トップ 差分 一覧 ソース 検索 ヘルプ PDF RSS ログイン

対応分析

*disclaimer
55346

R

対応分析


パッケージ

install.packages("ca", dependencies=T)
library(ca)

サンプルデータ

  • NICER のファイル5つ
> setwd("NICERsample/")

> list.files()
 [1] "JPN501.txt" "JPN502.txt" "JPN503.txt" "JPN504.txt" "JPN505.txt" "JPN506.txt" "JPN507.txt" "JPN508.txt" "JPN509.txt"
[10] "JPN510.txt"
> myIndices4()
Read 123 items
Read 120 items
Read 70 items
Read 114 items
Read 106 items
Read 93 items
Read 111 items
Read 93 items
Read 91 items
Read 72 items

> nicerSampleIndices <- read.table(choose.files())

> nicerSampleIndices
           V1 V2  V3  V4 V5        V6       V7        V8       V9      V10
1  JPN501.txt  4 319 135 30 0.4231975 7.558549 0.5921317 4.304075 10.63333
2  JPN502.txt  4 356 161 29 0.4522472 8.532983 0.6649157 4.233146 12.27586
3  JPN503.txt  3 201 121 13 0.6019900 8.534682 0.7170149 4.746269 15.46154
4  JPN504.txt  4 260 140 27 0.5384615 8.682431 0.6877692 4.761538  9.62963
5  JPN505.txt  4 420 175 25 0.4166667 8.539126 0.6341905 3.995238 16.80000
6  JPN506.txt  3 261 124 20 0.4750958 7.675407 0.6390038 4.072797 13.05000
7  JPN507.txt  4 362 151 26 0.4171271 7.936384 0.6485083 4.292818 13.92308
8  JPN508.txt  3 198  98 20 0.4949495 6.964557 0.6174747 4.545455  9.90000
9  JPN509.txt  4 263 104 19 0.3954373 6.412915 0.5726616 4.034221 13.84211
10 JPN510.txt  3 183  99 14 0.5409836 7.318291 0.6577049 4.387978 13.07143

> names(nicerSampleIndices) <- c("file", "Score", "Token", "Type", "NoS", "TTR", "GI", "MATTR", "AWL", "ASL")

> nicerSampleIndices
         file Score Token Type NoS       TTR       GI     MATTR      AWL      ASL
1  JPN501.txt     4   319  135  30 0.4231975 7.558549 0.5921317 4.304075 10.63333
2  JPN502.txt     4   356  161  29 0.4522472 8.532983 0.6649157 4.233146 12.27586
3  JPN503.txt     3   201  121  13 0.6019900 8.534682 0.7170149 4.746269 15.46154
4  JPN504.txt     4   260  140  27 0.5384615 8.682431 0.6877692 4.761538  9.62963
5  JPN505.txt     4   420  175  25 0.4166667 8.539126 0.6341905 3.995238 16.80000
6  JPN506.txt     3   261  124  20 0.4750958 7.675407 0.6390038 4.072797 13.05000
7  JPN507.txt     4   362  151  26 0.4171271 7.936384 0.6485083 4.292818 13.92308
8  JPN508.txt     3   198   98  20 0.4949495 6.964557 0.6174747 4.545455  9.90000
9  JPN509.txt     4   263  104  19 0.3954373 6.412915 0.5726616 4.034221 13.84211
10 JPN510.txt     3   183   99  14 0.5409836 7.318291 0.6577049 4.387978 13.07143

対応分析準備

  • 行名を番号ではなく、ファイル名にする
> rownames(nicerSampleIndices) <- nicerSampleIndices$file

> nicerSampleIndices
                 file Score Token Type NoS       TTR       GI     MATTR      AWL      ASL
JPN501.txt JPN501.txt     4   319  135  30 0.4231975 7.558549 0.5921317 4.304075 10.63333
JPN502.txt JPN502.txt     4   356  161  29 0.4522472 8.532983 0.6649157 4.233146 12.27586
JPN503.txt JPN503.txt     3   201  121  13 0.6019900 8.534682 0.7170149 4.746269 15.46154
JPN504.txt JPN504.txt     4   260  140  27 0.5384615 8.682431 0.6877692 4.761538  9.62963
JPN505.txt JPN505.txt     4   420  175  25 0.4166667 8.539126 0.6341905 3.995238 16.80000
JPN506.txt JPN506.txt     3   261  124  20 0.4750958 7.675407 0.6390038 4.072797 13.05000
JPN507.txt JPN507.txt     4   362  151  26 0.4171271 7.936384 0.6485083 4.292818 13.92308
JPN508.txt JPN508.txt     3   198   98  20 0.4949495 6.964557 0.6174747 4.545455  9.90000
JPN509.txt JPN509.txt     4   263  104  19 0.3954373 6.412915 0.5726616 4.034221 13.84211
JPN510.txt JPN510.txt     3   183   99  14 0.5409836 7.318291 0.6577049 4.387978 13.07143
  • 左端にファイル名が二つ並んで見えるが、
    • 一番左は行名
    • 二つ目は列名fileの各値

対応分析 ca()

  • ファイル名は、分析対象から外すので[ , -1]とすることで、一列目を除いて、対応分析を行う
> niserSample.ca <- ca(nicerSampleIndices[, -1])

> nicerSampl.ca

 Principal inertias (eigenvalues):
           1        2        3        4       5     6     7  8 
Value      0.005225 0.001995 0.000701 3.3e-05 9e-06 1e-06 0  0 
Percentage 65.61%   25.05%   8.8%     0.41%   0.11% 0.01% 0% 0%


 Rows:
        JPN501.txt JPN502.txt JPN503.txt JPN504.txt JPN505.txt JPN506.txt JPN507.txt JPN508.txt JPN509.txt JPN510.txt
Mass      0.109972   0.123870   0.079131   0.097887   0.140689   0.093288   0.122593   0.073425   0.089278   0.069868
ChiDist   0.077607   0.051114   0.171263   0.097029   0.085809   0.023531   0.061386   0.081665   0.079874   0.127017
Inertia   0.000662   0.000324   0.002321   0.000922   0.001036   0.000052   0.000462   0.000490   0.000570   0.001127
Dim. 1    0.828663   0.569189  -2.257347  -0.556775   0.882663  -0.241572   0.812881  -0.698749   0.447961  -1.695976
Dim. 2   -1.033676  -0.453632   1.034698  -1.902720   1.155776   0.248239   0.382980  -1.160287   0.974881   0.568028


 Columns:
            Score    Token      Type       NoS       TTR        GI     MATTR       AWL       ASL
Mass     0.007740 0.606927  0.281212  0.047944  0.001023  0.016803  0.001383  0.009325  0.027645
ChiDist  0.144788 0.051699  0.076812  0.165881  0.335743  0.198663  0.243273  0.261869  0.248121
Inertia  0.000162 0.001622  0.001659  0.001319  0.000115  0.000663  0.000082  0.000639  0.001702
Dim. 1  -1.053972 0.683722 -0.953127  0.381575 -4.493261 -2.699578 -3.205499 -3.243154 -2.620518
Dim. 2  -0.891426 0.329033 -0.324783 -3.513723 -0.783634 -0.639111 -0.435240 -1.080868  3.227127

プロットする

> plot(nicerSampl.ca)