Backward selection based on the BIC for all patients with
log_na_admit creatinine_admission log_inr_admit log_tb_admit
covariates_lab <- setdiff(names(ckd_data), c("time_90days","status_90days"))
covariates_lab <- covariates_lab[!covariates_lab %in% c("MELD_Na_baseline")]
new_covariates_lab <- paste(covariates_lab, collapse='+')
lab_function_new <- as.formula(paste0("Hist(time_90days, status_90days) ~ ",new_covariates_lab))
BIC_no_meld <- pec::selectFGR(lab_function_new, cause = 1, data = ckd_data,rule = "BIC", direction = "backward")
BIC_no_meld$fit
##
## Right-censored response of a competing.risks model
##
## No.Observations: 1949
##
## Pattern:
##
## Cause event right.censored
## 1 721 0
## 2 118 0
## unknown 0 1110
##
##
## Fine-Gray model: analysis of cause 1
##
## Competing Risks Regression
##
## Call:
## riskRegression::FGR(formula = Hist(time_90days, status_90days) ~
## age_admission + hispanic_race1 + liver_transplant_listed1 +
## final_type_of_aki2 + final_type_of_aki3 + final_type_of_aki4 +
## final_type_of_aki5 + sitejacksonville + sitekentukey +
## sitemgh + siterochester + siteusc + siteyale + etiology_cirrhosis2 +
## etiology_cirrhosis4 + etiology_cirrhosis5 + etiology_cirrhosis6 +
## etiology_cirrhosis7 + albumin_given_admission1 + lactulose1 +
## rifaximin1 + beta_blockers1 + encephalopathy_admission1 +
## hcc_admission1 + alcoholic_hepatitis_admission1 + log_co2_admit +
## log_alt_admit + log_tb_admit + log_alb_admit + log_inr_admit +
## log_wbc_admit + log_plt_admit + sbp_admission, data = data,
## cause = cause)
##
## coef exp(coef) se(coef) z p-value
## age_admission 0.01967 1.020 0.0040 4.92 8.8e-07
## hispanic_race1 -0.30113 0.740 0.1551 -1.94 5.2e-02
## liver_transplant_listed1 -1.48610 0.226 0.1621 -9.17 0.0e+00
## final_type_of_aki2 0.91430 2.495 0.1307 7.00 2.6e-12
## final_type_of_aki3 0.92650 2.526 0.0966 9.60 0.0e+00
## final_type_of_aki4 0.34498 1.412 0.1984 1.74 8.2e-02
## final_type_of_aki5 0.87545 2.400 0.1511 5.80 6.8e-09
## sitejacksonville -0.77322 0.462 0.2676 -2.89 3.9e-03
## sitekentukey 0.28848 1.334 0.1449 1.99 4.7e-02
## sitemgh -0.28861 0.749 0.1174 -2.46 1.4e-02
## siterochester -0.41614 0.660 0.1385 -3.00 2.7e-03
## siteusc -0.46441 0.629 0.2648 -1.75 7.9e-02
## siteyale -0.39158 0.676 0.1380 -2.84 4.5e-03
## etiology_cirrhosis2 0.28147 1.325 0.1316 2.14 3.2e-02
## etiology_cirrhosis4 0.69581 2.005 0.2807 2.48 1.3e-02
## etiology_cirrhosis5 0.21784 1.243 0.1360 1.60 1.1e-01
## etiology_cirrhosis6 0.37072 1.449 0.1481 2.50 1.2e-02
## etiology_cirrhosis7 0.42700 1.533 0.1341 3.18 1.5e-03
## albumin_given_admission1 0.28522 1.330 0.1118 2.55 1.1e-02
## lactulose1 0.15201 1.164 0.0932 1.63 1.0e-01
## rifaximin1 -0.17739 0.837 0.0969 -1.83 6.7e-02
## beta_blockers1 -0.21299 0.808 0.0829 -2.57 1.0e-02
## encephalopathy_admission1 0.41881 1.520 0.0970 4.32 1.6e-05
## hcc_admission1 0.50300 1.654 0.1120 4.49 7.1e-06
## alcoholic_hepatitis_admission1 -0.21267 0.808 0.1187 -1.79 7.3e-02
## log_co2_admit -0.54464 0.580 0.1493 -3.65 2.6e-04
## log_alt_admit 0.09039 1.095 0.0476 1.90 5.7e-02
## log_tb_admit 0.25826 1.295 0.0449 5.76 8.6e-09
## log_alb_admit -0.65015 0.522 0.1578 -4.12 3.8e-05
## log_inr_admit 0.54067 1.717 0.1068 5.06 4.2e-07
## log_wbc_admit 0.18522 1.203 0.0783 2.37 1.8e-02
## log_plt_admit -0.15258 0.858 0.0730 -2.09 3.7e-02
## sbp_admission -0.00737 0.993 0.0024 -3.07 2.2e-03
##
## exp(coef) exp(-coef) 2.5% 97.5%
## age_admission 1.020 0.981 1.012 1.028
## hispanic_race1 0.740 1.351 0.546 1.003
## liver_transplant_listed1 0.226 4.420 0.165 0.311
## final_type_of_aki2 2.495 0.401 1.931 3.223
## final_type_of_aki3 2.526 0.396 2.090 3.052
## final_type_of_aki4 1.412 0.708 0.957 2.083
## final_type_of_aki5 2.400 0.417 1.785 3.227
## sitejacksonville 0.462 2.167 0.273 0.780
## sitekentukey 1.334 0.749 1.004 1.773
## sitemgh 0.749 1.335 0.595 0.943
## siterochester 0.660 1.516 0.503 0.865
## siteusc 0.629 1.591 0.374 1.056
## siteyale 0.676 1.479 0.516 0.886
## etiology_cirrhosis2 1.325 0.755 1.024 1.715
## etiology_cirrhosis4 2.005 0.499 1.157 3.476
## etiology_cirrhosis5 1.243 0.804 0.953 1.623
## etiology_cirrhosis6 1.449 0.690 1.084 1.937
## etiology_cirrhosis7 1.533 0.652 1.178 1.993
## albumin_given_admission1 1.330 0.752 1.068 1.656
## lactulose1 1.164 0.859 0.970 1.397
## rifaximin1 0.837 1.194 0.693 1.013
## beta_blockers1 0.808 1.237 0.687 0.951
## encephalopathy_admission1 1.520 0.658 1.257 1.839
## hcc_admission1 1.654 0.605 1.328 2.060
## alcoholic_hepatitis_admission1 0.808 1.237 0.641 1.020
## log_co2_admit 0.580 1.724 0.433 0.777
## log_alt_admit 1.095 0.914 0.997 1.202
## log_tb_admit 1.295 0.772 1.186 1.414
## log_alb_admit 0.522 1.916 0.383 0.711
## log_inr_admit 1.717 0.582 1.393 2.117
## log_wbc_admit 1.203 0.831 1.032 1.403
## log_plt_admit 0.858 1.165 0.744 0.990
## sbp_admission 0.993 1.007 0.988 0.997
##
## Num. cases = 1949
## Pseudo Log-likelihood = -4873
## Pseudo likelihood ratio test = 768 on 33 df,
##
## Convergence: TRUE
Backward selection based on the BIC forcing ckd for all patients
with log_na_admit creatinine_admission log_inr_admit log_tb_admit
BIC_no_meld_ckd <- pec::selectFGR(lab_function_new, cause = 1, data = ckd_data,rule = "BIC",scope.min=~ckd1, direction = "backward")
BIC_no_meld_ckd$fit
##
## Right-censored response of a competing.risks model
##
## No.Observations: 1949
##
## Pattern:
##
## Cause event right.censored
## 1 721 0
## 2 118 0
## unknown 0 1110
##
##
## Fine-Gray model: analysis of cause 1
##
## Competing Risks Regression
##
## Call:
## riskRegression::FGR(formula = Hist(time_90days, status_90days) ~
## age_admission + hispanic_race1 + liver_transplant_listed1 +
## final_type_of_aki2 + final_type_of_aki3 + final_type_of_aki4 +
## final_type_of_aki5 + sitejacksonville + sitekentukey +
## sitemgh + siterochester + siteusc + siteyale + etiology_cirrhosis2 +
## etiology_cirrhosis4 + etiology_cirrhosis5 + etiology_cirrhosis6 +
## etiology_cirrhosis7 + albumin_given_admission1 + lactulose1 +
## rifaximin1 + beta_blockers1 + ckd1 + encephalopathy_admission1 +
## hcc_admission1 + alcoholic_hepatitis_admission1 + log_co2_admit +
## log_alt_admit + log_tb_admit + log_alb_admit + log_inr_admit +
## log_wbc_admit + log_plt_admit + sbp_admission, data = data,
## cause = cause)
##
## coef exp(coef) se(coef) z p-value
## age_admission 0.02011 1.020 0.00409 4.920 8.7e-07
## hispanic_race1 -0.30251 0.739 0.15514 -1.950 5.1e-02
## liver_transplant_listed1 -1.48210 0.227 0.16205 -9.146 0.0e+00
## final_type_of_aki2 0.92535 2.523 0.13277 6.969 3.2e-12
## final_type_of_aki3 0.93388 2.544 0.09740 9.588 0.0e+00
## final_type_of_aki4 0.34897 1.418 0.19869 1.756 7.9e-02
## final_type_of_aki5 0.88328 2.419 0.15168 5.823 5.8e-09
## sitejacksonville -0.77716 0.460 0.26725 -2.908 3.6e-03
## sitekentukey 0.29934 1.349 0.14586 2.052 4.0e-02
## sitemgh -0.28232 0.754 0.11766 -2.400 1.6e-02
## siterochester -0.41374 0.661 0.13888 -2.979 2.9e-03
## siteusc -0.47215 0.624 0.26503 -1.781 7.5e-02
## siteyale -0.39143 0.676 0.13784 -2.840 4.5e-03
## etiology_cirrhosis2 0.28120 1.325 0.13166 2.136 3.3e-02
## etiology_cirrhosis4 0.70462 2.023 0.28282 2.491 1.3e-02
## etiology_cirrhosis5 0.21319 1.238 0.13644 1.563 1.2e-01
## etiology_cirrhosis6 0.37153 1.450 0.14788 2.512 1.2e-02
## etiology_cirrhosis7 0.42498 1.530 0.13401 3.171 1.5e-03
## albumin_given_admission1 0.27627 1.318 0.11249 2.456 1.4e-02
## lactulose1 0.15560 1.168 0.09313 1.671 9.5e-02
## rifaximin1 -0.17066 0.843 0.09726 -1.755 7.9e-02
## beta_blockers1 -0.21100 0.810 0.08311 -2.539 1.1e-02
## ckd1 -0.07332 0.929 0.09998 -0.733 4.6e-01
## encephalopathy_admission1 0.41483 1.514 0.09714 4.270 2.0e-05
## hcc_admission1 0.49803 1.645 0.11252 4.426 9.6e-06
## alcoholic_hepatitis_admission1 -0.20959 0.811 0.11896 -1.762 7.8e-02
## log_co2_admit -0.54581 0.579 0.14888 -3.666 2.5e-04
## log_alt_admit 0.08832 1.092 0.04772 1.851 6.4e-02
## log_tb_admit 0.25442 1.290 0.04538 5.606 2.1e-08
## log_alb_admit -0.64454 0.525 0.15834 -4.071 4.7e-05
## log_inr_admit 0.53929 1.715 0.10705 5.038 4.7e-07
## log_wbc_admit 0.18135 1.199 0.07820 2.319 2.0e-02
## log_plt_admit -0.15323 0.858 0.07312 -2.096 3.6e-02
## sbp_admission -0.00722 0.993 0.00241 -2.992 2.8e-03
##
## exp(coef) exp(-coef) 2.5% 97.5%
## age_admission 1.020 0.980 1.012 1.029
## hispanic_race1 0.739 1.353 0.545 1.002
## liver_transplant_listed1 0.227 4.402 0.165 0.312
## final_type_of_aki2 2.523 0.396 1.945 3.273
## final_type_of_aki3 2.544 0.393 2.102 3.080
## final_type_of_aki4 1.418 0.705 0.960 2.093
## final_type_of_aki5 2.419 0.413 1.797 3.256
## sitejacksonville 0.460 2.175 0.272 0.776
## sitekentukey 1.349 0.741 1.014 1.795
## sitemgh 0.754 1.326 0.599 0.950
## siterochester 0.661 1.512 0.504 0.868
## siteusc 0.624 1.603 0.371 1.048
## siteyale 0.676 1.479 0.516 0.886
## etiology_cirrhosis2 1.325 0.755 1.023 1.715
## etiology_cirrhosis4 2.023 0.494 1.162 3.522
## etiology_cirrhosis5 1.238 0.808 0.947 1.617
## etiology_cirrhosis6 1.450 0.690 1.085 1.937
## etiology_cirrhosis7 1.530 0.654 1.176 1.989
## albumin_given_admission1 1.318 0.759 1.057 1.643
## lactulose1 1.168 0.856 0.973 1.402
## rifaximin1 0.843 1.186 0.697 1.020
## beta_blockers1 0.810 1.235 0.688 0.953
## ckd1 0.929 1.076 0.764 1.130
## encephalopathy_admission1 1.514 0.660 1.252 1.832
## hcc_admission1 1.645 0.608 1.320 2.052
## alcoholic_hepatitis_admission1 0.811 1.233 0.642 1.024
## log_co2_admit 0.579 1.726 0.433 0.776
## log_alt_admit 1.092 0.915 0.995 1.199
## log_tb_admit 1.290 0.775 1.180 1.410
## log_alb_admit 0.525 1.905 0.385 0.716
## log_inr_admit 1.715 0.583 1.390 2.115
## log_wbc_admit 1.199 0.834 1.028 1.397
## log_plt_admit 0.858 1.166 0.743 0.990
## sbp_admission 0.993 1.007 0.988 0.998
##
## Num. cases = 1949
## Pseudo Log-likelihood = -4872
## Pseudo likelihood ratio test = 769 on 34 df,
##
## Convergence: TRUE