Perform independent component analysis after processing missing values
Source:R/analysis_dimReduction_ica.R
performICA.RdPerform independent component analysis after processing missing values
Arguments
- data
an optional data frame (or similar: see
model.frame) containing the variables in the formulaformula. By default the variables are taken fromenvironment(formula).- n.comp
number of components to be extracted
- center
a logical value indicating whether the variables should be shifted to be zero centered. Alternately, a vector of length equal the number of columns of
xcan be supplied. The value is passed toscale.- scale.
a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. The default is
FALSEfor consistency with S, but in general scaling is advisable. Alternatively, a vector of length equal the number of columns ofxcan be supplied. The value is passed toscale.- missingValues
Integer: number of tolerated missing values per column to be replaced with the mean of the values of that same column
- alg.typ
if
alg.typ == "parallel"the components are extracted simultaneously (the default). ifalg.typ == "deflation"the components are extracted one at a time.- fun
the functional form of the \(G\) function used in the approximation to neg-entropy (see ‘details’).
- alpha
constant in range [1, 2] used in approximation to neg-entropy when
fun == "logcosh"- ...
Arguments passed on to
fastICA::fastICA
See also
Other functions to analyse independent components:
plotICA()
Examples
performICA(USArrests)
#> $X
#> Murder Assault UrbanPop Rape
#> Alabama 5.412 65.24 -7.54 -0.032
#> Alaska 2.212 92.24 -17.54 23.268
#> Arizona 0.312 123.24 14.46 9.768
#> Arkansas 1.012 19.24 -15.54 -1.732
#> California 1.212 105.24 25.46 19.368
#> Colorado 0.112 33.24 12.46 17.468
#> Connecticut -4.488 -60.76 11.46 -10.132
#> Delaware -1.888 67.24 6.46 -5.432
#> Florida 7.612 164.24 14.46 10.668
#> Georgia 9.612 40.24 -5.54 4.568
#> Hawaii -2.488 -124.76 17.46 -1.032
#> Idaho -5.188 -50.76 -11.54 -7.032
#> Illinois 2.612 78.24 17.46 2.768
#> Indiana -0.588 -57.76 -0.54 -0.232
#> Iowa -5.588 -114.76 -8.54 -9.932
#> Kansas -1.788 -55.76 0.46 -3.232
#> Kentucky 1.912 -61.76 -13.54 -4.932
#> Louisiana 7.612 78.24 0.46 0.968
#> Maine -5.688 -87.76 -14.54 -13.432
#> Maryland 3.512 129.24 1.46 6.568
#> Massachusetts -3.388 -21.76 19.46 -4.932
#> Michigan 4.312 84.24 8.46 13.868
#> Minnesota -5.088 -98.76 0.46 -6.332
#> Mississippi 8.312 88.24 -21.54 -4.132
#> Missouri 1.212 7.24 4.46 6.968
#> Montana -1.788 -61.76 -12.54 -4.832
#> Nebraska -3.488 -68.76 -3.54 -4.732
#> Nevada 4.412 81.24 15.46 24.768
#> New Hampshire -5.688 -113.76 -9.54 -11.732
#> New Jersey -0.388 -11.76 23.46 -2.432
#> New Mexico 3.612 114.24 4.46 10.868
#> New York 3.312 83.24 20.46 4.868
#> North Carolina 5.212 166.24 -20.54 -5.132
#> North Dakota -6.988 -125.76 -21.54 -13.932
#> Ohio -0.488 -50.76 9.46 0.168
#> Oklahoma -1.188 -19.76 2.46 -1.232
#> Oregon -2.888 -11.76 1.46 8.068
#> Pennsylvania -1.488 -64.76 6.46 -6.332
#> Rhode Island -4.388 3.24 21.46 -12.932
#> South Carolina 6.612 108.24 -17.54 1.268
#> South Dakota -3.988 -84.76 -20.54 -8.432
#> Tennessee 5.412 17.24 -6.54 5.668
#> Texas 4.912 30.24 14.46 4.268
#> Utah -4.588 -50.76 14.46 1.668
#> Vermont -5.588 -122.76 -33.54 -10.032
#> Virginia 0.712 -14.76 -2.54 -0.532
#> Washington -3.788 -25.76 7.46 4.968
#> West Virginia -2.088 -89.76 -26.54 -11.932
#> Wisconsin -5.188 -117.76 0.46 -10.432
#> Wyoming -0.988 -9.76 -5.54 -5.632
#> attr(,"scaled:center")
#> Murder Assault UrbanPop Rape
#> -2.842171e-16 9.094947e-15 -6.252776e-15 8.526513e-16
#>
#> $K
#> [,1] [,2] [,3] [,4]
#> [1,] -0.0005031233 0.003185718 -0.01243588 -0.40479570
#> [2,] -0.0120064074 0.004176394 0.01051799 0.01584251
#> [3,] -0.0005589971 -0.069430563 0.03121730 -0.02366681
#> [4,] -0.0009066803 -0.014266122 -0.15162666 0.02942629
#>
#> $W
#> [,1] [,2] [,3] [,4]
#> [1,] -0.3272940 -0.94429966 -0.02925497 -0.01791523
#> [2,] 0.2522182 -0.07988422 -0.66871761 0.69485341
#> [3,] 0.4959778 -0.20255298 0.70075675 0.47108204
#> [4,] 0.7637216 -0.24675688 -0.24678106 -0.54308332
#>
#> $A
#> [,1] [,2] [,3] [,4]
#> [1,] -0.83164439 27.496932 -1.679598 -1.641239
#> [2,] 3.92134419 77.722168 4.499120 7.331951
#> [3,] -0.07676045 2.141101 10.241290 -2.358271
#> [4,] 1.58637674 2.204880 -8.796661 -4.895097
#>
#> $S
#> IC1 IC2 IC3 IC4
#> Alabama -0.09449110 0.83631141 -0.00732968 1.294389562
#> Alaska 0.40717676 1.17895294 -3.42844353 -1.472300260
#> Arizona 1.81467992 0.97323601 0.21042435 -1.247542710
#> Arkansas 0.51751879 0.06841125 -0.86269229 0.698388250
#> California 0.37335669 1.28203521 0.09011010 -2.204951917
#> Colorado -0.52095560 0.69068271 -0.84785891 -1.950820618
#> Connecticut 0.39534489 -0.95597259 1.44144313 -0.189028385
#> Delaware 2.26855195 0.03793316 0.94412073 -0.048947617
#> Florida 0.38374628 1.94884283 0.80884355 0.221349760
#> Georgia -2.26982407 1.27146999 0.01142288 1.726777023
#> Hawaii -2.28989784 -0.80332272 1.05337559 -0.732120046
#> Idaho 1.12285326 -1.02787566 -0.63867754 -0.171810595
#> Illinois 0.42067854 0.82452406 1.31953235 -0.107225346
#> Indiana -1.07939230 -0.35600590 -0.12717930 -0.062665585
#> Iowa -0.07580912 -1.44366582 -0.21560434 -0.004088263
#> Kansas -0.50939954 -0.53997831 0.15398870 -0.051928527
#> Kentucky -1.43215202 -0.31158418 -0.38413986 1.206082283
#> Louisiana -0.71157202 1.19679959 0.69121407 1.500412771
#> Maine 0.87333007 -1.44250298 -0.27814040 0.424552704
#> Maryland 1.38081687 1.17730955 -0.12991985 0.021268558
#> Massachusetts 0.46849075 -0.47242248 1.63193282 -0.643342293
#> Michigan -0.42258871 1.26091697 -0.34422904 -0.636895460
#> Minnesota -0.25719862 -1.17099477 0.13848102 -0.440875337
#> Mississippi 0.01538190 1.06549723 -0.33767297 2.597548784
#> Missouri -0.69882097 0.36257553 -0.27822425 -0.512054042
#> Montana -0.29457702 -0.68316335 -0.64991598 0.375728830
#> Nebraska -0.10116024 -0.83951298 -0.15139963 -0.183897991
#> Nevada -1.27110597 1.57279745 -0.95228726 -1.819042227
#> New Hampshire 0.09870188 -1.50035992 -0.11054592 0.169585797
#> New Jersey -0.47133303 -0.02892030 1.94609988 -0.326020598
#> New Mexico 0.71420128 1.23930305 -0.36079679 -0.429574662
#> New York 0.13470029 0.99139572 1.39116891 -0.224911490
#> North Carolina 2.76529846 1.11471858 -0.35615731 1.962466327
#> North Dakota 0.60208537 -1.81642144 -0.89982085 0.357080335
#> Ohio -1.17635193 -0.24490367 0.58890363 -0.290441964
#> Oklahoma -0.04715184 -0.23761108 0.18455113 -0.177317602
#> Oregon 0.16446492 -0.14129310 -0.99959108 -1.433388290
#> Pennsylvania -0.75022078 -0.59920918 0.93874765 0.195317552
#> Rhode Island 1.74872549 -0.64333488 2.54826451 -0.135742538
#> South Carolina 0.61350611 1.15009861 -0.73337283 1.611213973
#> South Dakota 0.24519607 -1.15945721 -1.08838647 0.428020446
#> Tennessee -1.50413977 0.74866363 -0.57460381 0.744599918
#> Texas -1.39696370 0.84367322 1.09704592 0.331636005
#> Utah -0.07116232 -0.59954293 0.43862118 -1.426205230
#> Vermont 0.24941394 -1.62570154 -2.06741533 0.526774770
#> Virginia -0.47254364 -0.02794304 -0.08470155 0.266068117
#> Washington 0.18937013 -0.34849636 -0.32680775 -1.442925300
#> West Virginia -0.14793289 -1.11190127 -1.00540999 1.306085915
#> Wisconsin -0.41971477 -1.37991255 0.53639669 -0.053434541
#> Wyoming 0.51886918 -0.32413848 0.07663573 0.454151753
#>