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 -------------- next part -------------- A non-text attachment was scrubbed... Name: rpart.png Type: image/png Size: 12105 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20130127/849451f7/attachment.png>
Should I understand that this message was received? Thanks ----- Forwarded Message ----- From: carol white <wht_crl at yahoo.com> To: "r-help at stat.math.ethz.ch" <r-help at stat.math.ethz.ch> Sent: Sunday, January 27, 2013 8:31 PM Subject: rpart 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: rpart.png Type: image/png Size: 12105 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20130128/856a78a1/attachment.png>
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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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
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