feature selection cohort without transplant
model_14 threshold <- 0.1 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_1year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.518
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.665
## Area under the curve: 0.814
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 32991 1538
## died 26828 10960
##
## Accuracy : 0.6078
## 95% CI : (0.6042, 0.6113)
## No Information Rate : 0.8272
## P-Value [Acc > NIR] : 1
##
## Kappa : 0.238
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.8769
## Specificity : 0.5515
## Pos Pred Value : 0.2900
## Neg Pred Value : 0.9555
## Prevalence : 0.1728
## Detection Rate : 0.1516
## Detection Prevalence : 0.5225
## Balanced Accuracy : 0.7142
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.064917 0.007020 -294.15 <2e-16 ***
## age 0.655467 0.006471 101.30 <2e-16 ***
## ALBUMIN -0.710977 0.005822 -122.11 <2e-16 ***
## IRON_SAT_PERCENT -0.291617 0.005684 -51.31 <2e-16 ***
## HGB -0.277475 0.005780 -48.01 <2e-16 ***
## CLM_FROM_1year_cat 0.433463 0.005932 73.07 <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: 266319 on 289267 degrees of freedom
## Residual deviance: 209160 on 289262 degrees of freedom
## AIC: 209172
##
## Number of Fisher Scoring iterations: 5
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.93 |
1.90, 1.95 |
<0.001 |
| ALBUMIN |
0.49 |
0.49, 0.50 |
<0.001 |
| IRON_SAT_PERCENT |
0.75 |
0.74, 0.76 |
<0.001 |
| HGB |
0.76 |
0.75, 0.77 |
<0.001 |
| CLM_FROM_1year_cat |
1.54 |
1.52, 1.56 |
<0.001 |
## youden_index
## 0.428454
model_14 threshold <- 0.2 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_1year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.518
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.665
## Area under the curve: 0.814
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 46683 3912
## died 13136 8586
##
## Accuracy : 0.7643
## 95% CI : (0.7611, 0.7674)
## No Information Rate : 0.8272
## P-Value [Acc > NIR] : 1
##
## Kappa : 0.3618
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.6870
## Specificity : 0.7804
## Pos Pred Value : 0.3953
## Neg Pred Value : 0.9227
## Prevalence : 0.1728
## Detection Rate : 0.1187
## Detection Prevalence : 0.3004
## Balanced Accuracy : 0.7337
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.064917 0.007020 -294.15 <2e-16 ***
## age 0.655467 0.006471 101.30 <2e-16 ***
## ALBUMIN -0.710977 0.005822 -122.11 <2e-16 ***
## IRON_SAT_PERCENT -0.291617 0.005684 -51.31 <2e-16 ***
## HGB -0.277475 0.005780 -48.01 <2e-16 ***
## CLM_FROM_1year_cat 0.433463 0.005932 73.07 <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: 266319 on 289267 degrees of freedom
## Residual deviance: 209160 on 289262 degrees of freedom
## AIC: 209172
##
## Number of Fisher Scoring iterations: 5
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.93 |
1.90, 1.95 |
<0.001 |
| ALBUMIN |
0.49 |
0.49, 0.50 |
<0.001 |
| IRON_SAT_PERCENT |
0.75 |
0.74, 0.76 |
<0.001 |
| HGB |
0.76 |
0.75, 0.77 |
<0.001 |
| CLM_FROM_1year_cat |
1.54 |
1.52, 1.56 |
<0.001 |
## youden_index
## 0.4673941
model_14 threshold <- 0.3 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_1year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.518
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.665
## Area under the curve: 0.814
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 52975 6040
## died 6844 6458
##
## Accuracy : 0.8218
## 95% CI : (0.819, 0.8246)
## No Information Rate : 0.8272
## P-Value [Acc > NIR] : 0.9999
##
## Kappa : 0.3923
##
## Mcnemar's Test P-Value : 1.501e-12
##
## Sensitivity : 0.5167
## Specificity : 0.8856
## Pos Pred Value : 0.4855
## Neg Pred Value : 0.8977
## Prevalence : 0.1728
## Detection Rate : 0.0893
## Detection Prevalence : 0.1839
## Balanced Accuracy : 0.7012
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.064917 0.007020 -294.15 <2e-16 ***
## age 0.655467 0.006471 101.30 <2e-16 ***
## ALBUMIN -0.710977 0.005822 -122.11 <2e-16 ***
## IRON_SAT_PERCENT -0.291617 0.005684 -51.31 <2e-16 ***
## HGB -0.277475 0.005780 -48.01 <2e-16 ***
## CLM_FROM_1year_cat 0.433463 0.005932 73.07 <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: 266319 on 289267 degrees of freedom
## Residual deviance: 209160 on 289262 degrees of freedom
## AIC: 209172
##
## Number of Fisher Scoring iterations: 5
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.93 |
1.90, 1.95 |
<0.001 |
| ALBUMIN |
0.49 |
0.49, 0.50 |
<0.001 |
| IRON_SAT_PERCENT |
0.75 |
0.74, 0.76 |
<0.001 |
| HGB |
0.76 |
0.75, 0.77 |
<0.001 |
| CLM_FROM_1year_cat |
1.54 |
1.52, 1.56 |
<0.001 |
## youden_index
## 0.4023109
model_14 threshold <- 0.4 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_1year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.518
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.665
## Area under the curve: 0.814
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 56260 7737
## died 3559 4761
##
## Accuracy : 0.8438
## 95% CI : (0.8411, 0.8464)
## No Information Rate : 0.8272
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.3704
##
## Mcnemar's Test P-Value : < 2.2e-16
##
## Sensitivity : 0.38094
## Specificity : 0.94050
## Pos Pred Value : 0.57224
## Neg Pred Value : 0.87910
## Prevalence : 0.17282
## Detection Rate : 0.06584
## Detection Prevalence : 0.11505
## Balanced Accuracy : 0.66072
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.064917 0.007020 -294.15 <2e-16 ***
## age 0.655467 0.006471 101.30 <2e-16 ***
## ALBUMIN -0.710977 0.005822 -122.11 <2e-16 ***
## IRON_SAT_PERCENT -0.291617 0.005684 -51.31 <2e-16 ***
## HGB -0.277475 0.005780 -48.01 <2e-16 ***
## CLM_FROM_1year_cat 0.433463 0.005932 73.07 <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: 266319 on 289267 degrees of freedom
## Residual deviance: 209160 on 289262 degrees of freedom
## AIC: 209172
##
## Number of Fisher Scoring iterations: 5
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.93 |
1.90, 1.95 |
<0.001 |
| ALBUMIN |
0.49 |
0.49, 0.50 |
<0.001 |
| IRON_SAT_PERCENT |
0.75 |
0.74, 0.76 |
<0.001 |
| HGB |
0.76 |
0.75, 0.77 |
<0.001 |
| CLM_FROM_1year_cat |
1.54 |
1.52, 1.56 |
<0.001 |
## youden_index
## 0.3214448