Table 1 without transplant no missing, used for analysis
table1 <- final_cohort_1_no_missing %>%
tbl_summary(
by = group,
# first row: mean (SD), second row: median [IQR]
statistic = all_continuous() ~ "{mean} ({sd})",
missing_text = "Missing"
) %>%add_p()
## The following errors were returned during `add_p()`:
## ✖ For variable `HEMOSESSIONS_1year` (`group`) and "estimate", "p.value",
## "conf.low", and "conf.high" statistics: FEXACT error 40. Out of workspace.
## ✖ For variable `HEMOSESSIONS_3year` (`group`) and "estimate", "p.value",
## "conf.low", and "conf.high" statistics: FEXACT error 40. Out of workspace.
var1 <- names(final_cohort_1_no_missing)
var1_num <- names(final_cohort_1_no_missing)[sapply(final_cohort_1_no_missing, is.numeric)]
var1_cat <- setdiff(var1,var1_num)
#create table one for expourse response#
T1 <- CreateTableOne(vars = var1,strata ="group" ,includeNA = F,addOverall = TRUE,data = final_cohort_1_no_missing, factorVars = var1_cat)
#print table one
T1_print <- print(T1,showAllLevels = T,missing = T,quote = FALSE, noSpaces = TRUE, printToggle = FALSE)
#save
write.csv(T1_print, file = "/Users/to909/Desktop/Annie final/Table1.csv")
# final_cohort_1_no_missing %>%
# tbl_summary(
# by = transplant_dec_v2,
# # first row: mean (SD), second row: median [IQR]
# statistic = all_continuous() ~ "{median} [{p25}, {p75}]",
# missing_text = "Missing"
# ) %>% add_p()
feature selection cohort without transplant
1 year
Model1 : age sex_cat
## Area under the curve: 0.6675
## Confusion Matrix and Statistics
##
## Reference
## Prediction alive died
## alive 41613 5839
## died 18206 6659
##
## Accuracy : 0.6675
## 95% CI : (0.6641, 0.6709)
## No Information Rate : 0.8272
## P-Value [Acc > NIR] : 1
##
## Kappa : 0.1642
##
## Mcnemar's Test P-Value : <2e-16
##
## Sensitivity : 0.53281
## Specificity : 0.69565
## Pos Pred Value : 0.26781
## Neg Pred Value : 0.87695
## Prevalence : 0.17282
## Detection Rate : 0.09208
## Detection Prevalence : 0.34383
## Balanced Accuracy : 0.61423
##
## 'Positive' Class : died
##
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.731571 0.008106 -213.616 < 2e-16 ***
## age 0.658348 0.005949 110.658 < 2e-16 ***
## sex_catMale 0.060672 0.010202 5.947 2.73e-09 ***
## ---
## 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: 252119 on 289265 degrees of freedom
## AIC: 252125
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.93 |
1.91, 1.95 |
<0.001 |
sex_catMale |
1.06 |
1.04, 1.08 |
<0.001 |
Model2 : age sex_cat ALBUMIN
## Area under the curve: 0.7783
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.029104 0.009102 -222.92 <2e-16 ***
## age 0.647045 0.006269 103.21 <2e-16 ***
## sex_catMale 0.181583 0.010951 16.58 <2e-16 ***
## ALBUMIN -0.882147 0.005451 -161.85 <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: 221884 on 289264 degrees of freedom
## AIC: 221892
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.91 |
1.89, 1.93 |
<0.001 |
sex_catMale |
1.20 |
1.17, 1.23 |
<0.001 |
ALBUMIN |
0.41 |
0.41, 0.42 |
<0.001 |
Model_3 : age sex_cat ALBUMIN COMO_CHF
## Area under the curve: 0.7832
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.197386 0.010203 -215.37 <2e-16 ***
## age 0.625222 0.006317 98.97 <2e-16 ***
## sex_catMale 0.185548 0.010990 16.88 <2e-16 ***
## ALBUMIN -0.878988 0.005474 -160.56 <2e-16 ***
## COMO_CHFY 0.449989 0.011038 40.77 <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: 220241 on 289263 degrees of freedom
## AIC: 220251
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.87 |
1.85, 1.89 |
<0.001 |
sex_catMale |
1.20 |
1.18, 1.23 |
<0.001 |
ALBUMIN |
0.42 |
0.41, 0.42 |
<0.001 |
COMO_CHFY |
1.57 |
1.53, 1.60 |
<0.001 |
model_4 : age sex_cat ALBUMIN COMO_CHF COMO_DM_INS
## Area under the curve: 0.7833
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.165981 0.011364 -190.60 < 2e-16 ***
## age 0.618061 0.006411 96.40 < 2e-16 ***
## sex_catMale 0.183078 0.010999 16.64 < 2e-16 ***
## ALBUMIN -0.880710 0.005482 -160.65 < 2e-16 ***
## COMO_CHFY 0.457237 0.011104 41.18 < 2e-16 ***
## COMO_DM_INSY -0.068997 0.011165 -6.18 6.43e-10 ***
## ---
## 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: 220203 on 289262 degrees of freedom
## AIC: 220215
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.86 |
1.83, 1.88 |
<0.001 |
sex_catMale |
1.20 |
1.18, 1.23 |
<0.001 |
ALBUMIN |
0.41 |
0.41, 0.42 |
<0.001 |
COMO_CHFY |
1.58 |
1.55, 1.61 |
<0.001 |
COMO_DM_INSY |
0.93 |
0.91, 0.95 |
<0.001 |
model_5 : age sex_cat ALBUMIN COMO_CHF COMO_DM_INS COMO_HTN
## Area under the curve: 0.7843
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.918606 0.017960 -106.824 < 2e-16 ***
## age 0.620401 0.006419 96.654 < 2e-16 ***
## sex_catMale 0.179157 0.011008 16.275 < 2e-16 ***
## ALBUMIN -0.876448 0.005487 -159.742 < 2e-16 ***
## COMO_CHFY 0.459456 0.011114 41.341 < 2e-16 ***
## COMO_DM_INSY -0.063166 0.011176 -5.652 1.59e-08 ***
## COMO_HTNY -0.282824 0.016109 -17.557 < 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: 219903 on 289261 degrees of freedom
## AIC: 219917
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.86 |
1.84, 1.88 |
<0.001 |
sex_catMale |
1.20 |
1.17, 1.22 |
<0.001 |
ALBUMIN |
0.42 |
0.41, 0.42 |
<0.001 |
COMO_CHFY |
1.58 |
1.55, 1.62 |
<0.001 |
COMO_DM_INSY |
0.94 |
0.92, 0.96 |
<0.001 |
COMO_HTNY |
0.75 |
0.73, 0.78 |
<0.001 |
model_6 : age sex_cat ALBUMIN COMO_CHF COMO_DM_INS COMO_HTN
CLM_FROM_1year_cat
## Area under the curve: 0.8051
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.006086 0.018322 -109.491 < 2e-16 ***
## age 0.596321 0.006494 91.833 < 2e-16 ***
## sex_catMale 0.204939 0.011168 18.351 < 2e-16 ***
## ALBUMIN -0.812270 0.005568 -145.871 < 2e-16 ***
## COMO_CHFY 0.412920 0.011281 36.604 < 2e-16 ***
## COMO_DM_INSY -0.074979 0.011337 -6.614 3.75e-11 ***
## COMO_HTNY -0.266871 0.016336 -16.336 < 2e-16 ***
## CLM_FROM_1year_cat 0.464959 0.005870 79.212 < 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: 213297 on 289260 degrees of freedom
## AIC: 213313
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.82 |
1.79, 1.84 |
<0.001 |
sex_catMale |
1.23 |
1.20, 1.25 |
<0.001 |
ALBUMIN |
0.44 |
0.44, 0.45 |
<0.001 |
COMO_CHFY |
1.51 |
1.48, 1.55 |
<0.001 |
COMO_DM_INSY |
0.93 |
0.91, 0.95 |
<0.001 |
COMO_HTNY |
0.77 |
0.74, 0.79 |
<0.001 |
CLM_FROM_1year_cat |
1.59 |
1.57, 1.61 |
<0.001 |
model_ : age sex_cat ALBUMIN COMO_CHF COMO_DM_INS COMO_HTN
CLM_FROM_1year_cat ICU_DAYS_1year_cat
model_7 : age ALBUMIN COMO_CHF
## Area under the curve: 0.7828
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.089669 0.007811 -267.54 <2e-16 ***
## age 0.623609 0.006312 98.79 <2e-16 ***
## ALBUMIN -0.873782 0.005461 -159.99 <2e-16 ***
## COMO_CHFY 0.448184 0.011028 40.64 <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: 220528 on 289264 degrees of freedom
## AIC: 220536
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.87 |
1.84, 1.89 |
<0.001 |
ALBUMIN |
0.42 |
0.41, 0.42 |
<0.001 |
COMO_CHFY |
1.57 |
1.53, 1.60 |
<0.001 |
model_8 : age ALBUMIN COMO_CHF IRON_SAT_PERCENT
## Area under the curve: 0.7935
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.119267 0.007961 -266.19 <2e-16 ***
## age 0.645154 0.006395 100.88 <2e-16 ***
## ALBUMIN -0.855924 0.005513 -155.25 <2e-16 ***
## COMO_CHFY 0.400243 0.011152 35.89 <2e-16 ***
## IRON_SAT_PERCENT -0.351764 0.005595 -62.87 <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: 216393 on 289263 degrees of freedom
## AIC: 216403
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.91 |
1.88, 1.93 |
<0.001 |
ALBUMIN |
0.42 |
0.42, 0.43 |
<0.001 |
COMO_CHFY |
1.49 |
1.46, 1.53 |
<0.001 |
IRON_SAT_PERCENT |
0.70 |
0.70, 0.71 |
<0.001 |
model_9 : age ALBUMIN COMO_CHF IRON_SAT_PERCENT HGB
## Area under the curve: 0.8001
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.146100 0.008064 -266.12 <2e-16 ***
## age 0.660500 0.006456 102.31 <2e-16 ***
## ALBUMIN -0.756250 0.005775 -130.95 <2e-16 ***
## COMO_CHFY 0.420854 0.011253 37.40 <2e-16 ***
## IRON_SAT_PERCENT -0.296613 0.005655 -52.46 <2e-16 ***
## HGB -0.314519 0.005760 -54.61 <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: 213358 on 289262 degrees of freedom
## AIC: 213370
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.94 |
1.91, 1.96 |
<0.001 |
ALBUMIN |
0.47 |
0.46, 0.47 |
<0.001 |
COMO_CHFY |
1.52 |
1.49, 1.56 |
<0.001 |
IRON_SAT_PERCENT |
0.74 |
0.74, 0.75 |
<0.001 |
HGB |
0.73 |
0.72, 0.74 |
<0.001 |
model_8 : age ALBUMIN COMO_CHF IRON_SAT_PERCENT
## Area under the curve: 0.7935
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.119267 0.007961 -266.19 <2e-16 ***
## age 0.645154 0.006395 100.88 <2e-16 ***
## ALBUMIN -0.855924 0.005513 -155.25 <2e-16 ***
## COMO_CHFY 0.400243 0.011152 35.89 <2e-16 ***
## IRON_SAT_PERCENT -0.351764 0.005595 -62.87 <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: 216393 on 289263 degrees of freedom
## AIC: 216403
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.91 |
1.88, 1.93 |
<0.001 |
ALBUMIN |
0.42 |
0.42, 0.43 |
<0.001 |
COMO_CHFY |
1.49 |
1.46, 1.53 |
<0.001 |
IRON_SAT_PERCENT |
0.70 |
0.70, 0.71 |
<0.001 |
model_10 : age ALBUMIN COMO_CHF IRON_SAT_PERCENT HGB
CLM_FROM_1year_cat
## Area under the curve: 0.8166
##
## Call:
## NULL
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.202975 0.008353 -263.75 <2e-16 ***
## age 0.636937 0.006513 97.79 <2e-16 ***
## ALBUMIN -0.708801 0.005840 -121.37 <2e-16 ***
## COMO_CHFY 0.379328 0.011392 33.30 <2e-16 ***
## IRON_SAT_PERCENT -0.278749 0.005704 -48.87 <2e-16 ***
## HGB -0.284210 0.005794 -49.06 <2e-16 ***
## CLM_FROM_1year_cat 0.423964 0.005951 71.24 <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: 208062 on 289261 degrees of freedom
## AIC: 208076
##
## Number of Fisher Scoring iterations: 5
Characteristic |
OR |
95% CI |
p-value |
age |
1.89 |
1.87, 1.92 |
<0.001 |
ALBUMIN |
0.49 |
0.49, 0.50 |
<0.001 |
COMO_CHFY |
1.46 |
1.43, 1.49 |
<0.001 |
IRON_SAT_PERCENT |
0.76 |
0.75, 0.77 |
<0.001 |
HGB |
0.75 |
0.74, 0.76 |
<0.001 |
CLM_FROM_1year_cat |
1.53 |
1.51, 1.55 |
<0.001 |