PCCC subcondition summary returns NaN percentages when no conditions are flagged #27
Description
library(medicalcoder)
packageVersion("medicalcoder")
#> [1] '0.7.0.9000'
# `summary(pccc)` returns rows for each condition/subcondition where
# `percent_of_those_with_condition` is `NaN` (divide by zero) because `count` is 0
# for every condition in the cohort.
# SUGGESTED FIX: When the condition isn’t flagged (count = 0), the denominator
# is zero, so percent_of_those_with_condition should be NA rather than NaN. That
# keeps “share of those with the condition” undefined when nobody has the condition,
# while percent_of_cohort stays at 0. In practice: if counts[cnd] == 0, set
# percent_of_those_with_condition to NA_real_; otherwise compute the percentage.
# Codes that do not map to PCCC conditions
df_none <- data.frame(
patid = 1:3,
icdv = 10L,
dx = 1L,
code = c("XXX1", "XXX2", "XXX3")
)
pccc <- comorbidities(
data = df_none,
icd.codes = "code",
id.vars = "patid",
icdv.var = "icdv",
dx.var = "dx",
method = "pccc_v3.1",
flag.method = "current",
poa = 1L,
subconditions = TRUE
)
summary(pccc)
#> condition subcondition count
#> 1 congeni_genetic <NA> 0
#> 2 congeni_genetic bone_and_joint_anomalies 0
#> 3 congeni_genetic chromosomal_anomalies 0
#> 4 congeni_genetic diaphragm_and_abdominal_wall_anomalies 0
#> 5 congeni_genetic other_congenital_anomalies 0
#> 6 cvd <NA> 0
#> 7 cvd cardiomyopathies 0
#> 8 cvd conduction_disorder 0
#> 9 cvd device_and_technology_use 0
#> 10 cvd dysrhythmias 0
#> 11 cvd endocardium_diseases 0
#> 12 cvd heart_and_great_vessel_malformations 0
#> 13 cvd other 0
#> 14 cvd transplantation 0
#> 15 gi <NA> 0
#> 16 gi chronic_liver_disease_and_cirrhosis 0
#> 17 gi congenital_anomalies 0
#> 18 gi device_and_technology_use 0
#> 19 gi inflammatory_bowel_disease 0
#> 20 gi other 0
#> 21 gi transplantation 0
#> 22 hemato_immu <NA> 0
#> 23 hemato_immu acquired_immunodeficiency 0
#> 24 hemato_immu aplastic_anemias 0
#> 25 hemato_immu coagulation_hemorrhagic 0
#> 26 hemato_immu diffuse_diseases_of_connective_tissue 0
#> 27 hemato_immu hemophagocytic_syndromes 0
#> 28 hemato_immu hereditary_anemias 0
#> 29 hemato_immu hereditary_immunodeficiency 0
#> 30 hemato_immu leukopenia 0
#> 31 hemato_immu other 0
#> 32 hemato_immu polyarteritis_nodosa_and_related_conditions 0
#> 33 hemato_immu sarcoidosis 0
#> 34 hemato_immu transplantation 0
#> 35 malignancy <NA> 0
#> 36 malignancy neoplasms 0
#> 37 malignancy transplantation 0
#> 38 metabolic <NA> 0
#> 39 metabolic amino_acid_metabolism 0
#> 40 metabolic carbohydrate_metabolism 0
#> 41 metabolic device_and_technology_use 0
#> 42 metabolic endocrine_disorders 0
#> 43 metabolic lipid_metabolism 0
#> 44 metabolic other_metabolic_disorders 0
#> 45 metabolic storage_disorders 0
#> 46 misc <NA> 0
#> 47 misc device_and_technology_use 0
#> 48 misc transplantation 0
#> 49 neonatal <NA> 0
#> 50 neonatal birth_asphyxia 0
#> 51 neonatal cerebral_hemorrhage_at_birth 0
#> 52 neonatal extreme_immaturity 0
#> 53 neonatal fetal_malnutrition 0
#> 54 neonatal hypoxic_ischemic_encephalopathy 0
#> 55 neonatal other 0
#> 56 neonatal respiratory_diseases 0
#> 57 neonatal spinal_cord_injury_at_birth 0
#> 58 neuromusc <NA> 0
#> 59 neuromusc brain_and_spinal_cord_malformations 0
#> 60 neuromusc cns_degeneration_and_diseases 0
#> 61 neuromusc device_and_technology_use 0
#> 62 neuromusc epilepsy 0
#> 63 neuromusc infantile_cerebral_palsy 0
#> 64 neuromusc intellectual_disabilities 0
#> 65 neuromusc movement_diseases 0
#> 66 neuromusc muscular_dystrophies_and_myopathies 0
#> 67 neuromusc occlusion_of_cerebral_arteries 0
#> 68 neuromusc other_neurologic_disorders 0
#> 69 renal <NA> 0
#> 70 renal chronic_bladder_diseases 0
#> 71 renal chronic_renal_failure 0
#> 72 renal congenital_anomalies 0
#> 73 renal device_and_technology_use 0
#> 74 renal other 0
#> 75 renal transplantation 0
#> 76 respiratory <NA> 0
#> 77 respiratory chronic_respiratory_diseases 0
#> 78 respiratory cystic_fibrosis 0
#> 79 respiratory device_and_technology_use 0
#> 80 respiratory other 0
#> 81 respiratory respiratory_malformations 0
#> 82 respiratory transplantation 0
#> percent_of_cohort percent_of_those_with_condition
#> 1 0 NA
#> 2 0 NaN
#> 3 0 NaN
#> 4 0 NaN
#> 5 0 NaN
#> 6 0 NA
#> 7 0 NaN
#> 8 0 NaN
#> 9 0 NaN
#> 10 0 NaN
#> 11 0 NaN
#> 12 0 NaN
#> 13 0 NaN
#> 14 0 NaN
#> 15 0 NA
#> 16 0 NaN
#> 17 0 NaN
#> 18 0 NaN
#> 19 0 NaN
#> 20 0 NaN
#> 21 0 NaN
#> 22 0 NA
#> 23 0 NaN
#> 24 0 NaN
#> 25 0 NaN
#> 26 0 NaN
#> 27 0 NaN
#> 28 0 NaN
#> 29 0 NaN
#> 30 0 NaN
#> 31 0 NaN
#> 32 0 NaN
#> 33 0 NaN
#> 34 0 NaN
#> 35 0 NA
#> 36 0 NaN
#> 37 0 NaN
#> 38 0 NA
#> 39 0 NaN
#> 40 0 NaN
#> 41 0 NaN
#> 42 0 NaN
#> 43 0 NaN
#> 44 0 NaN
#> 45 0 NaN
#> 46 0 NA
#> 47 0 NaN
#> 48 0 NaN
#> 49 0 NA
#> 50 0 NaN
#> 51 0 NaN
#> 52 0 NaN
#> 53 0 NaN
#> 54 0 NaN
#> 55 0 NaN
#> 56 0 NaN
#> 57 0 NaN
#> 58 0 NA
#> 59 0 NaN
#> 60 0 NaN
#> 61 0 NaN
#> 62 0 NaN
#> 63 0 NaN
#> 64 0 NaN
#> 65 0 NaN
#> 66 0 NaN
#> 67 0 NaN
#> 68 0 NaN
#> 69 0 NA
#> 70 0 NaN
#> 71 0 NaN
#> 72 0 NaN
#> 73 0 NaN
#> 74 0 NaN
#> 75 0 NaN
#> 76 0 NA
#> 77 0 NaN
#> 78 0 NaN
#> 79 0 NaN
#> 80 0 NaN
#> 81 0 NaN
#> 82 0 NaNCreated on 2025-12-17 with reprex v2.1.1