Build summaries (counts and percentages) for each comorbidity and other summary statistics by method.
Usage
# S3 method for class 'medicalcoder_comorbidities'
summary(object, ...)Arguments
- object
a
medicalcoder_comorbiditiesobject generated by callingcomorbidities()- ...
additional parameters, not currently used
Examples
pccc_v3.1_results <-
comorbidities(data = mdcr,
icd.codes = "code",
id.vars = "patid",
dx.var = "dx",
method = "pccc_v3.1",
flag.method = 'current',
poa = 1)
summary(pccc_v3.1_results)
#> condition label dxpr_or_tech_count
#> 1 congeni_genetic Other Congenital or Genetic Defect 3225
#> 2 cvd Cardiovascular 5147
#> 3 gi Gastrointestinal 5652
#> 4 hemato_immu Hematologic or Immunologic 2832
#> 5 malignancy Malignancy 3784
#> 6 metabolic Metabolic 3407
#> 7 misc Miscellaneous, Not Elsewhere Classified 764
#> 8 neonatal Premature & Neonatal 1516
#> 9 neuromusc Neurologic or Neuromuscular 5828
#> 10 renal Renal Urologic 2787
#> 11 respiratory Respiratory 3260
#> 12 any_tech_dep Any Technology Dependence 7012
#> 13 any_transplant Any Transplantation 1585
#> 14 cmrb_flag Any Condition 20871
#> 15 num_cmrb >= 2 conditions 10657
#> 16 num_cmrb >= 3 conditions 4582
#> 17 num_cmrb >= 4 conditions 1571
#> 18 num_cmrb >= 5 conditions 418
#> 19 num_cmrb >= 6 conditions 88
#> 20 num_cmrb >= 7 conditions 13
#> 21 num_cmrb >= 8 conditions 2
#> 22 num_cmrb >= 9 conditions 0
#> 23 num_cmrb >= 10 conditions 0
#> 24 num_cmrb >= 11 conditions 0
#> dxpr_or_tech_percent dxpr_only_count dxpr_only_percent tech_only_count
#> 1 8.428728242 3225 8.4287282 0
#> 2 13.451988919 4560 11.9178297 283
#> 3 14.771836287 1420 3.7112540 3855
#> 4 7.401599498 2832 7.4015995 0
#> 5 9.889707804 3784 9.8897078 0
#> 6 8.904396006 3356 8.7711045 40
#> 7 1.996759187 121 0.3162407 643
#> 8 3.962155664 1516 3.9621557 0
#> 9 15.231822696 4564 11.9282839 316
#> 10 7.283989337 1876 4.9030370 555
#> 11 8.520202812 1848 4.8298573 755
#> 12 18.326276724 NA NA NA
#> 13 4.142491245 NA NA NA
#> 14 54.547592912 NA NA NA
#> 15 27.852699807 NA NA NA
#> 16 11.975328002 NA NA NA
#> 17 4.105901417 NA NA NA
#> 18 1.092467723 NA NA NA
#> 19 0.229993205 NA NA NA
#> 20 0.033976269 NA NA NA
#> 21 0.005227118 NA NA NA
#> 22 0.000000000 NA NA NA
#> 23 0.000000000 NA NA NA
#> 24 0.000000000 NA NA NA
#> tech_only_percent dxpr_and_tech_count dxpr_and_tech_percent
#> 1 0.0000000 0 0.00000000
#> 2 0.7396372 304 0.79452198
#> 3 10.0752705 377 0.98531180
#> 4 0.0000000 0 0.00000000
#> 5 0.0000000 0 0.00000000
#> 6 0.1045424 11 0.02874915
#> 7 1.6805185 0 0.00000000
#> 8 0.0000000 0 0.00000000
#> 9 0.8258847 948 2.47765407
#> 10 1.4505253 356 0.93042706
#> 11 1.9732372 657 1.71710836
#> 12 NA NA NA
#> 13 NA NA NA
#> 14 NA NA NA
#> 15 NA NA NA
#> 16 NA NA NA
#> 17 NA NA NA
#> 18 NA NA NA
#> 19 NA NA NA
#> 20 NA NA NA
#> 21 NA NA NA
#> 22 NA NA NA
#> 23 NA NA NA
#> 24 NA NA NA
charlson_results <-
comorbidities(data = mdcr,
icd.codes = "code",
id.vars = "patid",
dx.var = "dx",
method = "charlson_quan2011",
flag.method = 'current',
poa = 1)
#> Warning: Assuming all codes provided are secondary diagnostic codes. Define `primarydx.var` or `primarydx` if this assumption is incorrect.
summary(charlson_results)
#> $conditions
#> condition_description condition count percent
#> 1 AIDS/HIV aidshiv 7 0.018294914
#> 2 Any malignancy mal 2301 6.013799592
#> 3 Cerebrovascular disease cebvd 411 1.074172809
#> 4 Chronic pulmonary disease copd 3415 8.925304480
#> 5 Congestive heart failure chf 684 1.787674455
#> 6 Dementia dem 13 0.033976269
#> 7 Diabetes with chronic complications dmc 13 0.033976269
#> 8 Diabetes without chronic complications dm 441 1.152579583
#> 9 Hemiplegia or paraplegia hp 1177 3.076159113
#> 10 Liver disease, mild mld 593 1.549840573
#> 11 Liver disease, moderate to severe msld 206 0.538393184
#> 12 Metastatic solid tumor mst 453 1.183942293
#> 13 Myocardial infarction mi 10 0.026135591
#> 14 Peptic ulcer disease pud 45 0.117610162
#> 15 Peripheral vascular disease pvd 217 0.567142334
#> 16 Renal disease rnd 898 2.346976112
#> 17 Rheumatic disease rhd 136 0.355444044
#> 18 >= 1 <NA> 9841 25.720035544
#> 19 >= 2 <NA> 1075 2.809576081
#> 20 >= 3 <NA> 94 0.245674560
#> 21 >= 4 <NA> 9 0.023522032
#> 22 >= 5 <NA> 1 0.002613559
#>
#> $age_summary
#> age_score count percent
#> 1 <NA> 38262 100
#>
#> $index_summary
#> min q1 median q3 max
#> 1 0 0 0 0 10
#>
elixhauser_results <-
comorbidities(data = mdcr,
icd.codes = "code",
id.vars = "patid",
dx.var = "dx",
method = "elixhauser_ahrq2025",
primarydx = 1,
flag.method = 'current',
poa = 1)
summary(elixhauser_results)
#> $conditions
#> condition count percent
#> 1 AIDS 0 0
#> 2 ALCOHOL 0 0
#> 3 ANEMDEF 0 0
#> 4 AUTOIMMUNE 0 0
#> 5 BLDLOSS 0 0
#> 6 CANCER_LEUK 0 0
#> 7 CANCER_LYMPH 0 0
#> 8 CANCER_METS 0 0
#> 9 CANCER_NSITU 0 0
#> 10 CANCER_SOLID 0 0
#> 11 CBVD 0 0
#> 12 COAG 0 0
#> 13 DEMENTIA 0 0
#> 14 DEPRESS 0 0
#> 15 DIAB_CX 0 0
#> 16 DIAB_UNCX 0 0
#> 17 DRUG_ABUSE 0 0
#> 18 HF 0 0
#> 19 HTN_CX 0 0
#> 20 HTN_UNCX 0 0
#> 21 LIVER_MLD 0 0
#> 22 LIVER_SEV 0 0
#> 23 LUNG_CHRONIC 0 0
#> 24 NEURO_MOVT 0 0
#> 25 NEURO_OTH 0 0
#> 26 NEURO_SEIZ 0 0
#> 27 OBESE 0 0
#> 28 PARALYSIS 0 0
#> 29 PERIVASC 0 0
#> 30 PSYCHOSES 0 0
#> 31 PULMCIRC 0 0
#> 32 RENLFL_MOD 0 0
#> 33 RENLFL_SEV 0 0
#> 34 THYROID_HYPO 0 0
#> 35 THYROID_OTH 0 0
#> 36 ULCER_PEPTIC 0 0
#> 37 VALVE 0 0
#> 38 WGHTLOSS 0 0
#>
#> $index_summary
#> index min q1 median q3 max
#> 1 readmission 0 0 0 0 0
#> 2 mortality 0 0 0 0 0
#>