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(This article was first published on <strong><a href="https://datascienceplus.com/machine-learning-logistic-regression-for-credit-modelling-in-r/"> R Programming – DataScience+</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
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<li><a rel="nofollow" href="https://datascienceplus.com/tag/logistic-regression/" title="Permanent Link toLogistic Regression" target="_blank">Logistic Regression</a></li>
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<p>Machine learning logistic regressions is a widely popular method to model credit modeling. There are excellent and efficient packages in R, that can perform these types of analysis. Typically you will first create different machine learning visualizations before you perform the machine learning logistic regression analysis. </p>
<p>This article is the second step of a credit modeling analysis, where I recently published the <a rel="nofollow" href="https://datascienceplus.com/visualizations-for-credit-modeling-in-r/" target="_blank">first step in this article</a>.</p>
<p>The first thing we need to do is to load the R packages into the library:</p>
<pre>
# Load R packages into the library
# Data management packages
library(DescTools)
library(skimr)
library(plyr)
library(dplyr)
library(aod)
library(readxl)
# Visualization packages
library(Deducer)
library(ggplot2)
# Machine learnning method packages
library(ROCR)
library(pROC)
library(caret)
library(MASS)
</pre>
<p>Now it is time to load the dataset and do some data management. We will work with the <a rel="nofollow" href="https://www.kaggle.com/wendykan/lending-club-loan-data" target="_blank">loan lending club dataset</a>. The below coding is the data management:</p>
<pre>
# Import dataset
loan_data &lt;- read.csv(&quot;/loan.csv&quot;)
# Selecting the relevant variables in the dataset:
loan_data &lt;- loan_data[,c(&quot;grade&quot;,&quot;sub_grade&quot;,&quot;term&quot;,&quot;loan_amnt&quot;,&quot;issue_d&quot;,&quot;loan_status&quot;,&quot;emp_length&quot;,
                          &quot;home_ownership&quot;, &quot;annual_inc&quot;,&quot;verification_status&quot;,&quot;purpose&quot;,&quot;dti&quot;,
                          &quot;delinq_2yrs&quot;,&quot;addr_state&quot;,&quot;int_rate&quot;, &quot;inq_last_6mths&quot;,&quot;mths_since_last_delinq&quot;,
                          &quot;mths_since_last_record&quot;,&quot;open_acc&quot;,&quot;pub_rec&quot;,&quot;revol_bal&quot;,&quot;revol_util&quot;,&quot;total_acc&quot;)]
# Data management for missing observations
loan_data$mths_since_last_delinq[is.na(loan_data$mths_since_last_delinq)] &lt;- 0
loan_data$mths_since_last_record[is.na(loan_data$mths_since_last_record)] &lt;- 0
var.has.na &lt;- lapply(loan_data, function(x){any(is.na(x))})
num_na &lt;- which( var.has.na == TRUE )	
per_na &lt;- num_na/dim(loan_data)[1] 
loan_data &lt;- loan_data[complete.cases(loan_data),]
</pre>
<p>Although this is the second step of a credit modeling analysis, the visualization step can be found in <a rel="nofollow" href="https://datascienceplus.com/visualizations-for-credit-modeling-in-r/" target="_blank">my previous article</a>, let us do minimum of visualization in case the reader only reads this article:</p>
<pre>
# Visualization of the data
# Bar chart of the loan amount
loanamount_barchart &lt;- ggplot(data=loan_data, aes(loan_data$loan_amnt)) + 
  geom_histogram(breaks=seq(0, 35000, by=1000), 
                 col=&quot;black&quot;, aes(fill=..count..)) +
  scale_fill_gradient(&quot;Count&quot;, low=&quot;green1&quot;, high=&quot;yellowgreen&quot;)+
  labs(title=&quot;Loan Amount&quot;, x=&quot;Amount&quot;, y=&quot;Number of Loans&quot;)
loanamount_barchart
ggplotly(p = ggplot2::last_plot())
# Box plot of loan amount
box_plot_stat &lt;- ggplot(loan_data, aes(loan_status, loan_amnt))
box_plot_stat + geom_boxplot(aes(fill = loan_status)) +
  theme(axis.text.x = element_blank()) +
  labs(list(title = &quot;Loan amount by status&quot;, x = &quot;Loan Status&quot;, y = &quot;Amount&quot;))
ggplotly(p = ggplot2::last_plot())
</pre>
<p>The above coding gives us the following two visualizations:<br>
<a rel="nofollow" href="https://i1.wp.com/datascienceplus.com/wp-content/uploads/2018/10/V1.png?ssl=1" target="_blank"><img sizes="(max-width: 490px) 100vw, 490px" src="https://i2.wp.com/datascienceplus.com/wp-content/uploads/2018/10/V1-490x388.png?w=450&ssl=1" alt="" class="wp-image-17724" data-recalc-dims="1"></a><br>
<a rel="nofollow" href="https://i1.wp.com/datascienceplus.com/wp-content/uploads/2018/10/V2.png?ssl=1" target="_blank"><img sizes="(max-width: 490px) 100vw, 490px" src="https://i0.wp.com/datascienceplus.com/wp-content/uploads/2018/10/V2-490x388.png?w=450&ssl=1" alt="" class="wp-image-17725" data-recalc-dims="1"></a></p>
<p>Lets see some descriptive statistics of the data as well:</p>
<pre>
skim(loan_data)
<em>Skim summary statistics
n obs: 886877 n variables: 23 -- Variable type:factor --------------------------------------------------------
variable missing complete n n_unique top_counts ordered
addr_state 0 886877 886877 51 CA: 129456, NY: 74033, TX: 71100, FL: 60901 FALSE
emp_length 0 886877 886877 12 10+: 291417, 2 y: 78831, &lt; 1: 70538, 3 y: 69991 FALSE
grade 0 886877 886877 7 B: 254445, C: 245721, A: 148162, D: 139414 FALSE
home_ownership 0 886877 886877 6 MOR: 443319, REN: 355921, OWN: 87408, OTH: 180 FALSE
issue_d 0 886877 886877 103 Oct: 48619, Jul: 45938, Dec: 44323, Oct: 38760 FALSE
loan_status 0 886877 886877 8 Cur: 601533, Ful: 209525, Cha: 45956, Lat: 11582 FALSE
purpose 0 886877 886877 14 deb: 524009, cre: 206136, hom: 51760, oth: 42798 FALSE
sub_grade 0 886877 886877 35 B3: 56301, B4: 55599, C1: 53365, C2: 52206 FALSE
term 0 886877 886877 2 36: 620739, 60: 266138, NA: 0 FALSE
verification_status 0 886877 886877 3 Sou: 329393, Ver: 290896, Not: 266588, NA: 0 FALSE
-- Variable type:numeric -------------------------------------------------------
variable missing complete n mean sd p0 p25 p50 p75 p100 hist
annual_inc 0 886877 886877 75019.4 64687.38 0 45000 65000 90000 9500000 ????????
delinq_2yrs 0 886877 886877 0.31 0.86 0 0 0 0 39 ????????
dti 0 886877 886877 18.16 17.19 0 11.91 17.66 23.95 9999 ????????
inq_last_6mths 0 886877 886877 0.69 1 0 0 0 1 33 ????????
int_rate 0 886877 886877 13.25 4.38 5.32 9.99 12.99 16.2 28.99 ????????
loan_amnt 0 886877 886877 14756.97 8434.43 500 8000 13000 20000 35000 ????????
mths_since_last_delinq 0 886877 886877 16.62 22.89 0 0 0 30 188 ????????
mths_since_last_record 0 886877 886877 10.83 27.65 0 0 0 0 129 ????????
open_acc 0 886877 886877 11.55 5.32 1 8 11 14 90 ????????
pub_rec 0 886877 886877 0.2 0.58 0 0 0 0 86 ????????
revol_bal 0 886877 886877 16924.56 22414.33 0 6450 11879 20833 2904836 ????????
revol_util 0 886877 886877 55.07 23.83 0 37.7 56 73.6 892.3 ????????
total_acc 0 886877 886877 25.27 11.84 1 17 24 32 169 ????????
</em></pre>
<p>Next we need to do some more data management to prepare the dataset for machine learning analysis</p>
<pre>
# Focus on the historical loans
loan_data=as.data.frame(loan_data[loan_data$loan_status!=&quot;Current&quot;, ])
limits_inc = quantile(loan_data$annual_inc, seq(0,1,0.1))
labels &lt;- c(0, limits_inc[2:10], &quot;+inf&quot;)
labels &lt;- prettyNum(labels, big.mark = &quot;,&quot;)
labels &lt;- paste(labels[1:10], labels[2:11], sep = &quot;-&quot;)
loan_data$annual_inc &lt;- cut(loan_data$annual_inc, limits_inc, labels = labels, include.lowest = T)
loan_data[,&quot;annual_inc&quot;] &lt;- as.character(loan_data[,&quot;annual_inc&quot;])
# Create binary variables for the logistic regression analysis
# Annual_inc
loan_data$annual_inc[loan_data$annual_inc == &quot;70,000- 80,000&quot;| loan_data$annual_inc == &quot;80,000- 94,000&quot; | loan_data$annual_inc == &quot;94,000-120,000&quot; | loan_data$annual_inc == &quot;120,000-   +inf&quot; ] &lt;- 1
loan_data$annual_inc[loan_data$annual_inc != 1] &lt;- 0
loan_data$annual_inc &lt;- as.numeric(loan_data$annual_inc)
# Home_ownership
loan_data$home_ownership &lt;- as.character(loan_data$home_ownership)
loan_data$home_ownership[loan_data$home_ownership==&quot;OWN&quot; | loan_data$home_ownership==&quot;MORTGAGE&quot;  ] &lt;- 1       
loan_data$home_ownership[loan_data$home_ownership!=1] &lt;- 0
# Dealinq_2yrs
loan_data$delinq_2yrs &lt;- as.character(loan_data$delinq_2yrs)
loan_data$delinq_2yrs[loan_data$delinq_2yrs==&quot;0&quot;] &lt;- 0
loan_data$delinq_2yrs[loan_data$delinq_2yrs!= 0] &lt;- 1
# Verification status: if Verified = 1 ; otherwise = 0
loan_data$verification_status = as.character(loan_data$verification_status)
loan_data$verification_status[loan_data$verification_status == &quot;Verified&quot; | loan_data$verification_status == &quot;Source Verified&quot;] = 1
loan_data$verification_status[loan_data$verification_status != 1] = 0
loan_data$verification_status=as.numeric(loan_data$verification_status)
# Dti
dti_quant &lt;- quantile(loan_data$dti, seq(0, 1, 0.1))
labels = c(0,prettyNum(dti_quant[2:10], big.mark = &quot;,&quot;), &quot;+Inf&quot;)
labels = paste(labels[1:10],labels[2:11], sep = &quot;-&quot;)
loan_data &lt;- mutate(loan_data, dti= cut(loan_data$dti, breaks = dti_quant, labels = factor(labels), include.lowest = T))
loan_data$dti &lt;- as.character(loan_data$dti)
loan_data$dti[loan_data$dti == &quot;0-6.57&quot; | loan_data$dti == &quot;12.13-14.32&quot; | loan_data$dti == &quot;14.32-16.49&quot; ] &lt;- 1
loan_data$dti[loan_data$dti!=1] &lt;- 0
# Status
loan_data$loan_status &lt;- as.character(loan_data$loan_status)
loan_data$loan_status[loan_data$loan_status == &quot;Charged Off&quot; | loan_data$loan_status == &quot;Default&quot; ] &lt;- 1
loan_data$loan_status[loan_data$loan_status != 1] &lt;- 0
table(loan_data$loan_status)
PercTable(loan_data$loan_status)
# Change to nummeric variables:
loan_data[,&quot;revol_util&quot;] &lt;- as.numeric(sub(&quot;%&quot;, &quot;&quot;,loan_data$&quot;revol_util&quot;, fixed =TRUE))/100
loan_data[,&quot;int_rate&quot;] &lt;- as.numeric(sub(&quot;%&quot;, &quot;&quot;,loan_data$&quot;int_rate&quot;, fixed =TRUE))/100
loan_data$loan_status &lt;- as.numeric(loan_data$loan_status)
# Grouping variables
loan_data$purpose &lt;- as.character(loan_data$purpose)
loan_data$purpose[loan_data$purpose == &quot;car&quot; | loan_data$purpose == &quot;major_purchase&quot; | 
                    loan_data$purpose == &quot;home_improvement&quot;| loan_data$purpose == &quot;credit_card&quot; ] &lt;- 2
loan_data$purpose[loan_data$purpose == &quot;moving&quot; | loan_data$purpose == &quot;small_business&quot; | 
                    loan_data$purpose == &quot;renewable_energy&quot; ] &lt;- 0
loan_data$purpose[loan_data$purpose!= 0 &amp; loan_data$purpose!= 2 ] &lt;- 1
loan_data$purpose &lt;- as.factor(loan_data$purpose)
</pre>
<p>Now it is time to make the machine learning regression analysis. We will work with multiple logistic regression. <a rel="nofollow" href="https://datascienceplus.com/perform-logistic-regression-in-r/" target="_blank">Logistic regression</a> is applied when you have a binary variable (y) to explain. The logistic regression model uses the cumulative distribution function to estimate the logistic function of the model with a group of explanatory variables (the x’s). We will work with a stepwise model in order to find a final model for the logistic regression. The below coding generates the multiple logistic regression analysis:</p>
<pre>
##Machine Learning: Multiple  Logistic Regression Models
# Logistic: Logit stepwise Regression
logregmodI &lt;- glm(loan_status ~ loan_amnt + home_ownership + annual_inc
            + verification_status + purpose + dti + delinq_2yrs 
            + int_rate + inq_last_6mths + mths_since_last_delinq 
            + revol_bal + revol_util + total_acc,
            data = loan_data, family = binomial(link= &quot;logit&quot;))
step &lt;- stepAIC(logregmodI, direction=&quot;both&quot;)
step$anova
<em>Stepwise Model Path Analysis of Deviance Table
Initial Model:
loan_status ~ loan_amnt + home_ownership + annual_inc + verification_status + purpose + dti + delinq_2yrs + int_rate + inq_last_6mths + mths_since_last_delinq + revol_bal + revol_util + total_acc
Final Model:
loan_status ~ loan_amnt + home_ownership + verification_status + purpose + dti + delinq_2yrs + int_rate + inq_last_6mths + mths_since_last_delinq + revol_bal + revol_util + total_acc
Step Df Deviance Resid. Df Resid. Dev AIC
1 285330 241553.4 241581.4
2 - annual_inc 0 0 285330 241553.4 241581.4
</em></pre>
<p>Now we need to make a training dataset and testing dataset in order to train the model and perform a ROC curve:</p>
<pre>
# Create a training- and testing dataset
  percing &lt;- floor((nrow(loan_data)/4)*3)       
  loan &lt;- loan_data[sample(nrow(loan_data)), ]          
  loan.training &lt;- loan[1:percing, ]              
  loan.testing &lt;- loan[(percing+1):nrow(loan), ]
# Begin training of the model
  fitting.logistic &lt;- glm(loan_status ~ loan_amnt + home_ownership + verification_status + 
                   purpose + dti + delinq_2yrs + int_rate + inq_last_6mths + 
                   mths_since_last_delinq + revol_bal + revol_util + total_acc,
                 data=loan.training,family = binomial(link= &quot;logit&quot;))
  summary(fitting.logistic)
<em>Call:
glm(formula = loan_status ~ loan_amnt + home_ownership + verification_status + purpose + dti + delinq_2yrs + int_rate + inq_last_6mths + mths_since_last_delinq + revol_bal + revol_util + total_acc, family = binomial(link = &quot;logit&quot;), data = loan.training)
Deviance Residuals: Min 1Q Median 3Q Max -1.5509 -0.6336 -0.5098 -0.3799 2.5925 Coefficients:
Estimate Std. Error z value Pr(>|z|) (Intercept) -2.952e+00 4.221e-02 -69.931 &lt; 2e-16 ***
loan_amnt 2.213e-06 8.330e-07 2.657 0.007894 ** home_ownership1 -1.626e-01 1.261e-02 -12.892 &lt; 2e-16 ***
verification_status 7.695e-02 1.429e-02 5.385 7.23e-08 ***
purpose1 -3.342e-01 3.237e-02 -10.326 &lt; 2e-16 ***
purpose2 -3.882e-01 3.383e-02 -11.475 &lt; 2e-16 ***
dti1 -2.075e-01 1.385e-02 -14.982 &lt; 2e-16 ***
delinq_2yrs1 -5.411e-02 1.618e-02 -3.345 0.000823 ***
int_rate 1.157e+01 1.545e-01 74.868 &lt; 2e-16 ***
inq_last_6mths 7.640e-02 5.113e-03 14.943 &lt; 2e-16 ***
mths_since_last_delinq -2.289e-03 2.726e-04 -8.396 &lt; 2e-16 ***
revol_bal -1.818e-06 4.002e-07 -4.543 5.54e-06 ***
revol_util 3.391e-01 2.743e-02 12.366 &lt; 2e-16 ***
total_acc -6.473e-03 5.718e-04 -11.320 &lt; 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 191593 on 214007 degrees of freedom
Residual deviance: 180719 on 213994 degrees of freedom
AIC: 180747
Number of Fisher Scoring iterations: 4
</em></pre>
<p>Now we can create the ROC and AUC curves for the model. </p>
<pre>
# AUC and ROC curve
  fitted.results &lt;- predict(fit.log, newdata = loan.testing, type = &quot;response&quot;)
  loan.testing$prob &lt;- fitted.results
  pred &lt;- prediction(loan.testing$prob,loan.testing$loan_status)
  auc1 &lt;- performance(pred, measure = &quot;auc&quot;)
  auc1@y.values
</pre>
<p>And lastly we can display the ROC curve as a visualization. These codings are pretty heavy in computing power – so relax and let R do the calculations:</p>
<pre>
# Performance function
ROCRperf = performance(pred, &quot;tpr&quot;, &quot;fpr&quot;)
# Plot the ROC graph Add threshold labels 
plot(ROCRperf, colorize=TRUE, print.cutoffs.at=seq(0,1,by=0.1), text.adj=c(-0.2,1.7))
abline(0, 1, col= &quot;black&quot;)
</pre>
<p>The above coding gives us the following ROC graph visualizaiton:<br>
<a rel="nofollow" href="https://i1.wp.com/datascienceplus.com/wp-content/uploads/2018/10/V3.png?ssl=1" target="_blank"><img sizes="(max-width: 490px) 100vw, 490px" src="https://i0.wp.com/datascienceplus.com/wp-content/uploads/2018/10/V3-490x389.png?w=450&ssl=1" alt="" class="wp-image-17732" data-recalc-dims="1"></a></p>
<h3>References</h3>
<ol>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/DescTools/DescTools.pdf" target="_blank">Using DescTools in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/skimr/index.html" target="_blank">Using skimr in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/magrittr/vignettes/magrittr.html" target="_blank">Using magrittr in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/plyr/plyr.pdf" target="_blank">Using plyr in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/dplyr/dplyr.pdf" target="_blank">Using dplyr in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/aod/index.html" target="_blank">Using aod in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/readxl/readxl.pdf" target="_blank">Using readxl in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/Deducer/index.html" target="_blank">Using Deducer in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf" target="_blank">Using ggplot2 in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/plotly/plotly.pdf" target="_blank">Using plotly in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/ROCR/ROCR.pdf" target="_blank">Using ROCR in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/pROC/pROC.pdf" target="_blank">Using pROC in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/caret/caret.pdf" target="_blank">Using caret in R – CRAN.R-project.org</a></li>
<li><a rel="nofollow" href="https://cran.r-project.org/web/packages/MASS/MASS.pdf" target="_blank">Using MASS in R – CRAN.R-project.org</a></li>
</ol>
<p><strong>
<p>Related Post</p>
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	<p>
<div>
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