r - Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels

Question

I'm using the R caret package to generate a model. I'm using PCA in the pre-process for dimensionality reduction and then trying to generate a logistic regression model.

I'm getting this error:

Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels

    credit <- read.csv('~Loans Question/RequiredAttributesWithLoanStatus.csv')

    credit$LoanStatus <- as.factor(credit$LoanStatus)

    str(credit)
    'data.frame':   8580 obs. of  45 variables:
     $ ListingCategory            : int  1 7 3 1 1 7 1 1 1 1 ...
     $ IncomeRange                : int  3 4 6 4 4 3 3 4 3 3 ...
     $ StatedMonthlyIncome        : num  2583 4326 10500 4167 5667 ...
     $ IncomeVerifiable           : logi  TRUE TRUE TRUE FALSE TRUE TRUE ...
     $ DTIwProsperLoan            : num  1.8e-01 2.0e-01 1.7e-01 1.0e+06 1.8e-01 4.4e-01 2.2e-01 2.0e-01 2.0e-01 3.1e-01 ...
     $ EmploymentStatusDescription: Factor w/ 7 levels "Employed","Full-time",..: 1 4 1 7 1 1 1 1 1 1 ...
     $ Occupation                 : Factor w/ 65 levels "","Accountant/CPA",..: 37 37 20 14 43 58 48 37 37 37 ...
     $ MonthsEmployed             : int  4 44 159 67 26 16 209 147 24 9 ...
     $ BorrowerState              : Factor w/ 48 levels "AK","AL","AR",..: 22 32 5 5 14 28 4 10 10 34 ...
     $ BorrowerCity               : Factor w/ 3089 levels "AARONSBURG","ABERDEEN",..: 1737 3059 2488 654 482 719 895 1699 2747 1903 ...
     $ BorrowerMetropolitanArea   : Factor w/ 1 level "(Not Implemented)": 1 1 1 1 1 1 1 1 1 1 ...
     $ LenderIndicator            : int  0 0 0 1 0 0 0 0 1 0 ...
     $ GroupIndicator             : logi  FALSE FALSE FALSE TRUE FALSE FALSE ...
     $ GroupName                  : Factor w/ 83 levels "","00 Used Car Loans",..: 1 1 1 47 1 1 1 1 1 1 ...
     $ ChannelCode                : int  90000 90000 90000 80000 40000 40000 90000 90000 80000 90000 ...
     $ AmountParticipation        : int  0 0 0 0 0 0 0 0 0 0 ...
     $ MonthlyDebt                : int  247 785 1631 817 644 1524 427 817 654 749 ...
     $ CurrentDelinquencies       : int  0 0 0 0 0 0 0 1 0 1 ...
     $ DelinquenciesLast7Years    : int  0 10 0 0 0 0 0 0 0 0 ...
     $ PublicRecordsLast10Years   : int  0 1 0 0 0 0 1 0 1 0 ...
     $ PublicRecordsLast12Months  : int  0 0 0 0 0 0 0 0 0 0 ...
     $ FirstRecordedCreditLine    : Factor w/ 4719 levels "1/1/00 0:00",..: 3032 2673 1197 2541 4698 4345 3150 925 4452 2358 ...
     $ CreditLinesLast7Years      : int  53 30 36 26 7 22 15 20 34 32 ...
     $ InquiriesLast6Months       : int  2 8 5 0 0 0 0 3 0 0 ...
     $ AmountDelinquent           : int  0 0 0 0 0 0 0 63 0 15 ...
     $ CurrentCreditLines         : int  10 10 18 10 4 11 6 10 7 8 ...
     $ OpenCreditLines            : int  9 10 15 8 3 8 5 7 7 8 ...
     $ BankcardUtilization        : num  0.26 0.69 0.94 0.69 0.81 0.38 0.55 0.24 0.03 0 ...
     $ TotalOpenRevolvingAccounts : int  9 7 12 10 3 5 4 5 4 6 ...
     $ InstallmentBalance         : int  48648 14827 0 0 0 30916 0 21619 41340 15447 ...
     $ RealEstateBalance          : int  0 0 577745 0 0 0 191296 0 0 126039 ...
     $ RevolvingBalance           : int  5265 9967 94966 50511 37871 22463 19550 2436 1223 3236 ...
     $ RealEstatePayment          : int  0 0 4159 0 0 0 1303 0 0 1279 ...
     $ RevolvingAvailablePercent  : int  78 52 36 45 18 61 44 74 96 76 ...
     $ TotalInquiries             : int  8 11 15 2 0 0 1 7 1 1 ...
     $ TotalTradeItems            : int  53 30 36 26 7 22 15 20 34 32 ...
     $ SatisfactoryAccounts       : int  52 23 36 26 7 19 15 18 34 29 ...
     $ NowDelinquentDerog         : int  0 0 0 0 0 0 0 1 0 1 ...
     $ WasDelinquentDerog         : int  1 7 0 0 0 3 0 1 0 2 ...
     $ OldestTradeOpenDate        : int  5092001 5011977 12011984 4272000 9081993 9122000 6161987 11181999 9191990 4132000 ...
     $ DelinquenciesOver30Days    : int  0 6 0 0 0 13 0 2 0 2 ...
     $ DelinquenciesOver60Days    : int  0 4 0 0 0 0 0 0 0 1 ...
     $ DelinquenciesOver90Days    : int  0 10 0 0 0 0 0 0 0 0 ...
     $ IsHomeowner                : logi  FALSE FALSE TRUE FALSE FALSE FALSE ...
     $ LoanStatus                 : Factor w/ 4 levels "1","2","3","4": 4 2 2 4 4 4 4 4 4 3 ...

    summary(credit)
    ListingCategory   IncomeRange    StatedMonthlyIncome IncomeVerifiable
     Min.   : 0.000   Min.   :1.000   Min.   :     0      Mode :logical   
     1st Qu.: 1.000   1st Qu.:3.000   1st Qu.:  3167      FALSE:784       
     Median : 2.000   Median :4.000   Median :  4750      TRUE :7796      
     Mean   : 4.997   Mean   :4.089   Mean   :  5755      NA's :0         
     3rd Qu.: 7.000   3rd Qu.:5.000   3rd Qu.:  7083                      
     Max.   :20.000   Max.   :7.000   Max.   :250000                      

     DTIwProsperLoan     EmploymentStatusDescription
     Min.   :      0.0   Employed     :7182         
     1st Qu.:      0.1   Full-time    : 416         
     Median :      0.2   Not employed : 122         
     Mean   :  91609.4   Other        : 475         
     3rd Qu.:      0.3   Part-time    :   7         
     Max.   :1000000.0   Retired      :  32         
                         Self-employed: 346         
                        Occupation   MonthsEmployed   BorrowerState 
     Other                   :2421   Min.   :-23.00   CA     :1056  
     Professional            :1040   1st Qu.: 26.00   FL     : 608  
     Computer Programmer     : 345   Median : 68.00   NY     : 574  
     Executive               : 334   Mean   : 97.44   TX     : 532  
     Administrative Assistant: 325   3rd Qu.:139.00   IL     : 443  
     Teacher                 : 301   Max.   :755.00   GA     : 343  
     (Other)                 :3814   NA's   :5        (Other):5024  
        BorrowerCity       BorrowerMetropolitanArea LenderIndicator  
     CHICAGO  : 121   (Not Implemented):8580        Min.   :0.00000  
     NEW YORK :  91                                 1st Qu.:0.00000  

     BROOKLYN :  88                                 Median :0.00000  
     HOUSTON  :  64                                 Mean   :0.09196  
     LAS VEGAS:  53                                 3rd Qu.:0.00000  
     ATLANTA  :  51                                 Max.   :1.00000  
     (Other)  :8112                                                  
     GroupIndicator                                     GroupName   
     Mode :logical                                           :8326  
     FALSE:8325      We do not accept new membership requests:  39  
     TRUE :255       BORROWERS - LARGEST GROUP               :  29  
     NA's :0         LendersClub                             :  17  
                     Debt Consolidators                      :  12  
                     Have Money - Will Bid                   :  10  
                     (Other)                                 : 147  
      ChannelCode    AmountParticipation  MonthlyDebt      CurrentDelinquencies
     Min.   :40000   Min.   :0           Min.   :    0.0   Min.   : 0.0000     
     1st Qu.:80000   1st Qu.:0           1st Qu.:  364.0   1st Qu.: 0.0000     
     Median :80000   Median :0           Median :  708.0   Median : 0.0000     
     Mean   :77196   Mean   :0           Mean   :  885.5   Mean   : 0.4119     
     3rd Qu.:90000   3rd Qu.:0           3rd Qu.: 1205.2   3rd Qu.: 0.0000     
     Max.   :90000   Max.   :0           Max.   :30213.0   Max.   :21.0000     

     DelinquenciesLast7Years PublicRecordsLast10Years PublicRecordsLast12Months
     Min.   : 0.000          Min.   : 0.0000          Min.   :0.00000          
     1st Qu.: 0.000          1st Qu.: 0.0000          1st Qu.:0.00000          
     Median : 0.000          Median : 0.0000          Median :0.00000          
     Mean   : 4.009          Mean   : 0.2809          Mean   :0.01364          
     3rd Qu.: 3.000          3rd Qu.: 0.0000          3rd Qu.:0.00000          
     Max.   :99.000          Max.   :11.0000          Max.   :4.00000          

     FirstRecordedCreditLine CreditLinesLast7Years InquiriesLast6Months
     12/1/93 0:00:  20       Min.   :  2.0         Min.   : 0.0000     
     3/1/95 0:00 :  19       1st Qu.: 16.0         1st Qu.: 0.0000     
     6/1/90 0:00 :  17       Median : 24.0         Median : 1.0000     
     6/1/89 0:00 :  16       Mean   : 26.1         Mean   : 0.9994     
     12/1/90 0:00:  15       3rd Qu.: 34.0         3rd Qu.: 1.0000     
     2/1/94 0:00 :  14       Max.   :115.0         Max.   :15.0000     
     (Other)     :8479                                                 
     AmountDelinquent CurrentCreditLines OpenCreditLines  BankcardUtilization
     Min.   :     0   Min.   : 0.000     Min.   : 0.000   Min.   :0.0000     
     1st Qu.:     0   1st Qu.: 5.000     1st Qu.: 5.000   1st Qu.:0.2500     
     Median :     0   Median : 9.000     Median : 8.000   Median :0.5400     
     Mean   :  1195   Mean   : 9.345     Mean   : 8.306   Mean   :0.5182     
     3rd Qu.:     0   3rd Qu.:12.000     3rd Qu.:11.000   3rd Qu.:0.7900     
     Max.   :179158   Max.   :54.000     Max.   :42.000   Max.   :2.2300     

     TotalOpenRevolvingAccounts InstallmentBalance RealEstateBalance
     Min.   : 0.000             Min.   :     0     Min.   :      0  
     1st Qu.: 3.000             1st Qu.:  3338     1st Qu.:      0  
     Median : 6.000             Median : 14453     Median :  26154  
     Mean   : 6.441             Mean   : 24900     Mean   : 109306  
     3rd Qu.: 9.000             3rd Qu.: 32238     3rd Qu.: 176542  
     Max.   :44.000             Max.   :739371     Max.   :1938421  
                                NA's   :328                         
     RevolvingBalance RealEstatePayment RevolvingAvailablePercent TotalInquiries 
     Min.   :     0   Min.   :    0.0   Min.   :  0.00            Min.   : 0.00  
     1st Qu.:  2799   1st Qu.:    0.0   1st Qu.: 29.00            1st Qu.: 2.00  
     Median :  8784   Median :  346.5   Median : 52.00            Median : 3.00  
     Mean   : 19555   Mean   :  830.5   Mean   : 51.46            Mean   : 3.91  
     3rd Qu.: 21110   3rd Qu.: 1382.2   3rd Qu.: 75.00            3rd Qu.: 5.00  
     Max.   :695648   Max.   :13651.0   Max.   :100.00            Max.   :36.00  

     TotalTradeItems SatisfactoryAccounts NowDelinquentDerog WasDelinquentDerog
     Min.   :  2.0   Min.   :  1.00       Min.   : 0.0000    Min.   : 0.000    
     1st Qu.: 16.0   1st Qu.: 14.00       1st Qu.: 0.0000    1st Qu.: 0.000    
     Median : 24.0   Median : 21.00       Median : 0.0000    Median : 1.000    
     Mean   : 26.1   Mean   : 23.34       Mean   : 0.4119    Mean   : 2.343    
     3rd Qu.: 34.0   3rd Qu.: 30.25       3rd Qu.: 0.0000    3rd Qu.: 3.000    
     Max.   :115.0   Max.   :113.00       Max.   :21.0000    Max.   :32.000    

     OldestTradeOpenDate DelinquenciesOver30Days DelinquenciesOver60Days
     Min.   : 1011957    Min.   : 0.000          Min.   : 0.000         
     1st Qu.: 4101996    1st Qu.: 0.000          1st Qu.: 0.000         
     Median : 7191993    Median : 1.000          Median : 0.000         
     Mean   : 6934230    Mean   : 4.332          Mean   : 1.908         
     3rd Qu.:10011990    3rd Qu.: 5.000          3rd Qu.: 2.000         
     Max.   :12312004    Max.   :99.000          Max.   :73.000         

     DelinquenciesOver90Days IsHomeowner     LoanStatus
     Min.   : 0.000          Mode :logical   1:1847    
     1st Qu.: 0.000          FALSE:4264      2:1262    
     Median : 0.000          TRUE :4316      3: 256    
     Mean   : 4.009          NA's :0         4:5215    
     3rd Qu.: 3.000                                    
     Max.   :99.000                                    

    try(na.fail(credit))

    glmFit 

Answer 1

Looking at the error message and your dataset's variables, the variable BorrowerMetropolitanArea has only one level (Actually it has no predictive value at all if all samples have the same value). I guess this is causing the problem in the contrasts function when you use PCA to pre-process the dataset.

Try calling the train funcion on the dataset without the the variable BorrowerMetropolitanArea.