Carol,

Actually, you have only five nodes, numbered 1, 2, 3, 6, and 7.
And all five nodes are included in your plot.
Nodes 1 and 3 are branching nodes; nodes 2, 6, and 7 are terminal nodes.

Try typing just the name of the rpart object for a very brief text version
of the tree.
     rpart.res

Jean


On Sun, Jan 27, 2013 at 1:31 PM, carol white <wht_crl@yahoo.com> wrote:

> Hi,
> When I look at the summary of an rpart object run on my data, I get 7
> nodes but when I plot the rpart object, I get only 3 nodes. Should the
> number of nodes not match in the results of the 2 functions (summary and
> plot) or it is not always the same?
>
> Look forward to your reply,
>
> Carol
> --------------------------------------------
>  summary(rpart.res)
> Call:
> rpart(formula = mydata$class ~ ., data = as.data.frame(t(mydata)))
>   n= 62
>
>          CP nsplit rel error    xerror      xstd
> 1 0.6363636      0 1.0000000 1.0000000 0.1712469
> 2 0.1363636      1 0.3636364 0.6818182 0.1532767
> 3 0.0100000      2 0.2272727 0.7727273 0.1596659
>
> Variable importance
>   Hsa.627   Hsa.692 Hsa.692.2  Hsa.3306   Hsa.601   Hsa.831  Hsa.1832
> Hsa.2456
>        19        13        11        10        10         8
> 6         6
>  Hsa.8147  Hsa.1131 Hsa.692.1
>         6         5         5
>
> Node number 1: 62 observations,    complexity param=0.6363636
>   predicted class=t  expected loss=0.3548387  P(node) =1
>     class counts:    22    40
>    probabilities: 0.355 0.645
>   left son=2 (14 obs) right son=3 (48 obs)
>   Primary splits:
>       Hsa.627   < 59.83    to the left,  improve=15.05376, (0 missing)
>       Hsa.8147  < 1696.23  to the right, improve=14.46790, (0 missing)
>       Hsa.37937 < 379.39   to the right, improve=13.75358, (0 missing)
>       Hsa.692.2 < 842.305  to the right, improve=12.38710, (0 missing)
>       Hsa.1832  < 735.805  to the right, improve=11.90495, (0 missing)
>   Surrogate splits:
>       Hsa.692.2 < 1086.655 to the right, agree=0.903, adj=0.571, (0 split)
>       Hsa.3306  < 170.515  to the left,  agree=0.887, adj=0.500, (0 split)
>       Hsa.601   < 88.065   to the left,  agree=0.887, adj=0.500, (0 split)
>       Hsa.692   < 1251.99  to the right, agree=0.871, adj=0.429, (0 split)
>       Hsa.831   < 281.54   to the left,  agree=0.871, adj=0.429, (0 split)
>
> Node number 2: 14 observations
>   predicted class=n  expected loss=0  P(node) =0.2258065
>     class counts:    14     0
>    probabilities: 1.000 0.000
>
> Node number 3: 48 observations,    complexity param=0.1363636
>   predicted class=t  expected loss=0.1666667  P(node) =0.7741935
>     class counts:     8    40
>    probabilities: 0.167 0.833
>   left son=6 (7 obs) right son=7 (41 obs)
>   Primary splits:
>       Hsa.8147  < 1722.605 to the right, improve=4.915215, (0 missing)
>       Hsa.1832  < 681.145  to the right, improve=4.915215, (0 missing)
>       Hsa.1410  < 49.985   to the left,  improve=4.915215, (0 missing)
>       Hsa.2456  < 186.195  to the right, improve=4.915215, (0 missing)
>       Hsa.11616 < 969.085  to the right, improve=4.915215, (0 missing)
>   Surrogate splits:
>       Hsa.1832  < 681.145  to the right, agree=1.000, adj=1.000, (0 split)
>       Hsa.2456  < 186.195  to the right, agree=1.000, adj=1.000, (0 split)
>       Hsa.692   < 1048.375 to the right, agree=0.979, adj=0.857, (0 split)
>       Hsa.692.1 < 1136.75  to the right, agree=0.979, adj=0.857, (0 split)
>       Hsa.1131  < 1679.54  to the right, agree=0.979, adj=0.857, (0 split)
>
> Node number 6: 7 observations
>   predicted class=n  expected loss=0.2857143  P(node) =0.1129032
>     class counts:     5     2
>    probabilities: 0.714 0.286
>
> Node number 7: 41 observations
>   predicted class=t  expected loss=0.07317073  P(node) =0.6612903
>     class counts:     3    38
>    probabilities: 0.073 0.927
>
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