tests/test-vs-pccc_1.0.7.R

In medicalcoder: A Unified and Longitudinally Aware Framework for ICD-Based Comorbidity Assessment

library(medicalcoder)
source('utilities.R')
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# objective - the pccc_v2.0 in medicalcoder should reproduce the results from
# pccc version 1.0.7 _almost_ identically.
#
# There are a few differences.  The reason for this difference is that the old
# pccc package only mapped to conditions and did not map subconditions.  this
# creates a problem with a few codes that were not documented but in the
# software.  Those will be noted in this script.

# get the ICD codes from the medicalcoder package and add a code_id column
icd_codes <- get_icd_codes()
icd_codes[["code_id"]] <- seq_len(nrow(icd_codes))

# pccc_1.0.7 requires the input to be in a wide format and can only apply logic
# for ICD-9 or ICD-10 in one call.  Split the codes into the four sets ICD-9-CM,
# ICD-9-PCS, ICD-10-CM, and ICD-10-PCS.  Apply pccc::ccc to each and bind the
# results so we know when ICD codes map to which conditions.
#
# The following code generates the output object which is saved in the test
# directory such that the pccc_v1.0.7 package is not needed in the SUGGESTS
# section of the DESCRIPTION file.

### library(pccc)
### stopifnot(packageVersion("pccc") == "1.0.7")
###
### oldpccc <- rbind(
###   pccc::ccc(
###     data = icd_codes[icd_codes$icdv ==  9 & icd_codes$dx == 1, c("code_id", "code")],
###     id = code_id,
###     dx_cols = "code",
###     icdv = 9
###   )
###   ,
###   pccc::ccc(
###     data = icd_codes[icd_codes$icdv ==  9 & icd_codes$dx == 0, c("code_id", "code")],
###     id = code_id,
###     pc_cols = "code",
###     icdv = 9
###   )
###   ,
###   pccc::ccc(
###     data = icd_codes[icd_codes$icdv ==  10 & icd_codes$dx == 1, c("code_id", "code")],
###     id = code_id,
###     dx_cols = "code",
###     icdv = 10
###   )
###   ,
###   pccc::ccc(
###     data = icd_codes[icd_codes$icdv ==  10 & icd_codes$dx == 0, c("code_id", "code")],
###     id = code_id,
###     pc_cols = "code",
###     icdv = 10
###   )
### )
###
### saveRDS(oldpccc, file = "results_pccc_1.0.7.rds", compress = "xz")

oldpccc <- readRDS(file = "results_pccc_1.0.7.rds")

newpccc <-
  medicalcoder::comorbidities(
      data = icd_codes
    , icd.codes = "full_code"
    , id.vars = "code_id"
    , icdv.var = "icdv"
    , icdv = NULL
    , dx.var = "dx"
    , dx = NULL
    , poa = 1
    , poa.var = NULL
    , age.var = NULL
    , primarydx = NULL
    , primarydx.var = NULL
    , flag.method = "current"
    , full.codes = TRUE
    , compact.codes = TRUE
    , method = "pccc_v2.0"
  )

old_vs_mdcr <-
  merge(
    x = oldpccc,
    y = newpccc,
    all = TRUE,
    by = "code_id",
    suffixes = c("_old", "_mdcr")
  )

old_vs_mdcr <-
  merge(x = old_vs_mdcr,
    y = icd_codes[, c("code_id", "icdv", "dx", "full_code")],
    all = TRUE,
    by = "code_id"
  )

stopifnot(!any(is.na(old_vs_mdcr)))
stopifnot(nrow(old_vs_mdcr) == nrow(icd_codes))

# expect no difference in the following conditions:
#   cvd
#   neuromusc
#   respiratory
#   renal
#   gi
#   hemato_immu
#   metabolic
#   congeni_genetic
#   malignancy
#   neonatal
stopifnot(
  with(old_vs_mdcr, all(cvd_old == cvd_mdcr)),
  with(old_vs_mdcr, all(neuromusc_old == neuromusc_mdcr)),
  with(old_vs_mdcr, all(respiratory_old == respiratory_mdcr)),
  with(old_vs_mdcr, all(renal_old == renal_mdcr)),
  with(old_vs_mdcr, all(gi_old == gi_mdcr)),
  with(old_vs_mdcr, all(hemato_immu_old == hemato_immu_mdcr)),
  with(old_vs_mdcr, all(metabolic_old == metabolic_mdcr)),
  with(old_vs_mdcr, all(congeni_genetic_old == congeni_genetic_mdcr)),
  with(old_vs_mdcr, all(malignancy_old == malignancy_mdcr)),
  with(old_vs_mdcr, all(neonatal_old == neonatal_mdcr))
)

# we expect there is no difference in the ccc_flag (old) vs cmrb_flag (new)
stopifnot(
  with(old_vs_mdcr, all(ccc_flag == cmrb_flag))
)

#
# we _do_ expect differences in the tech_dep flag
#
# ICD-9-CM 349.1 - not in the v2 document, but in the software for neuromusc
# only. This raises a problem that the subcondition is not defined.  To allow
# for the methods in medicalcoder to work, a non-missing subcondition is needed.
# device and technology use seems appropriate
#
# ICD-9-CM V56 - same, not in v2 documents, in the software
#
# ICD-10-CM Z49 - same, not in v2 documents, in the software
#
# ICD-9-PCS 86.06 - this is in the document as metabolic (devices) but is only
# listed under metabolic in the software.  Again, because of the use of the
# subconditions in the implementation in medicalcoder the corrected mapping is
# needed in medicalcoder and thus the difference.
#
# ICD-9-CM V45.85 - same as ICD-9-PCS 86.06
#
# ICD-9-CM V53.3 - great, this is a header code used in cvd, the assignable
# codes, V53.31, V53.32, V53.39 are explicitly mapped to tech dep.  The result,
# the V53.3 needs to also have a tech dep flag
# subset(get_icd_codes(), grepl("^V53\\.3", full_code) & icdv == 9)
#
# ICD-9-CM V53.91 "Fitting and adjustment of insulin pump"
# This is listed in the documentation as metabolic (devices) but has been
# implemented in R as metabolic (transplant).  One major issue with this error is
# that there are no codes for metabolic (transplant). It doesn't make sense to
# retain this error so, method=pccc_v2.0 will differ from the R package
# pccc_1.0.7 for this code.
#
# subset(get_icd_codes(with.descriptions = TRUE), grepl("^V53\\.9", full_code) & icdv == 9)
#
# ICD-9-CM V65, and specifically V65.46 (encounter for insulin pump training),
# is not in the documentation but is in the R pccc_v1.0.7 implementation as
# metabolic.  The device flag has been added to this code.
# subset(get_icd_codes(with.descriptions = TRUE), grepl("^V65\\.4", full_code) & icdv == 9)

mismatch_tech_dep <- old_vs_mdcr[old_vs_mdcr$tech_dep != old_vs_mdcr$any_tech_dep, ]

stopifnot(nrow(mismatch_tech_dep) == 32L)

stopifnot(
  all(mismatch_tech_dep$tech_dep == 0L),
  all(mismatch_tech_dep$any_tech_dep == 1L)
)

stopifnot(
  isTRUE(
    identical(
      sort(unique(mismatch_tech_dep$full_code)),
      c("349.1",
        "86.06",
        "V45.85",
        "V53.3",
        "V53.91",
        "V56", "V56.0", "V56.1", "V56.2", "V56.3", "V56.31", "V56.32", "V56.8",
        "V65.46",
        "Z49.01", "Z49.02", "Z49.31", "Z49.32")
    )
  )
)

# we expect there are some differences in the transplant flag
#
# ICD-9-PCS 37.52 -- documented as cvd (device) implemented as cvd and
# transplant.

#subset(get_pccc_codes(), grepl("^37\\.52", full_code))
#subset(get_icd_codes(with.descriptions = TRUE), grepl("^37\\.52", full_code))

# ICD-9-CM V42.0
# documented as renal (transplant)
# missing from the transplant set in the pccc_1.0.7/src/pccc.cpp

#subset(get_pccc_codes(), grepl("^V42\\.0", full_code))
#subset(get_icd_codes(with.descriptions = TRUE), grepl("^V42\\.0", full_code) & icdv == 9)

# ICD-10-CM Z94
# specifically Z94.1, Z94.2, Z94.4, Z94.81, Z94.82, Z94.83, Z94.84
# All documented as subcondition transplant but are missing from the transplant
# set in the pccc_1.0.7/src/pccc.cpp
#
#subset(get_pccc_codes(), grepl("^Z94", full_code))
#subset(get_icd_codes(with.descriptions = TRUE), grepl("^Z94", full_code) & icdv == 10)

#
mismatch_transplant <- old_vs_mdcr[old_vs_mdcr$transplant != old_vs_mdcr$any_transplant, ]
stopifnot(nrow(mismatch_transplant) == 12L)
stopifnot(
  all(mismatch_transplant$transplant == 0L),
  all(mismatch_transplant$any_transplant == 1L)
)

stopifnot(
  isTRUE(
    identical(
      sort(unique(mismatch_transplant$full_code)),
      c("V42.0", "Z94.1", "Z94.2", "Z94.4", "Z94.81", "Z94.82", "Z94.83", "Z94.84")
    )
  )
)


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