## -------------------------------------------------------------------------
## Describe database[-c(1, 2)] (tbl_df, tbl, data.frame):
##
## data.frame: 423 obs. of 7 variables
##
## Nr ColName Class NAs Levels Label
## 1 Death factor . (2): 1-0, 2-1 Death
## 2 Age numeric . Age (years)
## 3 Neutrophiles numeric 3 (0.7%) Neutrophiles
## (#/μl)
## 4 Creatinine numeric . Creatinine
## (mg/dl)
## 5 Leucocytes numeric 2 (0.5%) Leucocytes
## (#/μl)
## 6 TI character . ICU stay
## 7 ICU factor . (2): 1-0, 2-1 ICU
##
##
## -------------------------------------------------------------------------
## 1 - Death (factor - dichotomous) :
## Death
##
##
## length n NAs unique
## 423 423 0 2
## 100.0% 0.0%
##
## freq perc lci.95 uci.95'
## 0 394 93.1% 90.3% 95.2%
## 1 29 6.9% 4.8% 9.7%
##
## ' 95%-CI Wilson
## -------------------------------------------------------------------------
## 2 - Age (numeric) :
## Age (years)
##
##
## length n NAs unique 0s mean meanCI
## 423 423 0 31 0 75.70 75.03
## 100.0% 0.0% 0.0% 76.38
##
## .05 .10 .25 median .75 .90 .95
## 66.00 67.00 70.00 76.00 80.00 86.00 88.00
##
## range sd vcoef mad IQR skew kurt
## 36.00 7.07 0.09 8.90 10.00 0.45 -0.45
##
## lowest : 65.0 (18), 66.0 (14), 67.0 (25), 68.0 (21), 69.0 (23)
## highest: 91.0, 92.0 (2), 93.0 (3), 94.0 (2), 101.0
## -------------------------------------------------------------------------
## 3 - Neutrophiles (numeric) :
## Neutrophiles (#/μl)
##
##
## length n NAs unique 0s mean meanCI
## 423 420 3 266 0 75.90 73.96
## 99.3% 0.7% 0.0% 77.84
##
## .05 .10 .25 median .75 .90 .95
## 49.99 57.29 65.57 76.85 85.00 91.00 92.61
##
## range sd vcoef mad IQR skew kurt
## 260.00 20.22 0.27 13.94 19.43 4.39 38.78
##
## lowest : 12.0, 20.76, 38.2, 38.4, 38.5
## highest: 97.0, 153.0, 227.0, 246.0, 272.0
## -------------------------------------------------------------------------
## 4 - Creatinine (numeric) :
## Creatinine (mg/dl)
##
##
## length n NAs unique 0s mean meanCI
## 423 423 0 155 3 1.21 1.13
## 100.0% 0.0% 0.7% 1.29
##
## .05 .10 .25 median .75 .90 .95
## 0.59 0.66 0.80 0.98 1.30 1.91 2.47
##
## range sd vcoef mad IQR skew kurt
## 7.41 0.84 0.69 0.33 0.50 3.73 18.43
##
## lowest : 0.0 (3), 0.28, 0.37, 0.4, 0.42
## highest: 5.4, 5.91, 6.15, 6.79, 7.41
## -------------------------------------------------------------------------
## 5 - Leucocytes (numeric) :
## Leucocytes (#/μl)
##
##
## length n NAs unique 0s mean meanCI
## 423 421 2 352 0 10.62 9.41
## 99.5% 0.5% 0.0% 11.82
##
## .05 .10 .25 median .75 .90 .95
## 3.75 4.60 6.29 8.53 11.98 16.29 19.19
##
## range sd vcoef mad IQR skew kurt
## 177.06 12.56 1.18 3.85 5.69 9.46 109.43
##
## lowest : 1.1, 1.67, 2.04 (2), 2.15, 2.27
## highest: 42.64, 53.98, 92.0, 146.44, 178.16
## -------------------------------------------------------------------------
## 6 - TI (character - dichotomous) :
## ICU stay
##
##
## length n NAs unique
## 423 423 0 2
## 100.0% 0.0%
##
## freq perc lci.95 uci.95'
## no 391 92.4% 89.5% 94.6%
## yes 32 7.6% 5.4% 10.5%
##
## ' 95%-CI Wilson
## -------------------------------------------------------------------------
## 7 - ICU (factor - dichotomous) :
## ICU
##
##
## length n NAs unique
## 423 423 0 2
## 100.0% 0.0%
##
## freq perc lci.95 uci.95'
## 0 391 92.4% 89.5% 94.6%
## 1 32 7.6% 5.4% 10.5%
##
## ' 95%-CI Wilson
## -------------------------------------------------------------------------
## Age ~ Death
##
## Summary:
## n pairs: 423, valid: 423 (100.0%), missings: 0 (0.0%), groups: 2
##
##
## 0 1
## mean 75.536 77.966
## median 75.000 78.000
## sd 7.067 6.869
## IQR 10.000 11.000
## n 394 29
## np 93.144% 6.856%
## NAs 0 0
## 0s 0 0
##
## Kruskal-Wallis rank sum test:
## Kruskal-Wallis chi-squared = 3, df = 1, p-value = 0.07
## -------------------------------------------------------------------------
## Neutrophiles ~ Death
##
## Summary:
## n pairs: 423, valid: 420 (99.3%), missings: 3 (0.7%), groups: 2
##
##
## 0 1
## mean 75.332 83.610
## median 76.100 89.200
## sd 20.555 12.834
## IQR 19.150 12.900
## n 391 29
## np 93.095% 6.905%
## NAs 3 0
## 0s 0 0
##
## Kruskal-Wallis rank sum test:
## Kruskal-Wallis chi-squared = 19, df = 1, p-value = 0.00001
## -------------------------------------------------------------------------
## Creatinine ~ Death
##
## Summary:
## n pairs: 423, valid: 423 (100.0%), missings: 0 (0.0%), groups: 2
##
##
## 0 1
## mean 1.148 2.097
## median 0.970 1.560
## sd 0.680 1.817
## IQR 0.490 1.250
## n 394 29
## np 93.144% 6.856%
## NAs 0 0
## 0s 3 0
##
## Kruskal-Wallis rank sum test:
## Kruskal-Wallis chi-squared = 14, df = 1, p-value = 0.0002
## -------------------------------------------------------------------------
## Leucocytes ~ Death
##
## Summary:
## n pairs: 423, valid: 421 (99.5%), missings: 2 (0.5%), groups: 2
##
##
## 0 1
## mean 10.244 15.625
## median 8.225 13.700
## sd 12.681 9.635
## IQR 5.490 9.690
## n 392 29
## np 93.112% 6.888%
## NAs 2 0
## 0s 0 0
##
## Kruskal-Wallis rank sum test:
## Kruskal-Wallis chi-squared = 22, df = 1, p-value = 0.000003
## -------------------------------------------------------------------------
## TI ~ Death
##
##
## Summary:
## n: 423, rows: 2, columns: 2
##
## Pearson's Chi-squared test (cont. adj):
## X-squared = 141, df = 1, p-value <0.0000000000000002
## Fisher's exact test p-value <0.0000000000000002
## McNemar's chi-squared = 0.2, df = 1, p-value = 0.7
##
## Warning message:
## Exp. counts < 5: Chi-squared approx. may be incorrect!!
##
##
## estimate lwr.ci upr.ci'
##
## odds ratio 55.6846 21.6563 143.1814
## rel. risk (col1) 2.3986 1.5773 3.6475
## rel. risk (col2) 0.0431 0.0219 0.0847
##
##
## Phi-Coefficient 0.595
## Contingency Coeff. 0.511
## Cramer's V 0.595
##
##
## Death 0 1 Sum
## TI
##
## no freq 381 10 391
## perc 90.1% 2.4% 92.4%
## p.row 97.4% 2.6% .
## p.col 96.7% 34.5% .
##
## yes freq 13 19 32
## perc 3.1% 4.5% 7.6%
## p.row 40.6% 59.4% .
## p.col 3.3% 65.5% .
##
## Sum freq 394 29 423
## perc 93.1% 6.9% 100.0%
## p.row . . .
## p.col . . .
##
##
## ----------
## ' 95% conf. level
## -------------------------------------------------------------------------
## ICU ~ Death
##
##
## Summary:
## n: 423, rows: 2, columns: 2
##
## Pearson's Chi-squared test (cont. adj):
## X-squared = 141, df = 1, p-value <0.0000000000000002
## Fisher's exact test p-value <0.0000000000000002
## McNemar's chi-squared = 0.2, df = 1, p-value = 0.7
##
## Warning message:
## Exp. counts < 5: Chi-squared approx. may be incorrect!!
##
##
## estimate lwr.ci upr.ci'
##
## odds ratio 55.6846 21.6563 143.1814
## rel. risk (col1) 2.3986 1.5773 3.6475
## rel. risk (col2) 0.0431 0.0219 0.0847
##
##
## Phi-Coefficient 0.595
## Contingency Coeff. 0.511
## Cramer's V 0.595
##
##
## Death 0 1 Sum
## ICU
##
## 0 freq 381 10 391
## perc 90.1% 2.4% 92.4%
## p.row 97.4% 2.6% .
## p.col 96.7% 34.5% .
##
## 1 freq 13 19 32
## perc 3.1% 4.5% 7.6%
## p.row 40.6% 59.4% .
## p.col 3.3% 65.5% .
##
## Sum freq 394 29 423
## perc 93.1% 6.9% 100.0%
## p.row . . .
## p.col . . .
##
##
## ----------
## ' 95% conf. level
Dependent: Death | alive (0) | dead (1) | OR | OR-adj |
Neutrophiles (#/μl) | 75.3 (20.6) | 83.6 (12.8) | 1.01 (1.00-1.03, p=0.050) | 1.01 (0.98-1.02, p=0.419) |
Creatinine (mg/dl) | 1.1 (0.7) | 2.1 (1.8) | 1.97 (1.47-2.68, p<0.001) | 1.60 (1.04-2.47, p=0.036) |
Leucocytes (#/μl) | 10.2 (12.7) | 15.6 (9.6) | 1.02 (1.00-1.03, p=0.064) | 1.01 (0.96-1.04, p=0.529) |
Age (years) | 75.5 (7.1) | 78.0 (6.9) | 1.05 (0.99-1.10, p=0.076) | 0.98 (0.91-1.05, p=0.516) |
ICU stay: no | 381 (96.7) | 10 (34.5) | - | - |
- yes | 13 (3.3) | 19 (65.5) | 55.68 (22.32-149.41, p<0.001) | 43.49 (15.74-132.11, p<0.001) |
Number in dataframe = 423, Number in model = 420, Missing = 3, AIC = 142.1, C-statistic = 0.84, H&L = Chi-sq(8) 8.16 (p=0.418) | ||||
Values are Means (SD), # (%), or OR (95% CI, p-values). |
Full | Full (Box-Cox) | Only creatinine | Only creatinine (Box-Cox) | |||||
---|---|---|---|---|---|---|---|---|
Predictors | Odds Ratios | p | Odds Ratios | p | Odds Ratios | p | Odds Ratios | p |
(Intercept) | 0.04 (0.00 – 6.70) | 0.216 | Inf (Inf – Inf) | <0.001 | 0.03 (0.01 – 0.05) | <0.001 | 0.05 (0.03 – 0.08) | <0.001 |
Neutrophiles(#/μl) | 1.01 (0.99 – 1.03) | 0.419 | 2.66 (0.14 – 51.06) | 0.516 | ||||
Creatinine(mg/dl) | 1.60 (1.03 – 2.49) | 0.036 | 2.22 (0.94 – 5.25) | 0.070 | 1.97 (1.46 – 2.64) | <0.001 | 4.43 (2.28 – 8.62) | <0.001 |
Leucocytes(#/μl) | 1.01 (0.98 – 1.05) | 0.529 | 4.86 (0.83 – 28.52) | 0.080 | ||||
Age(years) | 0.98 (0.91 – 1.05) | 0.516 | 0.00 (0.00 – 0.00) | <0.001 | ||||
TIyes | 43.49 (15.17 – 124.68) | <0.001 | ||||||
ICU 1 | 34.30 (11.77 – 99.99) | <0.001 | ||||||
Observations | 420 | 420 | 423 | 423 | ||||
Tjur’s R2 | 0.394 | 0.402 | 0.086 | 0.072 | ||||
Deviance | 130.129 | 127.380 | 191.816 | 192.891 | ||||
AIC | 142.129 | 139.380 | 195.816 | 196.891 | ||||
log-Likelihood | -65.064 | -63.690 | -95.908 | -96.446 |