Get preprocessed dataframe for continuous variables

Usage

get_caret_processed_df(features, method)

Arguments

features: Dataframe of features for machine learning
method: Methods to preprocess the data, described in caret::preProcess() (default: c("center","scale"), use NULL for no normalization).

Value

Named list:

processed: Dataframe of processed features.
removed: Names of any features removed during preprocessing.

Author

Zena Lapp, zenalapp@umich.edu

Examples

get_caret_processed_df(mikropml::otu_small[, 2:ncol(otu_small)], c("center", "scale"))
#> $processed
#>      Otu00001     Otu00002   Otu00003    Otu00004    Otu00005    Otu00006
#> 1  -0.4198476 -0.218855527 -0.1742962 -0.59073845 -0.04877422 -0.16741683
#> 2  -0.1045750  1.754032339 -0.7184194  0.03805034  1.53707297 -0.57321773
#> 3  -0.7076423  0.696324396  1.4281464  0.60439092 -0.26455904 -0.03641025
#> 4  -0.4936041 -0.665193276  2.0157993 -0.59289184 -0.67557776 -0.58599886
#> 5   1.1116829 -0.395140184 -0.7537874 -0.58643168 -0.75435634  2.72750923
#> 6  -0.6845031  0.613808173 -0.1742962 -0.58427829  0.37594511  0.80394909
#> 7  -0.7698291 -0.496410093 -0.3184889  0.15863997 -0.65845198  2.20028760
#> 8  -0.4241862 -0.477656406 -0.3973867 -0.55628427 -0.39128981 -0.06197251
#> 9  -0.5557909  1.144537514  1.6158688 -0.35171258 -0.27483451 -0.46457812
#> 10  1.4573258 -0.451401245 -0.6939338 -0.05669866 -0.70640416  0.68891891
#> 11  0.2931312 -0.721454336 -0.7537874  3.03341063 -0.44951746 -0.24090833
#> 12  1.1044519  0.002437979 -0.4735640 -0.41846755  0.41362183 -0.35593851
#> 13 -0.5933922 -0.297621012 -0.3402538 -0.59289184 -0.65502682 -0.49972623
#> 14 -0.8016456  0.077452727 -0.4191516 -0.59073845 -0.04534906 -0.77452053
#> 15 -0.7915222  0.291244758 -0.2695178 -0.59289184 -0.22003202 -0.68824790
#> 16  1.4862499 -0.683946963 -0.7456255 -0.54551734 -0.74408087  0.91897926
#>       Otu00007     Otu00008    Otu00009    Otu00010    Otu00011    Otu00012
#> 1  -0.56874580 -0.062364359  0.05469266 -0.63787623  0.72598299 -0.02599851
#> 2  -0.64274431 -0.132045208 -0.40907548 -0.38331472  0.01116897  0.41335612
#> 3  -0.61247219 -0.207086122 -0.73691158  2.58656951 -0.77512645 -0.67898429
#> 4  -0.55192796 -0.469729320  0.13465268  0.02598025 -0.02010414 -0.65479963
#> 5   0.19142068 -0.676091833  1.26208901  1.70309134  1.58822740 -0.67495351
#> 6  -0.33665957 -0.006083674 -0.26514744 -0.34837491  0.55621466 -0.26784509
#> 7  -0.71674282  0.063597174 -0.84485761 -0.68279885 -0.48920084 -0.63867653
#> 8   0.37641695 -0.022163870  0.61841082  2.38192202 -0.75278851 -0.05824472
#> 9  -0.80419560  0.294079981 -0.40907548  0.28054175  0.18540489 -0.03809084
#> 10 -0.37029526  1.588535743 -0.72091957  0.49517204 -0.82873750  0.18360187
#> 11  0.06696865 -0.196365991  0.09067467  0.50016344  0.38644633  0.42544845
#> 12 -0.77728705  0.342320568  0.48247878  0.63493130 -0.48920084 -0.21141422
#> 13 -0.14157260 -0.217806252 -0.14520740 -0.24854687  1.11019552 -0.19932189
#> 14 -0.62256290 -0.421488732 -0.64495755 -0.60792781 -0.04690967 -0.61046109
#> 15 -0.58220008  0.899767356 -0.79688159 -0.89243773 -0.62769606 -0.50163013
#> 16  1.18030983 -0.424168765 -0.06524738 -0.05887359 -0.06478002 -0.50969168
#>      Otu00013     Otu00014    Otu00015   Otu00016   Otu00017     Otu00018
#> 1   1.5243040  1.671766383  1.25749765 -0.4950312  0.4761147  0.399615523
#> 2  -0.5512515  0.971673864  0.30580586 -0.5033126 -0.3211097 -0.679309939
#> 3  -0.9800853  0.007910136 -0.66585150 -0.4757081  0.4908327 -0.679309939
#> 4  -0.8428585 -0.542162557 -0.47950625 -0.5005521 -0.2671438  0.030253653
#> 5   0.5179740 -0.792195600 -0.96533493  0.3441451 -0.5296146 -0.674449915
#> 6   1.2155437  2.385497069  0.40563367 -0.1085684  3.3068745 -0.008626544
#> 7   0.3235694 -0.737642936 -0.49281662 -0.3984155 -0.5026316 -0.518929127
#> 8   0.2949805 -0.437603285 -0.60595481  3.7836639 -0.5345206  0.419055622
#> 9  -0.2196201  0.953489643 -0.94536936 -0.3294043  1.2929631 -0.679309939
#> 10 -0.6999139 -0.751281102 -0.89212787  0.1647160 -0.5222556 -0.436308709
#> 11  0.3921828 -0.792195600  0.65853079 -0.5033126 -0.5345206 -0.679309939
#> 12 -0.9114719  2.280937796  0.08618468  1.7271298  2.6592830 -0.664729865
#> 13 -0.5340982  0.485245945 -0.74571374 -0.4950312 -0.4437596 -0.650149792
#> 14 -0.6713250  0.958035698  0.13277099 -0.1223707  0.9470903 -0.120407110
#> 15 -0.7170673  0.262489234 -0.01364313 -0.4729476  0.6821665 -0.280787922
#> 16 -0.3396935 -0.769465323 -0.52609256 -0.1969028 -0.5345206  2.304745168
#>       Otu00019    Otu00020   Otu00021    Otu00022     Otu00023   Otu00024
#> 1   0.55293856  0.55481623 -0.3553701  1.64761210 -0.006925459 -0.1772044
#> 2   0.61541514 -0.36000866  0.1515983 -0.37570583 -0.664257143 -0.6784410
#> 3  -0.13846893 -0.52918860 -0.6310034 -0.08161892 -0.374718187  0.1771180
#> 4   0.08644676 -0.26601980  0.7422412 -0.18749021 -0.319940546  0.9548989
#> 5  -0.64244668 -0.68583670 -0.6310034 -0.36786351 -0.906843836 -0.6957250
#> 6  -0.08432256  0.17259487  0.7816173 -0.35610003 -0.343416678  0.8511948
#> 7  -0.52165862 -0.40387013 -0.6310034 -0.02672270  0.407819532 -0.6697990
#> 8   0.69871725 -0.02791469 -0.6063933 -0.20709600 -0.085179231 -0.5920209
#> 9   0.29053693 -0.67330485 -0.6310034  0.14188713 -0.899018459 -0.3932547
#> 10 -0.03017619  0.91823982 -0.5227189 -0.28159802 -0.406019696 -0.3414026
#> 11 -0.35921951  1.00596275 -0.6310034 -0.38354815  0.196534348  3.9623184
#> 12 -0.21344082 -0.64197523  0.4666078 -0.27375570  1.245134892  0.3240322
#> 13 -0.64244668 -0.52292268 -0.6260814 -0.37178467  0.071328313  0.4882304
#> 14 -0.34255909 -0.47906121  3.6019369 -0.27767686 -0.562527239 -0.2809085
#> 15 -0.30923825 -0.58558192 -0.1191130 -0.36002119 -0.695558652  0.1079819
#> 16 -0.35921951  1.08741976 -0.6260814 -0.30120381  1.691181392 -0.7130090
#>       Otu00025    Otu00026    Otu00027   Otu00028    Otu00029   Otu00030
#> 1  -0.24303824 -0.22202016 -0.24641906 -0.2925540  0.69582149  0.3919317
#> 2  -0.43616774 -0.29146475 -0.38539990 -0.3073944 -0.25226077  0.4472047
#> 3   0.04157367 -0.47086329 -0.41259180 -0.1688839  0.06672018 -0.5937702
#> 4  -0.28369708  0.43770350 -0.36425064 -0.3148146 -0.47377531 -0.7135284
#> 5  -0.39550890 -0.61553953 -0.06816104 -0.3148146 -0.57124171  0.3366587
#> 6   0.03649131 -0.45350214 -0.38842122 -0.3197614 -0.21681844 -0.5292851
#> 7  -0.42600303  0.87751927 -0.23131245 -0.2950274  3.07931802  0.1984761
#> 8  -0.35485005 -0.57503018  0.01945732 -0.3222348  0.03127785 -0.1700105
#> 9  -0.45141481 -0.62132658 -0.31288816 -0.3197614 -0.73073219 -0.1147375
#> 10  1.42397434 -0.62132658 -0.40957048  0.2144934  0.13760484 -0.7688014
#> 11 -0.07023815  0.46085170 -0.20412055 -0.3222348 -0.30542426  0.1616275
#> 12 -0.14647348 -0.58660428  0.02852128 -0.3197614 -0.73073219 -0.5477094
#> 13 -0.30402650 -0.37248345 -0.39748519 -0.3148146 -0.26998193 -0.6214067
#> 14 -0.26845001  1.35205733 -0.37935725 -0.3222348 -0.52693880  0.5485385
#> 15 -0.37009712 -0.26252951 -0.31288816 -0.3123412 -0.53579939 -0.3358296
#> 16 -0.43616774 -0.01368637 -0.32497345 -0.3073944 -0.34086658 -0.3818904
#>      Otu00031    Otu00032    Otu00033    Otu00034    Otu00035   Otu00036
#> 1   0.2730666  1.85022773 -0.35236586 -0.14829148 -0.28857253 -0.3377980
#> 2  -0.1402888 -0.49393851  0.15285109 -0.15073149  1.32771762 -0.3377980
#> 3  -0.4629076 -0.35782563 -0.28806552 -0.13609144 -0.09645535 -0.3096270
#> 4   1.5937875 -0.50150034 -0.43503772 -0.15073149 -0.24263146 -0.3377980
#> 5  -0.5637260 -0.57711860  0.95201244  0.04690915 -0.38463111 -0.3321638
#> 6  -0.2411072  0.33786241  0.07936499 -0.15073149 -0.31363129 -0.3377980
#> 7  -0.3520074 -0.39563477 -0.61875297 -0.15073149 -0.38880757  3.0990589
#> 8  -0.3822529 -0.35782563 -0.44422348 -0.15073149 -0.25098438 -0.3377980
#> 9   0.3335576 -0.07047622 -0.16865060 -0.07753125 -0.38880757 -0.3377980
#> 10 -0.4830713 -0.51662399  0.74073990 -0.06045120 -0.30110191  0.8115771
#> 11 -0.5939716 -0.57711860 -0.60038145 -0.15073149  1.31518824 -0.3377980
#> 12 -0.5233987  0.14881675  0.46516702  0.69351126 -0.25098438 -0.3377980
#> 13 -0.2209435  0.10344579 -0.45340924 -0.14585147  5.21182571 -0.3377980
#> 14  0.1420027  0.57227904 -0.64631026 -0.15073149 -0.31780775 -0.3377980
#> 15 -0.2411072  0.43616616 -0.65549602 -0.15073149 -0.20921978  0.1580109
#> 16 -0.4729895 -0.56955678  1.07142736 -0.08241127 -0.36792527 -0.3377980
#>       Otu00037    Otu00038    Otu00039    Otu00040    Otu00041    Otu00042
#> 1  -0.28026882 -0.26900974 -0.36969168 -0.20704023  0.12272828  0.69052599
#> 2  -0.40104181 -0.26900974  0.50452482 -0.32139200 -0.63077588 -0.30167974
#> 3   5.43380328 -0.25196493 -0.43941446  0.35201286  0.85558850 -0.29347970
#> 4  -0.28781713 -0.25480573  0.06473493 -0.33409775 -0.62045391  0.64132571
#> 5  -0.55200805 -0.26900974  0.25245013 -0.85503359  4.86051474  2.21163478
#> 6  -0.02362622 -0.26900974 -0.21415623  0.05978056  0.27755790 -0.30167974
#> 7  -0.19723739 -0.26900974 -0.38578155 -0.81691633 -0.42433639 -0.30167974
#> 8  -0.13685089 -0.26616894 -0.27851572  0.30118985 -0.66174181 -0.30167974
#> 9   0.32359613 -0.08435761 -0.13370685 -0.33409775  3.46704813 -0.29757972
#> 10 -0.51426649 -0.25480573 -0.41259801 -0.46115527  0.07111841 -0.30167974
#> 11  0.52740055 -0.26900974  0.10227797  0.50448189 -0.66174181 -0.30167974
#> 12 -0.54445974 -0.26616894 -0.41796130 -0.63903580  0.08144038 -0.30167974
#> 13 -0.55200805 -0.25764653  0.08082480  0.37742437  0.20530408 -0.01057806
#> 14 -0.43878337 -0.26900974 -0.39650813 -0.55009554  0.29820185  4.58144848
#> 15 -0.40859012 -0.26900974 -0.28924231 -0.37221501  1.71231241  3.25714082
#> 16  1.16145875 -0.26900974 -0.43941446  0.75859693 -0.65141983 -0.30167974
#>       Otu00043    Otu00044   Otu00045   Otu00046    Otu00047     Otu00048
#> 1   0.71982858 -0.61170426 -0.2339134  0.6935514 -0.20351219 -0.253544727
#> 2  -0.24396750 -0.62270910 -0.2339134 -0.5691107 -0.20866114 -0.253544727
#> 3  -0.46108640  0.02657670 -0.2339134 -0.5843235  0.34227636  0.007337307
#> 4  -0.12746468  0.09260576 -0.2339134 -0.5234723 -0.20866114 -0.253544727
#> 5  -0.46108640 -0.30356862 -0.1407517 -0.5843235 -0.20866114 -0.194846269
#> 6   0.54507434 -0.25954925 -0.2339134  0.7848281 -0.20866114 -0.253544727
#> 7   0.12672330  0.82993032 -0.2339134 -0.5843235 -0.03359689 -0.247022676
#> 8  -0.38165266 -0.20452503 -0.2339134  0.2219547 -0.20866114 -0.253544727
#> 9  -0.45579082 -0.53467035 -0.2339134 -0.5843235 -0.20866114 -0.070927303
#> 10 -0.46108640 -0.44663160 -0.2339134 -0.5843235  0.50189377 -0.207890371
#> 11 -0.46108640  0.23566874 -0.2339134  1.8953622 -0.20351219 -0.247022676
#> 12  0.31206870 -0.62270910 -0.2339134 -0.1887908 -0.20866114 -0.116581659
#> 13 -0.46108640 -0.31457347 -0.2339134 -0.5843235 -0.20866114 -0.227456524
#> 14 -0.09569118 -0.57868973 -0.1873326  0.2980187 -0.20866114 -0.253544727
#> 15 -0.02684861  0.88495454 -0.2339134  1.1803608 -0.20866114 -0.253544727
#> 16  0.53977876 -0.61170426 -0.1034871 -0.5843235 -0.19321430 -0.253544727
#>       Otu00049   Otu00050    Otu00051    Otu00052    Otu00053    Otu00054
#> 1   0.60651290 -0.4753858 -0.20991733  0.19735560 -0.08276103 -0.18688626
#> 2  -0.42970775 -0.4506422 -0.20991733 -0.25745566  0.65153274 -0.45315341
#> 3  -0.42161228  0.3040366 -0.16859502  5.36271211 -0.18984553  1.12780781
#> 4  -0.43780323  1.3803818 -0.20991733 -0.25745566 -0.12865439 -0.08703608
#> 5   0.42841248 -0.5496165  2.09035789 -0.25745566 -0.46520570 -0.53636190
#> 6  -0.43780323 -0.4753858 -0.20991733 -0.25745566 -0.34282340 -0.58628699
#> 7   0.01554331 -0.5248729 -0.20991733  0.06740953 -0.08276103 -0.33666153
#> 8  -0.33256207  1.6525611 -0.20991733 -0.22496914 -0.38871676 -0.51972020
#> 9  -0.31637112  0.3906391 -0.20991733 -0.25745566  1.09516856  0.76169047
#> 10 -0.42970775 -0.4753858 -0.20991733 -0.25745566 -0.37341898  0.26243956
#> 11 -0.43780323  3.3846108 -0.20991733 -0.25745566 -0.46520570 -0.58628699
#> 12 -0.40542133 -0.5496165 -0.20991733 -0.25745566 -0.41931234 -0.38658662
#> 13 -0.42161228 -0.5496165 -0.20991733 -0.25745566  0.08551463 -0.30337814
#> 14 -0.43780323 -0.4258987  0.04490358 -0.25745566 -0.35812119 -0.50307850
#> 15 -0.40542133  0.1926905 -0.20991733 -0.25745566  0.02432348 -0.58628699
#> 16  8.67770035 -0.2032066  0.84380156 -0.25745566 -0.46520570 -0.53636190
#>       Otu00055    Otu00056    Otu00057    Otu00058    Otu00059    Otu00060
#> 1  -0.25600918 -0.67302626 -0.06308524  0.24402844 -0.04265350 -0.41506494
#> 2  -0.41855470  2.49956176 -0.37827265  0.95629418 -0.33573273 -0.41506494
#> 3  -0.37791832 -0.80430576  2.65898785 -0.31339693 -0.40900254 -0.40518715
#> 4  -0.40500924  0.18029052 -0.34006811 -0.06565232 -0.29386427 -0.41506494
#> 5  -0.20182735 -0.80430576 -0.42602832 -0.56114154 -0.39853543 -0.40518715
#> 6  -0.28310010  0.77104829  0.78696566  0.15112421  0.66911037 -0.41506494
#> 7  -0.43210016 -0.82618568 -0.24455678 -0.54565750 -0.29386427 -0.41506494
#> 8  -0.41855470 -0.62926642 -0.42602832 -0.40630116  7.84955171 -0.16812007
#> 9   0.13680914  0.24593027 -0.42602832 -0.48372135 -0.40900254 -0.41506494
#> 10  0.09617276 -0.23542791 -0.40692605 -0.57662557 -0.40900254  2.69644047
#> 11 -0.29664556 -0.82618568 -0.40692605  2.79889470 -0.40900254  0.40479204
#> 12 -0.29664556 -0.56362667  0.55773845 -0.20500866  0.09341901  0.04919142
#> 13 -0.41855470  0.66164870 -0.42602832  1.73049608 -0.40900254 -0.41506494
#> 14 -0.35082740  0.04901101  0.52908505  0.21306036  0.69004460 -0.41506494
#> 15 -0.29664556  1.82128432  1.40778935  0.83242188 -0.05312061 -0.41506494
#> 16 -0.43210016  1.66812490 -0.39737492 -0.15855655 -0.40900254 -0.41506494
#>  [ reached 'max' / getOption("max.print") -- omitted 184 rows ]
#> 
#> $removed
#> character(0)
#>