feature selection cohort without transplant
model_14 threshold <- 0.1 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_3year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.703
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.401
## Area under the curve: 0.7509
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 2565 258
## died 38188 31306
##
## Accuracy : 0.4684
## 95% CI : (0.4647, 0.472)
## No Information Rate : 0.5635
## P-Value [Acc > NIR] : 1
##
## Kappa : 0.0482
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.99183
## Specificity : 0.06294
## Pos Pred Value : 0.45048
## Neg Pred Value : 0.90861
## Prevalence : 0.43647
## Detection Rate : 0.43290
## Detection Prevalence : 0.96096
## Balanced Accuracy : 0.52738
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.323447 0.004199 -77.04 <2e-16 ***
## age 0.634053 0.004599 137.88 <2e-16 ***
## ALBUMIN -0.577922 0.004785 -120.77 <2e-16 ***
## IRON_SAT_PERCENT -0.202689 0.004294 -47.20 <2e-16 ***
## HGB -0.184980 0.004550 -40.65 <2e-16 ***
## CLM_FROM_3year_cat 0.283274 0.004280 66.19 <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: 395983 on 289267 degrees of freedom
## Residual deviance: 337338 on 289262 degrees of freedom
## AIC: 337350
##
## Number of Fisher Scoring iterations: 4
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.89 |
1.87, 1.90 |
<0.001 |
| ALBUMIN |
0.56 |
0.56, 0.57 |
<0.001 |
| IRON_SAT_PERCENT |
0.82 |
0.81, 0.82 |
<0.001 |
| HGB |
0.83 |
0.82, 0.84 |
<0.001 |
| CLM_FROM_3year_cat |
1.33 |
1.32, 1.34 |
<0.001 |
## youden_index
## 0.05476628
model_14 threshold <- 0.2 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_3year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.703
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.401
## Area under the curve: 0.7509
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 9718 1592
## died 31035 29972
##
## Accuracy : 0.5488
## 95% CI : (0.5452, 0.5525)
## No Information Rate : 0.5635
## P-Value [Acc > NIR] : 1
##
## Kappa : 0.1701
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.9496
## Specificity : 0.2385
## Pos Pred Value : 0.4913
## Neg Pred Value : 0.8592
## Prevalence : 0.4365
## Detection Rate : 0.4145
## Detection Prevalence : 0.8436
## Balanced Accuracy : 0.5940
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.323447 0.004199 -77.04 <2e-16 ***
## age 0.634053 0.004599 137.88 <2e-16 ***
## ALBUMIN -0.577922 0.004785 -120.77 <2e-16 ***
## IRON_SAT_PERCENT -0.202689 0.004294 -47.20 <2e-16 ***
## HGB -0.184980 0.004550 -40.65 <2e-16 ***
## CLM_FROM_3year_cat 0.283274 0.004280 66.19 <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: 395983 on 289267 degrees of freedom
## Residual deviance: 337338 on 289262 degrees of freedom
## AIC: 337350
##
## Number of Fisher Scoring iterations: 4
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.89 |
1.87, 1.90 |
<0.001 |
| ALBUMIN |
0.56 |
0.56, 0.57 |
<0.001 |
| IRON_SAT_PERCENT |
0.82 |
0.81, 0.82 |
<0.001 |
| HGB |
0.83 |
0.82, 0.84 |
<0.001 |
| CLM_FROM_3year_cat |
1.33 |
1.32, 1.34 |
<0.001 |
## youden_index
## 0.1880238
model_14 threshold <- 0.3 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_3year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.703
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.401
## Area under the curve: 0.7509
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 17947 4384
## died 22806 27180
##
## Accuracy : 0.624
## 95% CI : (0.6205, 0.6275)
## No Information Rate : 0.5635
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.2829
##
## Mcnemar's Test P-Value : < 2.2e-16
##
## Sensitivity : 0.8611
## Specificity : 0.4404
## Pos Pred Value : 0.5438
## Neg Pred Value : 0.8037
## Prevalence : 0.4365
## Detection Rate : 0.3758
## Detection Prevalence : 0.6912
## Balanced Accuracy : 0.6507
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.323447 0.004199 -77.04 <2e-16 ***
## age 0.634053 0.004599 137.88 <2e-16 ***
## ALBUMIN -0.577922 0.004785 -120.77 <2e-16 ***
## IRON_SAT_PERCENT -0.202689 0.004294 -47.20 <2e-16 ***
## HGB -0.184980 0.004550 -40.65 <2e-16 ***
## CLM_FROM_3year_cat 0.283274 0.004280 66.19 <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: 395983 on 289267 degrees of freedom
## Residual deviance: 337338 on 289262 degrees of freedom
## AIC: 337350
##
## Number of Fisher Scoring iterations: 4
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.89 |
1.87, 1.90 |
<0.001 |
| ALBUMIN |
0.56 |
0.56, 0.57 |
<0.001 |
| IRON_SAT_PERCENT |
0.82 |
0.81, 0.82 |
<0.001 |
| HGB |
0.83 |
0.82, 0.84 |
<0.001 |
| CLM_FROM_3year_cat |
1.33 |
1.32, 1.34 |
<0.001 |
## youden_index
## 0.3014923
model_14 threshold <- 0.4 : age ALBUMIN IRON_SAT_PERCENT HGB
CLM_FROM_3year_cat
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 pr_auc binary 0.703
## # A tibble: 1 × 3
## .metric .estimator .estimate
## <chr> <chr> <dbl>
## 1 brier_class binary 0.401
## Area under the curve: 0.7509
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 25554 8442
## died 15199 23122
##
## Accuracy : 0.6731
## 95% CI : (0.6697, 0.6765)
## No Information Rate : 0.5635
## P-Value [Acc > NIR] : < 2.2e-16
##
## Kappa : 0.3511
##
## Mcnemar's Test P-Value : < 2.2e-16
##
## Sensitivity : 0.7325
## Specificity : 0.6270
## Pos Pred Value : 0.6034
## Neg Pred Value : 0.7517
## Prevalence : 0.4365
## Detection Rate : 0.3197
## Detection Prevalence : 0.5299
## Balanced Accuracy : 0.6798
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.323447 0.004199 -77.04 <2e-16 ***
## age 0.634053 0.004599 137.88 <2e-16 ***
## ALBUMIN -0.577922 0.004785 -120.77 <2e-16 ***
## IRON_SAT_PERCENT -0.202689 0.004294 -47.20 <2e-16 ***
## HGB -0.184980 0.004550 -40.65 <2e-16 ***
## CLM_FROM_3year_cat 0.283274 0.004280 66.19 <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: 395983 on 289267 degrees of freedom
## Residual deviance: 337338 on 289262 degrees of freedom
## AIC: 337350
##
## Number of Fisher Scoring iterations: 4
| Characteristic |
OR |
95% CI |
p-value |
| age |
1.89 |
1.87, 1.90 |
<0.001 |
| ALBUMIN |
0.56 |
0.56, 0.57 |
<0.001 |
| IRON_SAT_PERCENT |
0.82 |
0.81, 0.82 |
<0.001 |
| HGB |
0.83 |
0.82, 0.84 |
<0.001 |
| CLM_FROM_3year_cat |
1.33 |
1.32, 1.34 |
<0.001 |
## youden_index
## 0.3595893