# [R] define number of clusters in kmeans/apcluster analysis

Bert Gunter bgunter.4567 at gmail.com
Sun Dec 13 17:28:25 CET 2015

```It sounds to me like you don't understand cluster analysis. You should
not expect perfect "allocation" of points. I suggest that you consult
references in the man pages of your functions or on the web. You might
also find it useful to post on stats.stackexchange.com or a machine
learning help site, as this is a statistical issue, not an R
programming issue AFAICS (corrections welcome if I'm wrong about
this), and so is somewhat OT here.

Cheers,
Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Sun, Dec 13, 2015 at 8:17 AM, Luigi Marongiu
<marongiu.luigi at gmail.com> wrote:
> Dear all,
> I am trying to do some cluster analysis, both with the base R and the
> apcluster. Both methods give 2 clusters, which is what I am looking
> for since I am interested in identifying positive and negative
> results. However  I could not find a way to fine-tuning the analysis
> in order to properly allocate the points; essentially the negative
> points should be all those in the lower left portion of the plot (see
> example) but some in the top centre are also given to the negative
> cluster.
> So how can I change the parameters to get better results?
> Thank you
> L
>
>>>>
> x <- c(3.15,    3.07,    2,    3,    2.97,    45,    3.21,    45,
> 40.55,    2,    22.09,    2.47,    2.97,    2.77,    2.6,    7.35,
> 4.11,    37.12,    2.73,    36.36,    45,    2.33,    2.49,    45,
> 2.4,    2.74,    2.64,    45,    2.47,    38.1,    2.47,    37.4,
> 2.77,    2.37,    45,    2.69,    2.97,    2.7,    2,    2,    2.55,
>  11.86,    2.51,    2.68,    2.31,    2.6,    2.45,    2,    2.72,
> 2.57,    2.09,    3.04,    45,    45,    2.13,    43.82,    2.92,
> 4.94,    24.82,    2.64,    4.96,    3.65,    2.67,    2.64,    8.04,
>   4.56,    44.87,    37.42,    45,    6.2,    2.84,    4.08,    2,
> 5.03,    2.27,    44.89,    2.41,    2.47,    2.78,    37.47,    45,
>  2.76,    45,    2.51,    2.8,    44.8,    6.2,    2.87,    2.23,
> 18.32,    3.14,    2.1,    2.38,    2.72,    2,    2,    44.41,
> 3.15,    3.06,    4.8,    2.77,    2.8,    2.71,    44.77,    2.25,
> 2.69,    28.38,    2,    2.95,    45,    2.79,    2.46,    2.61,
> 2.78,    2.94,    38.47,    3.29,    2.89,    2.4,    2.23,    2.62,
>  4.21,    2.61,    2.81,    2.41,    41.98,    2.39,    36.41,
> 44.84,    4.73,    2,    2.66,    4.57,    3.01,    42.64,    2.04,
> 5.49,    15.48,    3.08,    2.7,    2,    2,    2.09,    2,    2.29,
>  2.92,    3.39,    3.1,    2,    6.14,    7.03,    4.77,    2.55,
> 32.36,    20.61,    3.09,    4.46,    44.75,    2,    2.73,    2,
> 36.05,    3.61,    34.84,    2.69,    5.28,    3.04,    45,    2.47,
>  2.58,    2.16,    2.59,    45,    44.08,    2,    37.05,    2.48,
> 2.46,    38.71,    7.32,    2.95,    2.8,    44.58,    42.24,
> 36.99,    13.84,    45,    2,    2,    2.38,    45,    45,    43.59,
>  2.69,    2.81,    3.05,    2.8,    4.65,    45,    41.46,    2.33,
> 7.12,    19.18,    4.82,    4.76,    2.51,    3.1,    2.74,    4.99,
>  38.06,    2.53,    2.94,    2.93,    6.59,    2.72,    2.94,    2.56,
>    2.91,    44.79,    2.98,    42.95,    45,    2.63,    38.44,
> 2.71,    2,    37.92,    2.69,    2.91,    2.65,    44.48,    6.35,
> 2.56,    21.94,    3.08,    2.6,    45,    2,    2.62,    2.47,
> 2.62,    2.73,    2.87,    2.83,    4.56,    44.22,    5.15,    5.13,
>   2.76,    7.02,    28.61,    4.87,    5.02,    44.35,    2.26,
> 2.89,    5.26,    38.01,    44.79,    39.26,    2.91,    4.59,
> 2.69,    2.61,    34.97,    3,    45,    2.81,    2,    2.65,    2,
> 37.33,    4.69,    3.26,    38.24,    4.97,    4.62,    2.47,    45,
>  4.52,    2.73,    15.66,    6.06,    2.79,    2.87,    45,    45,
> 45,    4.84,    3.05,    4.89,    4.64,    4.92,    2.74,    7.83,
> 42.31,    2.88,    6.89,    23.06,    2.94,    4.72,    4.55,    5.52,
>    4.48,    4.86,    3.12,    7.68,    43.89,    2.82,    2.64,
> 3.05,    42.95,    2.33,    3.55,    45,    2.79,    2.47,    45,
> 2.56,    38.33,    2.73,    2.87,    2.61,    3.01,    2.86,    2.74,
>   44.46,    44.54,    2.62,    16.94,    2.53,    2.24,    2.72,    2,
>    3.1,    2.88,    7.4,    4.64,    8.25,    3.01,    2.86,    2.46,
>   5.67,    44.52,    2.47,    2,    29.01,    2.61,    3.23,    12.3,
>   3.9,    2.91,    43.99,    36.99,    43.72,    42.29,    2.63,
> 3.03,    2.85,    2.58,    2.63,    2.73,    2.57,    2.37,    2.57,
>  2.75,    44.14,    39.4,    40.02,    3.08,    45,    4.96,    3,
> 2.83,    2.74,    2.8,    2.8,    18.88,    4.69,    2.51,    4.32,
> 2,    2.56,    2.81
> )
> y <- c(0.014,    0.04,    0.001,    0.023,    0.008,    0,    0.008,
>  0.001,    -0.001,    0.002,    0.103,    0,    0.013,    0.005,
> 0.008,    0.001,    0.011,    0.076,    0.005,    0.045,    -0.001,
> 0,    0.008,    -0.002,    0.002,    0.016,    0.006,    0.001,
> 0.002,    0.001,    0.004,    0.086,    0.009,    0.011,    0.002,
> 0.013,    0.019,    0.007,    0,    0.002,    0.024,    0.119,
> 0.015,    0.009,    0.013,    0.017,    0.009,    0.009,    0.006,
> 0.012,    0.002,    0.015,    0,    0.001,    0.002,    0.001,
> 0.007,    0.004,    0.113,    0.016,    0.013,    0.004,    0.015,
> 0.005,    0.004,    0.007,    0,    0.081,    0.001,    0.002,
> 0.014,    0.002,    0,    0.01,    0.003,    0.002,    0.004,
> 0.004,    0.006,    0.064,    0,    0.014,    0,    0.01,    0.019,
> 0.002,    0.006,    0.005,    0.003,    0.103,    0.007,    0.008,
> 0.002,    0.013,    0.007,    0.004,    0.001,    0.04,    0.017,
> 0.018,    0.002,    0.006,    0.011,    0.003,    0.004,    0.008,
> 0.115,    0,    0.02,    0,    0.012,    0.009,    0.011,    0.013,
> 0.004,    0.058,    0.019,    0.006,    0.005,    0.004,    0.012,
> 0.003,    0.003,    0.004,    0.002,    0.001,    0.002,    0.102,
> -0.001,    0.008,    0.002,    0.016,    0.023,    0.014,    0.053,
> 0.009,    0.001,    0.124,    0.009,    0.008,    0.002,    0.002,
> 0.013,    0.002,    0.001,    0.042,    0.011,    0.009,    0,
> 0.004,    0.003,    0.002,    0.005,    0,    0.101,    0.013,
> 0.009,    0.005,    0.002,    0.007,    0.008,    0.067,    0.002,
> 0.064,    0.028,    0.007,    0.006,    0,    0.007,    0.006,    0,
>  0.001,    0.001,    0.001,    0,    0.088,    0.005,    0.008,
> 0.098,    0.005,    0.019,    0.007,    0.05,    -0.002,    0.002,
> 0.129,    0.001,    0.004,    -0.001,    0.002,    -0.001,    0,
> 0.043,    0.018,    0.019,    0.015,    0.003,    0.006,    0.002,
> 0.001,    0.002,    0.004,    0.097,    0.025,    0.022,    0.007,
> 0.011,    0.007,    0.013,    0.061,    0.008,    0.013,    0.028,
> 0.004,    0.013,    0.005,    0.01,    0.004,    0,    0.006,
> -0.001,    0.001,    0.01,    0.061,    0.002,    0.004,    0,
> 0.011,    0.029,    0.018,    0,    0.003,    0.012,    0.085,
> 0.015,    0.007,    0.002,    0.003,    0.008,    0.002,    0.007,
> 0.02,    0.011,    0.02,    0.008,    0.001,    0.003,    0.01,
> 0.014,    0.001,    0.096,    0.027,    0.024,    0,    0.005,
> 0.006,    0.024,    0.087,    0.001,    0.083,    0.02,    0.009,
> 0.009,    0.001,    0,    0.019,    0,    0.003,    -0.001,    0.002,
>   0,    0.089,    0.016,    0.01,    0.103,    0.003,    0.01,
> 0.002,    0.008,    0.005,    0.014,    0.1,    0.007,    0.009,
> 0.011,    -0.001,    0,    0.002,    0.015,    0.036,    0.018,
> 0.026,    0.009,    0.008,    0.004,    0.001,    0.014,    0.009,
> 0.1,    0.026,    0.032,    0.008,    0.011,    0.004,    0.013,
> 0.019,    0.004,    0.02,    0.015,    0.005,    0.013,    -0.001,
> 0.013,    0.012,    0,    0.01,    0.002,    0.001,    0.013,
> 0.066,    0.009,    0.005,    0.002,    0.013,    0.025,    0.006,
> 0,    0,    0.015,    0.121,    0.006,    0.003,    0.008,    0,
> 0.012,    0.011,    0.003,    0.022,    0.008,    0.032,    0.007,
> 0.002,    0.006,    0.007,    0,    0.003,    0.11,    0.01,    0.008,
>    0,    0.018,    0.008,    0.001,    0.087,    0,    0.028,
> 0.011,    0.014,    0.007,    0.001,    0.018,    0.033,    0.021,
> 0.003,    0.003,    0.007,    -0.001,    0.07,    0.022,    0.009,
> 0.001,    0.007,    0.031,    0.008,    0.013,    0.01,    0.018,
> 0.125,    0.01,    0.015,    0.006,    0,    0.015,    0.019
> )
> z <- cbind(x, y)
> k <- kmeans(z, 2)
> plot(z, col=k\$cluster)
>
> library(apcluster)
> m <- apclusterK(negDistMat(r=2), z, K=2, verbose=TRUE)
> plot(m, z)
>
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