Summaries of Comorbidities with Subconditions
Source:R/summary.R
summary.medicalcoder_comorbidities_with_subconditions.RdBuild summaries (counts and percentages) for each Pediatric Complex Chronic Condition (PCCC) condition and subcondition.
Usage
# S3 method for class 'medicalcoder_comorbidities_with_subconditions'
summary(object, ...)Arguments
- object
a
medicalcoder_comorbidities_with_subcondtionsobject generated by callingcomorbidities()withsubconditions = TRUE. This is currently only applicable to PCCC.- ...
additional parameters, not currently used
Value
a data.frame with five columns.
conditionthe primary conditionsubconditionthe subcondition(s) within thecondition. There will be a row wheresubconditionisNAwhich is used to report thecountandpercent_of_cohortfor theconditionoverall.countthe number of rows inobjectwith the applicableconditionandsubcondition.percent_of_cohort: a numeric value within [0, 100] for the percent of rows inobjectwith the flaggedconditionandsubcondition.percent_of_those_with_condition: a numeric value within [0, 100] for the subset of rows inobjectwith the primaryconditionand the flaggedsubcondition. Will beNAfor the primarycondition.
Examples
pccc_v3.1_subcondition_results <-
comorbidities(data = mdcr,
icd.codes = "code",
id.vars = "patid",
dx.var = "dx",
method = "pccc_v3.1",
flag.method = 'current',
poa = 1,
subconditions = TRUE)
summary(pccc_v3.1_subcondition_results)
#> condition subcondition count
#> 1 congeni_genetic <NA> 3225
#> 2 congeni_genetic bone_and_joint_anomalies 825
#> 3 congeni_genetic chromosomal_anomalies 1544
#> 4 congeni_genetic diaphragm_and_abdominal_wall_anomalies 300
#> 5 congeni_genetic other_congenital_anomalies 754
#> 6 cvd <NA> 5147
#> 7 cvd cardiomyopathies 240
#> 8 cvd conduction_disorder 653
#> 9 cvd device_and_technology_use 587
#> 10 cvd dysrhythmias 1130
#> 11 cvd endocardium_diseases 278
#> 12 cvd heart_and_great_vessel_malformations 2320
#> 13 cvd other 1247
#> 14 cvd transplantation 271
#> 15 gi <NA> 5652
#> 16 gi chronic_liver_disease_and_cirrhosis 290
#> 17 gi congenital_anomalies 709
#> 18 gi device_and_technology_use 4232
#> 19 gi inflammatory_bowel_disease 264
#> 20 gi other 295
#> 21 gi transplantation 343
#> 22 hemato_immu <NA> 2832
#> 23 hemato_immu acquired_immunodeficiency 11
#> 24 hemato_immu aplastic_anemias 823
#> 25 hemato_immu coagulation_hemorrhagic 100
#> 26 hemato_immu diffuse_diseases_of_connective_tissue 125
#> 27 hemato_immu hemophagocytic_syndromes 59
#> 28 hemato_immu hereditary_anemias 771
#> 29 hemato_immu hereditary_immunodeficiency 909
#> 30 hemato_immu leukopenia 28
#> 31 hemato_immu other 12
#> 32 hemato_immu polyarteritis_nodosa_and_related_conditions 46
#> 33 hemato_immu sarcoidosis 3
#> 34 hemato_immu transplantation 181
#> 35 malignancy <NA> 3784
#> 36 malignancy neoplasms 3525
#> 37 malignancy transplantation 452
#> 38 metabolic <NA> 3407
#> 39 metabolic amino_acid_metabolism 194
#> 40 metabolic carbohydrate_metabolism 130
#> 41 metabolic device_and_technology_use 51
#> 42 metabolic endocrine_disorders 884
#> 43 metabolic lipid_metabolism 354
#> 44 metabolic other_metabolic_disorders 1870
#> 45 metabolic storage_disorders 82
#> 46 misc <NA> 764
#> 47 misc device_and_technology_use 643
#> 48 misc transplantation 121
#> 49 neonatal <NA> 1516
#> 50 neonatal birth_asphyxia 11
#> 51 neonatal cerebral_hemorrhage_at_birth 84
#> 52 neonatal extreme_immaturity 349
#> 53 neonatal fetal_malnutrition 45
#> 54 neonatal hypoxic_ischemic_encephalopathy 130
#> 55 neonatal other 247
#> 56 neonatal respiratory_diseases 950
#> 57 neonatal spinal_cord_injury_at_birth 0
#> 58 neuromusc <NA> 5828
#> 59 neuromusc brain_and_spinal_cord_malformations 1767
#> 60 neuromusc cns_degeneration_and_diseases 1474
#> 61 neuromusc device_and_technology_use 1264
#> 62 neuromusc epilepsy 833
#> 63 neuromusc infantile_cerebral_palsy 1322
#> 64 neuromusc intellectual_disabilities 161
#> 65 neuromusc movement_diseases 146
#> 66 neuromusc muscular_dystrophies_and_myopathies 147
#> 67 neuromusc occlusion_of_cerebral_arteries 92
#> 68 neuromusc other_neurologic_disorders 848
#> 69 renal <NA> 2787
#> 70 renal chronic_bladder_diseases 519
#> 71 renal chronic_renal_failure 627
#> 72 renal congenital_anomalies 915
#> 73 renal device_and_technology_use 911
#> 74 renal other 217
#> 75 renal transplantation 322
#> 76 respiratory <NA> 3260
#> 77 respiratory chronic_respiratory_diseases 1092
#> 78 respiratory cystic_fibrosis 400
#> 79 respiratory device_and_technology_use 1412
#> 80 respiratory other 22
#> 81 respiratory respiratory_malformations 1091
#> 82 respiratory transplantation 39
#> percent_of_cohort percent_of_those_with_condition
#> 1 8.428728242 NA
#> 2 2.156186294 25.5813953
#> 3 4.035335320 47.8759690
#> 4 0.784067743 9.3023256
#> 5 1.970623595 23.3798450
#> 6 13.451988919 NA
#> 7 0.627254195 4.6629104
#> 8 1.706654122 12.6870021
#> 9 1.534159218 11.4047018
#> 10 2.953321834 21.9545366
#> 11 0.726569442 5.4012046
#> 12 6.063457216 45.0748009
#> 13 3.259108254 24.2277055
#> 14 0.708274528 5.2652030
#> 15 14.771836287 NA
#> 16 0.757932152 5.1309271
#> 17 1.853013434 12.5442321
#> 18 11.060582301 74.8761500
#> 19 0.689979614 4.6709130
#> 20 0.770999948 5.2193914
#> 21 0.896450787 6.0686483
#> 22 7.401599498 NA
#> 23 0.028749151 0.3884181
#> 24 2.150959176 29.0607345
#> 25 0.261355914 3.5310734
#> 26 0.326694893 4.4138418
#> 27 0.154199990 2.0833333
#> 28 2.015054101 27.2245763
#> 29 2.375725263 32.0974576
#> 30 0.073179656 0.9887006
#> 31 0.031362710 0.4237288
#> 32 0.120223721 1.6242938
#> 33 0.007840677 0.1059322
#> 34 0.473054205 6.3912429
#> 35 9.889707804 NA
#> 36 9.212795986 93.1553911
#> 37 1.181328733 11.9450317
#> 38 8.904396006 NA
#> 39 0.507030474 5.6941591
#> 40 0.339762689 3.8156736
#> 41 0.133291516 1.4969181
#> 42 2.310386284 25.9465806
#> 43 0.925199937 10.3903728
#> 44 4.887355601 54.8869974
#> 45 0.214311850 2.4068095
#> 46 1.996759187 NA
#> 47 1.680518530 84.1623037
#> 48 0.316240657 15.8376963
#> 49 3.962155664 NA
#> 50 0.028749151 0.7255937
#> 51 0.219538968 5.5408971
#> 52 0.912132142 23.0211082
#> 53 0.117610162 2.9683377
#> 54 0.339762689 8.5751979
#> 55 0.645549109 16.2928760
#> 56 2.482881188 62.6649077
#> 57 0.000000000 0.0000000
#> 58 15.231822696 NA
#> 59 4.618159009 30.3191489
#> 60 3.852386179 25.2916953
#> 61 3.303538759 21.6884008
#> 62 2.177094768 14.2930679
#> 63 3.455125189 22.6835964
#> 64 0.420783022 2.7625257
#> 65 0.381579635 2.5051476
#> 66 0.384193194 2.5223061
#> 67 0.240447441 1.5785861
#> 68 2.216298155 14.5504461
#> 69 7.283989337 NA
#> 70 1.356437196 18.6221744
#> 71 1.638701584 22.4973089
#> 72 2.391406618 32.8310011
#> 73 2.380952381 32.6874776
#> 74 0.567142334 7.7861500
#> 75 0.841566045 11.5536419
#> 76 8.520202812 NA
#> 77 2.854006586 33.4969325
#> 78 1.045423658 12.2699387
#> 79 3.690345513 43.3128834
#> 80 0.057498301 0.6748466
#> 81 2.851393027 33.4662577
#> 82 0.101928807 1.1963190