.180815e-03
9.979202e-01
9.999990e-01
1.416779e-01
c
7.289231e-01
2.597752e-06
6.383218e-29
9.599874e-34
7.132110e-06
1.782123e-15
2.274741e-05
1.674928e-18
1.064219e-09
1.180411e-04
3.635929e-07
7.904032e-01
3.034166e-03
5.562795e-11
1.314517e-11
3.148891e-02
9.859633e-01
9.969349e-01
3.220436e-05
9.885363e-07
8.583198e-01
$call
qda(x = cush.ltp, cush.class, CV = T)
> table(Actual=cush.class, Classified=cush.pred.q$class)
Classified
Actual a b c
a 6 0 0
b 0 9 1
c 0 1 4
>
> table(Actual=cush.class, Classified=cush.qda.cv$class)
Classified
Actual a b c
a 5 0 1
b 1 8 1
c 0 2 3
> (1+1)/length(cush.class)
[1] 0.0952381
> (5)/length(cush.class)
[1] 0.2380952
> cush.ltp
Tetrahydrocortisone Pregnanetriol
a1
1.1314021
2.45958884
a2
1.0986123
0.26236426
a3
0.6418539
-2.30258509
a4
1.3350011
-3.21887582
a5
1.4109870
0.09531018
a6
0.6418539
-0.91629073
b1
2.1162555
0.00000000
b2
1.3350011
-1.60943791
b3
1.3609766
-0.51082562
b4
2.0541237
0.18232156
b5
2.2082744
-0.51082562
b6
2.7343675
1.28093385
b7
2.0412203
0.47000363
b8
1.8718022
-0.91629073
b9
1.7404662
-0.91629073
b10
2.6100698
0.47000363
c1
2.3223877
1.85629799
c2
2.2192035
2.06686276
c3
2.2617631
1.13140211
c4
3.9852735
0.91629073
c5
2.7600099
2.02814825
> x=cush.ltp[1,]
> x
Tetrahydrocortisone Pregnanetriol
a1
1.131402
2.459589
> cush.qda.cv$posterior[1,]
a
b
c
2.710769e-01 1.063718e-15 7.289231e-01
> round(cush.qda.cv$posterior[1,],3)
a
b
c
0.271 0.000 0.729
> ans=round(cush.qda.cv$posterior[1,],3)
> cush.ltp[-1,]
Tetrahydrocortisone Pregnanetriol
a2
1.0986123
0.26236426
a3
0.6418539
-2.30258509
a4
1.3350011
-3.21887582
a5
1.4109870
0.09531018
a6
0.6418539
-0.91629073
b1
2.1162555
0.00000000
b2
1.3350011
-1.60943791
b3
1.3609766
-0.51082562
b4
2.0541237
0.18232156
b5
2.2082744
-0.51082562
b6
2.7343675
1.28093385
b7
2.0412203
0.47000363
b8
1.8718022
-0.91629073
b9
1.7404662
-0.91629073
b10
2.6100698
0.47000363
c1
2.3223877
1.85629799
c2
2.2192035
2.06686276
c3
2.2617631
1.13140211
c4
3.9852735
0.91629073
c5
2.7600099
2.02814825
> x1=cush.ltp[-1,cush.class=='a']
Error in `[.data.frame`(cush.ltp, -1, cush.class == "a") :
undefined columns selected
> x1=cush.ltp[-1,cush.class=="a"]
Error in `[.data.frame`(cush.ltp, -1, cush.class == "a") :
undefined columns selected
> x1=cush.ltp[cush.class,-1]=='a',]
Error: unexpected ',' in "x1=cush.ltp[cush.class,-1]=='a',"
> x1=cush.ltp[cush.class,-1]=="a",]
Error: unexpected ',' in "x1=cush.ltp[cush.class,-1]=="a","
> x1=cush.ltp[-1,][1:5,]
> x1
Tetrahydrocortisone Pregnanetriol
a2
1.0986123
0.26236426
a3
0.6418539
-2.30258509
a4
1.3350011
-3.21887582
a5
1.4109870
0.09531018
a6
0.6418539
-0.91629073
> x2=cush.ltp[-1,][1:5+10,]
> x2
Tetrahydrocortisone Pregnanetriol
b6
2.734368
1.2809338
b7
2.041220
0.4700036
b8
1.871802
-0.9162907
b9
1.740466
-0.9162907
b10
2.610070
0.4700036
> x2=cush.ltp[-1,][6:15,]
> x2
Tetrahydrocortisone Pregnanetriol
b1
2.116256
0.0000000
b2
1.335001
-1.6094379
b3
1.360977
-0.5108256
b4
2.054124
0.1823216
b5
2.208274
-0.5108256
b6
2.734368
1.2809338
b7
2.041220
0.4700036
b8
1.871802
-0.9162907
b9
1.740466
-0.9162907
b10
2.610070
0.4700036
> x3=cush.ltp[-1,][16:21,]
> x3
Tetrahydrocortisone Pregnanetriol
c1
2.322388
1.8562980
c2
2.219203
2.0668628
c3
2.261763
1.1314021
c4
3.985273
0.9162907
c5
2.760010
2.0281482
NA
NA
NA
> x3=cush.ltp[-1,][16:20,]
> x1;x2;x3
Tetrahydrocortisone Pregnanetriol
a2
1.0986123
0.26236426
a3
0.6418539
-2.30258509
a4
1.3350011
-3.21887582
a5
1.4109870
0.09531018
a6
0.6418539
-0.91629073
Tetrahydrocortisone Pregnanetriol
b1
2.116256
0.0000000
b2
1.335001
-1.6094379
b3
1.360977
-0.5108256
b4
2.054124
0.1823216
b5
2.208274
-0.5108256
b6
2.734368
1.2809338
b7
2.041220
0.4700036
b8
1.871802
-0.9162907
b9
1.740466
-0.9162907
b10
2.610070
0.4700036
Tetrahydrocortisone Pregnanetriol
c1
2.322388
1.8562980
c2
2.219203
2.0668628
c3
2.261763
1.1314021
c4
3.985273
0.9162907
c5
2.760010
2.0281482
> mean(x1)
Tetrahydrocortisone
Pregnanetriol
1.025662
-1.216015
> var(x1)
Tetrahydrocortisone Pregnanetriol
Tetrahydrocortisone
0.13602627
0.07389231
Pregnanetriol
0.07389231
2.29677492
> s1=var(x1)
> s2=var(x2)
> s3=var(x3)
> s=(4*s1+9*s2+4*s3)/(4+9+4)
> s
Tetrahydrocortisone Pregnanetriol
Tetrahydrocortisone
0.2748125
0.1319893
Pregnanetriol
0.1319893
0.9896334
> var(cush.ltp[-1,])
Tetrahydrocortisone Pregnanetriol
Tetrahydrocortisone
0.6241786
0.7274309
Pregnanetriol
0.7274309
1.9703983
> p1=5/20
> p3=5/20
> p2=10/20
> p1;p2;p3
[1] 0.25
[1] 0.5
[1] 0.25
> library(mvtnorm)
> ?dmvnorm
> p1*dmvnorm(x,mean=mean(x1),sigma=s)
a1
6.422051e-05
> j1=p1*dmvnorm(x,mean=mean(x1),sigma=s)
> j2=p2*dmvnorm(x,mean=mean(x2),sigma=s)
> j3=p3*dmvnorm(x,mean=mean(x3),sigma=s)
> j1;j2;j3
a1
6.422051e-05
a1
0.00022839
a1
0.0002064751
> j=j1+j2+j3
> j1/j;j2/j;j3/j
a1
0.1286763
a1
0.4576169
a1
0.4137068
> ans
a
b
c
0.271 0.000 0.729
> j1=p1*dmvnorm(x,mean=mean(x1),sigma=s)
> j1=p1*dmvnorm(x,mean=mean(x1),sigma=var(x1))
> j2=p2*dmvnorm(x,mean=mean(x2),sigma=var(x2))
> j3=p3*dmvnorm(x,mean=mean(x3),sigma=var(x3))
> j=j1+j2+j3
> j1/j;j2/j;j3/j
a1
0.2365863
a1
1.114050e-15
a1
0.7634137
>