##
## Attaching package: 'dplyr'
## The following object is masked from 'package:MASS':
##
## select
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
## crim zn indus chas nox rm age dis rad tax ptratio black lstat
## 1 0.00632 18 2.31 0 0.538 6.575 65.2 4.0900 1 296 15.3 396.90 4.98
## 2 0.02731 0 7.07 0 0.469 6.421 78.9 4.9671 2 242 17.8 396.90 9.14
## 3 0.02729 0 7.07 0 0.469 7.185 61.1 4.9671 2 242 17.8 392.83 4.03
## 4 0.03237 0 2.18 0 0.458 6.998 45.8 6.0622 3 222 18.7 394.63 2.94
## 5 0.06905 0 2.18 0 0.458 7.147 54.2 6.0622 3 222 18.7 396.90 5.33
## 6 0.02985 0 2.18 0 0.458 6.430 58.7 6.0622 3 222 18.7 394.12 5.21
## medv
## 1 24.0
## 2 21.6
## 3 34.7
## 4 33.4
## 5 36.2
## 6 28.7
## Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
## of ggplot2 3.3.4.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
##
## Call:
## glm(formula = crime_factor ~ poly(rad, 3) + poly(nox, 3) + poly(tax,
## 3) + poly(age, 3) + poly(dis, 3) + poly(indus, 3), family = "binomial",
## data = boston_training)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.790e+14 3.339e+06 -113518879 <2e-16 ***
## poly(rad, 3)1 8.745e+16 4.751e+08 184071758 <2e-16 ***
## poly(rad, 3)2 8.225e+15 1.075e+08 76514466 <2e-16 ***
## poly(rad, 3)3 1.953e+15 7.773e+07 25122280 <2e-16 ***
## poly(nox, 3)1 1.888e+16 1.771e+08 106597240 <2e-16 ***
## poly(nox, 3)2 1.054e+15 1.016e+08 10377240 <2e-16 ***
## poly(nox, 3)3 2.177e+15 9.908e+07 21975041 <2e-16 ***
## poly(tax, 3)1 -6.941e+16 4.130e+08 -168075367 <2e-16 ***
## poly(tax, 3)2 -3.403e+16 1.859e+08 -183065250 <2e-16 ***
## poly(tax, 3)3 1.628e+16 8.421e+07 193318513 <2e-16 ***
## poly(age, 3)1 -1.028e+15 1.234e+08 -8335643 <2e-16 ***
## poly(age, 3)2 2.885e+15 7.958e+07 36254178 <2e-16 ***
## poly(age, 3)3 1.990e+15 7.152e+07 27820397 <2e-16 ***
## poly(dis, 3)1 -4.984e+15 1.606e+08 -31035200 <2e-16 ***
## poly(dis, 3)2 3.258e+15 9.902e+07 32900446 <2e-16 ***
## poly(dis, 3)3 1.957e+15 8.154e+07 23994946 <2e-16 ***
## poly(indus, 3)1 1.115e+16 1.411e+08 78989311 <2e-16 ***
## poly(indus, 3)2 4.318e+15 1.171e+08 36885916 <2e-16 ***
## poly(indus, 3)3 8.514e+15 1.210e+08 70376384 <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: 560.06 on 403 degrees of freedom
## Residual deviance: 2811.40 on 385 degrees of freedom
## AIC: 2849.4
##
## Number of Fisher Scoring iterations: 25
## Loading required package: lattice
## Warning in confusionMatrix.default(predict_binary_glm$predicted_value,
## predict_binary_glm$actual_value): Levels are not in the same order for
## reference and data. Refactoring data to match.
## Confusion Matrix and Statistics
##
## Reference
## Prediction Low High
## Low 49 4
## High 2 47
##
## Accuracy : 0.9412
## 95% CI : (0.8764, 0.9781)
## No Information Rate : 0.5
## P-Value [Acc > NIR] : <2e-16
##
## Kappa : 0.8824
##
## Mcnemar's Test P-Value : 0.6831
##
## Sensitivity : 0.9608
## Specificity : 0.9216
## Pos Pred Value : 0.9245
## Neg Pred Value : 0.9592
## Prevalence : 0.5000
## Detection Rate : 0.4804
## Detection Prevalence : 0.5196
## Balanced Accuracy : 0.9412
##
## 'Positive' Class : Low
##
## Call:
## lda(crime_factor ~ poly(rad, 3) + poly(nox, 3) + poly(tax, 3) +
## poly(age, 3) + poly(dis, 3) + poly(indus, 3), data = boston_training)
##
## Prior probabilities of groups:
## Low High
## 0.5 0.5
##
## Group means:
## poly(rad, 3)1 poly(rad, 3)2 poly(rad, 3)3 poly(nox, 3)1 poly(nox, 3)2
## Low -0.02986818 0.00527937 -0.00410086 -0.035856 0.01135621
## High 0.02986818 -0.00527937 0.00410086 0.035856 -0.01135621
## poly(nox, 3)3 poly(tax, 3)1 poly(tax, 3)2 poly(tax, 3)3 poly(age, 3)1
## Low 0.003725802 -0.02961653 0.002564994 -0.0006208593 -0.03045625
## High -0.003725802 0.02961653 -0.002564994 0.0006208593 0.03045625
## poly(age, 3)2 poly(age, 3)3 poly(dis, 3)1 poly(dis, 3)2 poly(dis, 3)3
## Low -0.009153263 0.001180473 0.02998473 -0.01131224 0.00113431
## High 0.009153263 -0.001180473 -0.02998473 0.01131224 -0.00113431
## poly(indus, 3)1 poly(indus, 3)2 poly(indus, 3)3
## Low -0.02966437 0.01012727 0.01050137
## High 0.02966437 -0.01012727 -0.01050137
##
## Coefficients of linear discriminants:
## LD1
## poly(rad, 3)1 54.0984813
## poly(rad, 3)2 3.3023799
## poly(rad, 3)3 1.6940323
## poly(nox, 3)1 24.9539062
## poly(nox, 3)2 -9.7129156
## poly(nox, 3)3 0.9273337
## poly(tax, 3)1 -45.9158270
## poly(tax, 3)2 -20.7927520
## poly(tax, 3)3 9.3380422
## poly(age, 3)1 5.0154409
## poly(age, 3)2 5.0754930
## poly(age, 3)3 0.6445356
## poly(dis, 3)1 4.3726330
## poly(dis, 3)2 -2.6098746
## poly(dis, 3)3 4.6884000
## poly(indus, 3)1 7.0953914
## poly(indus, 3)2 8.0702091
## poly(indus, 3)3 -2.6227889
## New names:
## • `` -> `...1`
## Confusion Matrix and Statistics
##
## Reference
## Prediction Low High
## Low 46 1
## High 5 50
##
## Accuracy : 0.9412
## 95% CI : (0.8764, 0.9781)
## No Information Rate : 0.5
## P-Value [Acc > NIR] : <2e-16
##
## Kappa : 0.8824
##
## Mcnemar's Test P-Value : 0.2207
##
## Sensitivity : 0.9020
## Specificity : 0.9804
## Pos Pred Value : 0.9787
## Neg Pred Value : 0.9091
## Prevalence : 0.5000
## Detection Rate : 0.4510
## Detection Prevalence : 0.4608
## Balanced Accuracy : 0.9412
##
## 'Positive' Class : Low
##
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
##
## Attaching package: 'e1071'
## The following object is masked from 'package:rsample':
##
## permutations
##
## Naive Bayes Classifier for Discrete Predictors
##
## Call:
## naiveBayes.default(x = X, y = Y, laplace = laplace)
##
## A-priori probabilities:
## Y
## Low High
## 0.5 0.5
##
## Conditional probabilities:
## rad
## Y [,1] [,2]
## Low 4.168317 1.645554
## High 14.475248 9.592798
##
## nox
## Y [,1] [,2]
## Low 0.4709698 0.05651158
## High 0.6326337 0.09464589
##
## tax
## Y [,1] [,2]
## Low 306.1089 83.91098
## High 503.1485 168.82912
##
## age
## Y [,1] [,2]
## Low 50.87376 24.98412
## High 85.07129 18.87520
##
## indus
## Y [,1] [,2]
## Low 6.998465 5.471512
## High 15.143713 5.522585
## New names:
## • `` -> `...1`
## Confusion Matrix and Statistics
##
## Reference
## Prediction Low High
## Low 47 11
## High 4 40
##
## Accuracy : 0.8529
## 95% CI : (0.7691, 0.9153)
## No Information Rate : 0.5
## P-Value [Acc > NIR] : 8.267e-14
##
## Kappa : 0.7059
##
## Mcnemar's Test P-Value : 0.1213
##
## Sensitivity : 0.9216
## Specificity : 0.7843
## Pos Pred Value : 0.8103
## Neg Pred Value : 0.9091
## Prevalence : 0.5000
## Detection Rate : 0.4608
## Detection Prevalence : 0.5686
## Balanced Accuracy : 0.8529
##
## 'Positive' Class : Low
##
## [1] Low Low Low High Low Low
## Levels: Low High
## New names:
## • `` -> `...1`
## Confusion Matrix and Statistics
##
## Reference
## Prediction Low High
## Low 48 1
## High 3 50
##
## Accuracy : 0.9608
## 95% CI : (0.9026, 0.9892)
## No Information Rate : 0.5
## P-Value [Acc > NIR] : <2e-16
##
## Kappa : 0.9216
##
## Mcnemar's Test P-Value : 0.6171
##
## Sensitivity : 0.9412
## Specificity : 0.9804
## Pos Pred Value : 0.9796
## Neg Pred Value : 0.9434
## Prevalence : 0.5000
## Detection Rate : 0.4706
## Detection Prevalence : 0.4804
## Balanced Accuracy : 0.9608
##
## 'Positive' Class : Low
##
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
##
## Attaching package: 'ISLR2'
## The following object is masked _by_ '.GlobalEnv':
##
## Boston
## The following object is masked from 'package:MASS':
##
## Boston
##
## Call:
## glm(formula = default ~ income + balance, family = "binomial",
## data = Default)
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.154e+01 4.348e-01 -26.545 < 2e-16 ***
## income 2.081e-05 4.985e-06 4.174 2.99e-05 ***
## balance 5.647e-03 2.274e-04 24.836 < 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: 2920.6 on 9999 degrees of freedom
## Residual deviance: 1579.0 on 9997 degrees of freedom
## AIC: 1585
##
## Number of Fisher Scoring iterations: 8
## [1] 0.0248
## [1] 0.0256
## [1] 0.0254
## [1] 0.0222
## [1] 0.0262
## [1] 1188.832
## Loading required package: Matrix
##
## Attaching package: 'Matrix'
## The following objects are masked from 'package:tidyr':
##
## expand, pack, unpack
## Loaded glmnet 4.1-9
## [1] 1539.344
## [1] 1539.344
## [1] 1497.048
## 19 x 1 sparse Matrix of class "dgCMatrix"
## s0
## (Intercept) -586.05287161
## (Intercept) .
## PrivateYes -563.25598510
## Accept 1.21205847
## Enroll .
## Top10perc 35.58069720
## Top25perc -6.29046439
## F.Undergrad 0.06094957
## P.Undergrad .
## Outstate -0.03740620
## Room.Board 0.14301915
## Books .
## Personal .
## PhD -4.28904039
## Terminal -4.48542960
## S.F.Ratio .
## perc.alumni -6.65372612
## Expend 0.07473866
## Grad.Rate 8.41829047
##
## Attaching package: 'pls'
## The following object is masked from 'package:caret':
##
## R2
## The following object is masked from 'package:stats':
##
## loadings
## [1] NaN
## [1] NaN
## Warning in mean.default(y): argument is not numeric or logical: returning NA
## Warning in mean.default(y): argument is not numeric or logical: returning NA
## Warning in mean.default(y): argument is not numeric or logical: returning NA
## Warning in mean.default(y): argument is not numeric or logical: returning NA
## Warning in mean.default(y): argument is not numeric or logical: returning NA
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning in install.packages("ISLR", repos = "https://cloud.r-project.org"):
## installation of package 'ISLR' had non-zero exit status
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning in install.packages("ISLR"): installation of package 'ISLR' had
## non-zero exit status
## [1] "R version 4.4.3 (2025-02-28)"
## Warning: package 'cluster' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Warning: package 'foreign' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Warning: package 'lattice' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Warning: package 'MASS' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Warning: package 'Matrix' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Warning: package 'mgcv' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Warning: package 'nlme' in library '/opt/R/4.4.3/lib/R/library' will not be
## updated
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Downloading GitHub repo cran/ISLR@HEAD
## Running `R CMD build`...
## * checking for file ‘/tmp/RtmpfWz520/remotes1da110b5669/cran-ISLR-b72e0ce/DESCRIPTION’ ... OK
## * preparing ‘ISLR’:
## * checking DESCRIPTION meta-information ... OK
## * checking for LF line-endings in source and make files and shell scripts
## * checking for empty or unneeded directories
## * building ‘ISLR_1.4.tar.gz’
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning in i.p(...): installation of package
## '/tmp/RtmpfWz520/file1da77b6cfa2/ISLR_1.4.tar.gz' had non-zero exit status
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## system (cmd0): /opt/R/4.4.3/lib/R/bin/R CMD INSTALL
## foundpkgs: ISLR, /tmp/RtmpfWz520/downloaded_packages/ISLR_1.4.tar.gz
## files: /tmp/RtmpfWz520/downloaded_packages/ISLR_1.4.tar.gz
## Warning in install.packages("ISLR", verbose = TRUE): installation of package
## 'ISLR' had non-zero exit status
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)
## Warning in install.packages("ISLR", repos = "https://cloud.r-project.org"):
## installation of package 'ISLR' had non-zero exit status
## Installing package into '/cloud/lib/x86_64-pc-linux-gnu-library/4.4'
## (as 'lib' is unspecified)