R help - Dec 2015 - how to use confusionMatrix function in solving multi-classes problem

Dear Colleagues
I need someone to kindly help me solving this problem.
A sample of 89 patients was tested for 4 tumor types (T1, T2, T3, T4).
The results of the operative predicted T stage and those of the pathology
tests are tabulated in the following table:

     .------------.-----------------------------------------------.
     .            .     Operative predicted T stage  .
     .            ------------------------------------------------.
     . Pathology  .    T1   .   T2  .   T3      T4  .
     .------------.----------------------------------------------.
     .    T1      .        1   .      0  .     0  .     0 .
     .------------.---------------------------------------------.
     .    T2      .        0   .     24 .     2  .     0 .
     .------------.--------------------------------------------.
     .    T3      .        0   .     1  .     49       3 .
     .------------.--------------------------------------------.
     .    T4      .        0   .     0  .       0  .    9 .
     .-----------------------------------------------------------

I need to calculate the sensitivity, specificity,accuracy,positive and
negative prediction values, p-value and kappa value of these tests.
I tried to convert the tabulated results into a two-class (0,1) table and
use the function (confusionMatrix) taking the pathology results as the
(goldstandard), but unfortunately,I got unreasonable output. Most
probably,I used the function wrongly.

Thank you and regards

Hamed

	[[alternative HTML version deleted]]

This looks like homework to me and this list has a No-Homework policy. Now, once
you have done your homework (and that includes reading the documentation of the
functions you are using), and you are still confused about details, you are
welcome to ask again. Please keep the following in mind:

http://adv-r.had.co.nz/Reproducibility.html
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
... and definitely read the posting guide for this list and don't post in
HTML.

B.




On Dec 13, 2015, at 5:02 AM, Hamed Nofal <hamednofal85 at gmail.com>
wrote:
> Dear Colleagues
> I need someone to kindly help me solving this problem.
> A sample of 89 patients was tested for 4 tumor types (T1, T2, T3, T4).
> The results of the operative predicted T stage and those of the pathology
> tests are tabulated in the following table:
> 
>     .------------.-----------------------------------------------.
>     .            .     Operative predicted T stage  .
>     .            ------------------------------------------------.
>     . Pathology  .    T1   .   T2  .   T3      T4  .
>     .------------.----------------------------------------------.
>     .    T1      .        1   .      0  .     0  .     0 .
>     .------------.---------------------------------------------.
>     .    T2      .        0   .     24 .     2  .     0 .
>     .------------.--------------------------------------------.
>     .    T3      .        0   .     1  .     49       3 .
>     .------------.--------------------------------------------.
>     .    T4      .        0   .     0  .       0  .    9 .
>     .-----------------------------------------------------------
> 
> I need to calculate the sensitivity, specificity,accuracy,positive and
> negative prediction values, p-value and kappa value of these tests.
> I tried to convert the tabulated results into a two-class (0,1) table and
> use the function (confusionMatrix) taking the pathology results as the
> (goldstandard), but unfortunately,I got unreasonable output. Most
> probably,I used the function wrongly.
> 
> Thank you and regards
> 
> Hamed
> 
> 	[[alternative HTML version deleted]]
> 
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