Transition From The pccc Package to the medicalcoder Package
Source:vignettes/articles/transition-pccc-to-medicalcoder.Rmd
transition-pccc-to-medicalcoder.RmdIntroduction
The R package pccc (Feinstein et al. 2024; DeWitt, Feinstein, and Russell 2025) was published to support version 2 of the Pediatric Complex Chronic Conditions (PCCC) (Feudtner et al. 2014). This document is provided to help users of pccc to transition to medicalcoder.
Major differences between pccc::ccc() and
medicalcoder::comorbidities():
-
Input data format
-
pccc::ccc()expects a data.frame with each row representing one patient and/or encounter. There is a column for each diagnosic and procedure code. For example, a data set were the max number of diagnosic codes is six and the max number of procedure codes is five, an entry for patient XX could look like the following:
-
patid dx1 dx2 dx3 dx4 dx5 dx6 pr1 pr2 pr3 pr4 pr5
patXX T8619 E8809 E876 Z7982 NA NA 02PAX3Z 5A1D70Z 04Q90ZZ 0TS60ZZ NA-
medicalcoder::comorbidities()expects the input data to be in a data.frame where each row is single ICD code. For example, the same record for patient XX above would be three columns below, one row for each code, one column to identify the patient/encounter, and a column to denote if the code is a diagnosic (dx = 1) or procedure (dx = 0).
patid code dx
patXX T8619 1
patXX E8809 1
patXX E876 1
patXX Z7982 1
patXX 02PAX3Z 0
patXX 5A1D70Z 0
patXX 04Q90ZZ 0
patXX 0TS60ZZ 0- ICD Version
pccc::ccc()only considers ICD-9 and ICD-10 independently. If the input data consists of both ICD-9 and ICD-10 data false negatives will be inevitable. The version is set by theicdvargument topccc::ccc().medicalcoder::comorbidities()considers both ICD-9 and ICD-10 at the same time. A column added to the input data to identify the code version allows for a single patient/encounter record to consist of both version and to have PCCC flagged accordingly. Users specify the ICD version via the argumentsicdvandicdv.vartomedicalcoder::comorbidities().
- PCCC Versions
pccc::ccc()only impliments PCCC version 2 (Feudtner et al. 2014)-
medicalcoder::comorbidities()impliments:pccc_v2.0: consistent results withpccc::ccc()for pccc version 1.0.6.pccc_v2.1: improved mappings of ICD codes to PCCC using the PCCC v2 scoring algorithm.pccc_v3.0: consistent with SAS code published with PCCC version 3 (Feinstein et al. 2024).pccc_v3.1: extended set of ICD code to condition mappings.Note: medicalcoder also provides several variants of the Charlson and Elixhauser comorbidities.
- Subconditions
pccc::ccc()only returns flags for primary conditionsmedicalcoder::comorbidities(): when the argumentsubconditons = TRUEis passed in, for PCCC the primary conditions and subconditions are flagged. Examples to follow.
- Present-on-Admission and Longitudinal data
pccc::ccc()only considers singular encounters and considers all codes to be present-on-admission.medicalcoder::comorbidities()can account for present-on-admission flags and longitudinal flagging of comorbidities within a patient over multiple encounters.
pccc::ccc() vs
medicalcoder::comorbidities()
library(pccc)
packageVersion("pccc")
## [1] '1.0.6'
library(medicalcoder)Prepare Data
We’ll use the mdcr data set from the medicalcoder
package.
head(mdcr)
## patid icdv code dx
## 1 71412 9 99931 1
## 2 71412 9 75169 1
## 3 71412 9 99591 1
## 4 71412 9 V5865 1
## 5 71412 9 V427 1
## 6 17087 10 V441 1We will split the data set into two sets, one for ICD-9 and one for ICD-10.
Using the tidyverse we can build the needed input data sets
mdcr_tbls <-
mdcr |>
dplyr::group_by(patid, icdv, dx) |>
dplyr::mutate(n = seq_len(dplyr::n())) |>
dplyr::ungroup() |>
dplyr::mutate(dxv = dplyr::if_else(dx == 1, "dx", "pr")) |>
dplyr::group_by(icdv) |>
dplyr::group_split()
mdcr_tbls <-
lapply(mdcr_tbls,
tidyr::pivot_wider,
id_cols = "patid",
names_from = c("dxv", "n"),
names_sep = "",
values_from = "code"
)A data.table approach:
mdcr_DTs <- data.table::as.data.table(data.table::copy(mdcr))
mdcr_DTs[
,
dxv := paste0(data.table::fifelse(dx == 1, "dx", "pr"), seq_len(.N)),
by = .(patid, icdv, dx)
]
mdcr_DTs <- split(mdcr_DTs, by = "icdv")
mdcr_DTs <-
lapply(
mdcr_DTs,
data.table::dcast,
formula = patid ~ dxv,
value.var = "code",
na.rm = FALSE
)Applying pccc::ccc()
To flag PCCC via pccc::ccc() we need to call
pccc::ccc() twice and to then aggregate the results.
tic <- Sys.time()
pccc_9_results_tbl <-
pccc::ccc(
data = mdcr_tbls[[1]],
id = patid,
dx_cols = grep("dx", names(mdcr_tbls[[1]]), value = TRUE),
pc_cols = grep("pr", names(mdcr_tbls[[1]]), value = TRUE),
icdv = 9
)
pccc_10_results_tbl <-
pccc::ccc(
data = mdcr_tbls[[2]],
id = patid,
dx_cols = grep("dx", names(mdcr_tbls[[2]]), value = TRUE),
pc_cols = grep("pr", names(mdcr_tbls[[2]]), value = TRUE),
icdv = 10
)
pccc_results_tbl <-
dplyr::bind_rows(pccc_9_results_tbl, pccc_10_results_tbl) |>
dplyr::group_by(patid) |>
dplyr::summarize_all(max) |>
dplyr::ungroup() |>
dplyr::arrange(patid)
toc <- Sys.time()
pccc_ccc_tbl_time <- difftime(toc, tic, units = "secs")
tic <- Sys.time()
pccc_9_results_DT <-
pccc::ccc(
data = mdcr_DTs[[1]],
id = patid,
dx_cols = grep("dx", names(mdcr_DTs[[1]]), value = TRUE),
pc_cols = grep("pr", names(mdcr_DTs[[1]]), value = TRUE),
icdv = 9
)
pccc_10_results_DT <-
pccc::ccc(
data = mdcr_DTs[[2]],
id = patid,
dx_cols = grep("dx", names(mdcr_DTs[[2]]), value = TRUE),
pc_cols = grep("pr", names(mdcr_DTs[[2]]), value = TRUE),
icdv = 10
)
pccc_results_DT <- data.table::rbindlist(list(pccc_9_results_DT, pccc_10_results_DT))
pccc_results_DT <-
pccc_results_DT[, lapply(.SD, max), by = .(patid), .SDcols = -"patid"]
data.table::setkey(pccc_results_DT, patid)
toc <- Sys.time()
pccc_ccc_dt_time <- difftime(toc, tic)A quick sanity check that we have the same results for both the tidyverse and data.table input data sets.
Calling medicalcoder::comorbidities()
tic <- Sys.time()
medicalcoder_results <-
medicalcoder::comorbidities(
data = mdcr,
id.vars = "patid",
icd.codes = "code",
icdv.var = "icdv",
dx.var = "dx",
method = "pccc_v2.0",
poa = 1
)
toc <- Sys.time()
medicalcoder_df_time <- difftime(toc, tic)Differences in results?
old_vs_new <-
merge(
x = pccc_results_DT,
y = medicalcoder_results,
all = TRUE,
by = "patid",
suffixes = c("_old", "_new")
)Most importantly, the condition flag (ccc_flag from
pccc::ccc() and cmrb_flag from
medicalcoder::comorbidities()) are identical.
Second, the flags for all but the technology dependence and transplant flags are identical.
stopifnot(
with(old_vs_new, identical(neuromusc_old, neuromusc_new)),
with(old_vs_new, identical(cvd_old, cvd_new)),
with(old_vs_new, identical(respiratory_old, respiratory_new)),
with(old_vs_new, identical(renal_old, renal_new)),
with(old_vs_new, identical(gi_old, gi_new)),
with(old_vs_new, identical(hemato_immu_old, hemato_immu_new)),
with(old_vs_new, identical(metabolic_old, metabolic_new)),
with(old_vs_new, identical(congeni_genetic_old, congeni_genetic_new)),
with(old_vs_new, identical(malignancy_old, malignancy_new)),
with(old_vs_new, identical(neonatal_old, neonatal_new))
)Omitting the columns which are as expected from the
old_vs_new data.table we can focus in on the differences in
the results.
good <- c("neuromusc", "cvd", "respiratory", "renal", "gi", "hemato_immu",
"metabolic", "congeni_genetic", "malignancy", "neonatal", "ccc_flag",
"cmrb_flag")
for(g in good) {
for (j in grep(g, names(old_vs_new), value = TRUE)) {
data.table::set(old_vs_new, j = j, value = NULL)
}
}
old_vs_new
## Key: <patid>
## patid tech_dep transplant misc any_tech_dep any_transplant num_cmrb
## <int> <int> <int> <int> <int> <int> <int>
## 1: 10000 0 0 0 0 0 0
## 2: 10002 0 0 0 0 0 1
## 3: 10005 0 0 0 0 0 1
## 4: 10006 0 0 0 0 0 1
## 5: 10008 0 0 0 0 0 1
## ---
## 38258: 99992 0 0 0 0 0 0
## 38259: 99995 0 0 0 0 0 0
## 38260: 99997 0 0 0 0 0 0
## 38261: 99998 0 0 0 0 0 1
## 38262: 99999 1 0 0 1 0 3First, the num_cmrb column is a count of the number of
conditions and is reported by
medicalcoder::comorbidities(). There is not similar flag
from pccc::ccc().
old_vs_new[, num_cmrb := NULL]The misc column is the “miscellaneous” category reported
by medicalcoder::comorbidities() and is not reported by
pccc::ccc(). The existence of the misc column
and some differences in the returned results between
pccc::ccc() version 1.0.6, and
medicalcoder::comorbidities() is due to how medicalcoder is
implemented.
old_vs_new
## Key: <patid>
## patid tech_dep transplant misc any_tech_dep any_transplant
## <int> <int> <int> <int> <int> <int>
## 1: 10000 0 0 0 0 0
## 2: 10002 0 0 0 0 0
## 3: 10005 0 0 0 0 0
## 4: 10006 0 0 0 0 0
## 5: 10008 0 0 0 0 0
## ---
## 38258: 99992 0 0 0 0 0
## 38259: 99995 0 0 0 0 0
## 38260: 99997 0 0 0 0 0
## 38261: 99998 0 0 0 0 0
## 38262: 99999 1 0 0 1 0There are several ICD codes which need to be corrected in pccc
GitHub links:
Additional Benfits of medicalcoder
Computation Performance
medicalcoder was built such that only base R is needed to install and use the package. That said, there is specific support for the tidyverse and data.table. For example, the same calls as above but with either a tibble or a data.table instead of a simple base R data.table take less time to compute. The differences here are small. See benchmarking for more details.
mdcr_tbl <- tibble::as_tibble(mdcr)
tic <- Sys.time()
medicalcoder_results <-
medicalcoder::comorbidities(
data = mdcr_tbl,
id.vars = "patid",
icd.codes = "code",
icdv.var = "icdv",
dx.var = "dx",
method = "pccc_v2.0",
poa = 1
)
toc <- Sys.time()
medicalcoder_tbl_time <- difftime(toc, tic, units = "secs")
mdcr_DT <- data.table::as.data.table(data.table::copy(mdcr))
tic <- Sys.time()
medicalcoder_results <-
medicalcoder::comorbidities(
data = mdcr_tbl,
id.vars = "patid",
icd.codes = "code",
icdv.var = "icdv",
dx.var = "dx",
method = "pccc_v2.0",
poa = 1
)
toc <- Sys.time()
medicalcoder_dt_time <- difftime(toc, tic, units = "secs")
pccc_ccc_tbl_time
## Time difference of 8.832043 secs
pccc_ccc_dt_time
## Time difference of 7.528091 secs
medicalcoder_df_time
## Time difference of 0.865835 secs
medicalcoder_tbl_time
## Time difference of 0.3059685 secs
medicalcoder_dt_time
## Time difference of 0.3336756 secsSummary of results
A simple call to summary() will return a data.frame with
counts and percentages for the
summary(medicalcoder_results)
## condition label count percent
## 1 congeni_genetic Other Congenital or Genetic Defect 3399 8.883487533
## 2 cvd Cardiovascular 4952 12.942344885
## 3 gi Gastrointestinal 6233 16.290314150
## 4 hemato_immu Hematologic or Immunologic 2695 7.043541895
## 5 malignancy Malignancy 3733 9.756416288
## 6 metabolic Metabolic 2983 7.796246929
## 7 misc Miscellaneous, Not Elsewhere Classified 822 2.148345617
## 8 neonatal Premature & Neonatal 1559 4.074538707
## 9 neuromusc Neurologic or Neuromuscular 5580 14.583660028
## 10 renal Renal Urologic 2807 7.336260520
## 11 respiratory Respiratory 3040 7.945219800
## 12 any_tech_dep Any Technology Dependence 7897 20.639276567
## 13 any_transplant Any Transplantation 1453 3.797501437
## 14 cmrb_flag Any Condition 21283 55.624379280
## 15 num_cmrb >= 2 conditions 10448 27.306465945
## 16 num_cmrb >= 3 conditions 4313 11.272280592
## 17 num_cmrb >= 4 conditions 1353 3.536145523
## 18 num_cmrb >= 5 conditions 335 0.875542314
## 19 num_cmrb >= 6 conditions 64 0.167267785
## 20 num_cmrb >= 7 conditions 6 0.015681355
## 21 num_cmrb >= 8 conditions 1 0.002613559
## 22 num_cmrb >= 9 conditions 0 0.000000000
## 23 num_cmrb >= 10 conditions 0 0.000000000
## 24 num_cmrb >= 11 conditions 0 0.000000000Subconditions
In the documentation for both PCCC v2 and v3 there are subconditions. For example, there are 8 subconditions under cardiovascular disease:
- cardiomyopathies
- conduction disorder
- device and technology use
- dysrhythmias
- endocardium diseases
- heart and great vessel malformations
- other
- transplantation
Calling medicalcoder::comorbidities() with
subconditions = TRUE when working with PCCC will flag these
conditions as well as the primary conditions.
with_subconditions <-
medicalcoder::comorbidities(
data = mdcr,
id.vars = "patid",
icd.codes = "code",
icdv.var = "icdv",
dx.var = "dx",
method = "pccc_v2.0",
poa = 1,
subconditions = TRUE
)
with_subconditions
##
## Comorbidities and Subconditions via pccc_v2.0
##
## List of 2
## $ conditions :'data.frame': 38262 obs. of 16 variables:
## $ subconditions:List of 11
## ..$ congeni_genetic:'data.frame': 3399 obs. of 5 variables:
## ..$ cvd :'data.frame': 4952 obs. of 9 variables:
## ..$ gi :'data.frame': 6233 obs. of 7 variables:
## ..$ hemato_immu :'data.frame': 2695 obs. of 13 variables:
## ..$ malignancy :'data.frame': 3733 obs. of 3 variables:
## ..$ metabolic :'data.frame': 2983 obs. of 8 variables:
## ..$ misc :'data.frame': 822 obs. of 3 variables:
## ..$ neonatal :'data.frame': 1559 obs. of 9 variables:
## ..$ neuromusc :'data.frame': 5580 obs. of 11 variables:
## ..$ renal :'data.frame': 2807 obs. of 7 variables:
## ..$ respiratory :'data.frame': 3040 obs. of 7 variables:The summary includes counts and percentages as before. Additionally, for a subconditon, the percentage is reported as percent of the cohort and as the percent of those with the primary condition.
str(summary(with_subconditions))
## 'data.frame': 82 obs. of 5 variables:
## $ condition : chr "congeni_genetic" "congeni_genetic" "congeni_genetic" "congeni_genetic" ...
## $ subcondition : chr NA "bone_and_joint_anomalies" "chromosomal_anomalies" "diaphragm_and_abdominal_wall_anomalies" ...
## $ count : num 3399 1239 1509 300 552 ...
## $ percent_of_cohort : num 8.883 3.238 3.944 0.784 1.443 ...
## $ percent_of_those_with_condition: num NA 36.45 44.4 8.83 16.24 ...Using tools such as kableExtra, these summaries can be formatted into publication ready tables. For example, say we want to report on the cardiovascular and metabolic conditions and subconditions.
cvd_and_metabolic <- subset(summary(with_subconditions), condition %in% c("cvd", "metabolic"))
cvd_and_metabolic$subcondition[is.na(cvd_and_metabolic$subcondition)] <- "Any subcondition"
kableExtra::kbl(
x = cvd_and_metabolic[, c("subcondition", "count", "percent_of_cohort", "percent_of_those_with_condition")],
caption = "Patients with cardiovascular and/or metabolic conditions and the associated with_subconditions.",
row.names = FALSE,
digits = 2,
col.names = c("Subcondition", "Patients", "% of chort", "% of those with the primary condition")
) |>
kableExtra::kable_styling(bootstrap_options = "striped") |>
kableExtra::pack_rows(index = table(cvd_and_metabolic$condition))| Subcondition | Patients | % of chort | % of those with the primary condition |
|---|---|---|---|
| cvd | |||
| Any subcondition | 4952 | 12.94 | |
| cardiomyopathies | 240 | 0.63 | 4.85 |
| conduction_disorder | 653 | 1.71 | 13.19 |
| device_and_technology_use | 438 | 1.14 | 8.84 |
| dysrhythmias | 1130 | 2.95 | 22.82 |
| endocardium_diseases | 247 | 0.65 | 4.99 |
| heart_and_great_vessel_malformations | 2298 | 6.01 | 46.41 |
| other | 1071 | 2.80 | 21.63 |
| transplantation | 237 | 0.62 | 4.79 |
| metabolic | |||
| Any subcondition | 2983 | 7.80 | |
| amino_acid_metabolism | 187 | 0.49 | 6.27 |
| carbohydrate_metabolism | 130 | 0.34 | 4.36 |
| device_and_technology_use | 71 | 0.19 | 2.38 |
| endocrine_disorders | 748 | 1.95 | 25.08 |
| lipid_metabolism | 294 | 0.77 | 9.86 |
| other_metabolic_disorders | 1736 | 4.54 | 58.20 |
| storage_disorders | 69 | 0.18 | 2.31 |
PCCC version 3
For more detail on the differences between PCCC v2 (Feudtner et al. 2014) and PCCC v3 (Feudtner et al. 2014) see the PCCC article.