title: Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels
body: <p>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.</p>
  
  <p>I'm getting this error:</p>
  
  <p>Error in <code>contrasts&lt;-</code>(<code>*tmp*</code>, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels</p>
  
  <pre><code>    credit &lt;- read.csv('~Loans Question/RequiredAttributesWithLoanStatus.csv')
  
      credit$LoanStatus &lt;- as.factor(credit$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 &lt;- train(LoanStatus~., credit, method = "glm", family=binomial, preProcess=c("pca"), 
          trControl = trainControl(method = "cv"))
  </code></pre>
  
  <p>Error in <code>contrasts&lt;-</code>(<code>*tmp*</code>, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels</p>
  
  <pre><code>logregFit &lt;- train(LoanStatus~., credit, method = "logreg", family=binomial, preProcess=c("pca"), 
      trControl = trainControl(method = "cv"))
  </code></pre>
  
  <p>Error in <code>contrasts&lt;-</code>(<code>*tmp*</code>, value = contr.funs[1 + isOF[nn]]): contrasts can be applied only to factors with 2 or more levels</p>