The goal of {coder}
is to classify items from one dataset, using codes
from a secondary source with classification schemes based on regular
expressions and weighted indices.
You can install the released version of coder from CRAN with:
# install.packages("coder")
And the development version from GitHub with:
# install.packages("remotes")
remotes::install_github("eribul/coder")
- Determining comorbidities before clinical trials
- Discovering adverse events after surgery
Patient data: The initial rationale for the package was to classify patient data based on medical coding. A typical use case would consider patients from a medical/administrative data base, as identified by some patient id and possibly with some associated date of interest (date of diagnoses/treatment/intervention/hospitalization/rehabilitation). This data source could be for example an administrative hospital register or a national quality register.
Codify: The primary source could then be linked to a secondary (possibly larger) data base including the same patients with corresponding id:s and some coded patient data. This could be a national patient register with medical codes from the International Classification of Diseases (ICD) with corresponding dates of hospital visits/admission/discharge, or a medical prescription register with codes from the Anatomic Therapeutic Chemical (ATC) classification system with dates of medical prescription/dispatch/usage. A time window could be specified relating the date of the primary source (i. e. the date of a primary total hip arthroplasty; THA), to dates from the secondary source (i.e. the date of a medical prescription). ATC codes associated with medical prescriptions during one year prior to THA, could thus be identified and used as a measure of comorbidity. Another time window of 90 days after THA, might instead be used to identify adverse events after surgery.
Classify: To work with medical/chemical codes directly might be
cumbersome, since those classifications tend to be massive and therefore
hard to interpret. It is thus common to use data aggregation as proposed
by some classification or combined index from the literature. This could
be the Charlson or Elixhauser comorbidity indices based on
ICD-codes, or the RxRisk V classification based on ATC-codes. Each of
those tools appear with different code versions (ICD-8, ICD-9, ICD-9-CM,
ICD-10, ICD-10-CA, ICD-10-SE, ICD-10-CM et cetera) and with different
codes recognized as relevant comorbidities (the Charlson index proposed
by Charlson et al, Deyo et al, Romano et al. Quan et al. et cetera).
Using a third object (in addition to the primary and secondary patient
data sets) helps to formalize and structure the use of such
classifications. This is implemented in the coder
package by
classcodes
objects based on regular expressions (often with several
alternative versions). Those classcodes
objects could be prepared by
the user, although a number of default classcodes
are also included in
the package (table below).
Index: Now, instead of working with tens of thousands of individual ICD-codes, each patient might be recognized to have none or some familiar comorbidity such as hypertension, cancer or dementia. This granularity might be too fine-grained still, wherefore an even simpler index score might be searched for. Such scores/indices/weighted sums have been proposed as well and exist in many versions for each of the standard classifications. Some are simple counts, some are weighted sums, and some accounts for some inherited hierarchy (such that ICD-codes for diabetes with and without complications might be recognized in the same patient, although the un-complicated version might be masked by the complicated version in the index).
Conditions: Some further complexity might appear if some codes are only supposed to be recognized based on certain conditions. Patients with THA for example might have an adverse event after surgery if a certain ICD-code is recorded as the main diagnose at a later hospital visit, although the same code could be ignored if recorded only as a secondary diagnosis.
To summarize: The coder package takes three objects: (1) a data
frame/table/tibble with id and possible dates from a primary source; (2)
coded data from a secondary source with the same id and possibly
different dates and; (3) a classcodes
object, either a default one
from the package, or as specified by the user. The outcome is then: (i)
codes associated with each element from (1) identified from (2),
possibly limited to a relevant time window; (ii) a broader
categorization of the relevant codes as prescribed by (3), and; (iii) a
summarized index score based on the relevant categories from (3).
(i-iii) corresponds to the output from functions codify()
,
classify()
and index()
, which could be chained explicitly as
codify() %>% classify() %>% index()
, or implicitly by the
categorize()
function.
Assume we have some patients with surgery at specified dates:
library(coder)
ex_people
#> # A tibble: 100 x 2
#> name surgery
#> <chr> <date>
#> 1 Chen, Trevor 2021-01-04
#> 2 Graves, Acineth 2020-09-26
#> 3 Trujillo, Yanelly 2020-09-13
#> 4 Simpson, Kenneth 2020-12-16
#> 5 Chin, Nelson 2020-11-29
#> 6 Le, Christina 2020-07-03
#> 7 Kang, Xuan 2020-10-05
#> 8 Shuemaker, Lauren 2020-07-04
#> 9 Boucher, Teresa 2020-12-10
#> 10 Le, Soraiya 2020-11-14
#> # ... with 90 more rows
Those patients (among others) were also recorded in a national patient register with date of hospital admissions and diagnoses codes coded by the International Classification of Diseases (ICD) version 10:
ex_icd10
#> # A tibble: 2,376 x 4
#> name admission icd10 hdia
#> <chr> <date> <chr> <lgl>
#> 1 Tran, Kenneth 2020-07-18 S134A FALSE
#> 2 Tran, Kenneth 2021-01-01 W3319 FALSE
#> 3 Tran, Kenneth 2020-12-11 Y0262 TRUE
#> 4 Tran, Kenneth 2020-11-03 X0488 FALSE
#> 5 Sommerville, Dominic 2020-12-23 V8104 FALSE
#> 6 Sommerville, Dominic 2020-08-03 B853 FALSE
#> 7 Sommerville, Dominic 2020-12-18 Q174 FALSE
#> 8 Sommerville, Dominic 2020-08-08 A227 FALSE
#> 9 Sommerville, Dominic 2020-12-13 H702 FALSE
#> 10 Sommerville, Dominic 2020-04-06 X6051 TRUE
#> # ... with 2,366 more rows
Using those two data sets, as well as a classification scheme
(classcodes
object; see below), we can easily identify all Charlson
comorbidities for each patient:
ch <-
categorize(
ex_people, # patients of interest
codedata = ex_icd10, # Medical codes from national patient register
cc = "charlson", # Calculate Charlson comorbidity
id = "name", code = "icd10" # Specify column names
)
#> Classification based on: icd10
ch
#> # A tibble: 100 x 25
#> name surgery myocardial.infa~ congestive.hear~ peripheral.vasc~
#> <chr> <date> <lgl> <lgl> <lgl>
#> 1 Chen~ 2021-01-04 FALSE FALSE FALSE
#> 2 Grav~ 2020-09-26 FALSE FALSE FALSE
#> 3 Truj~ 2020-09-13 FALSE FALSE FALSE
#> 4 Simp~ 2020-12-16 FALSE FALSE FALSE
#> 5 Chin~ 2020-11-29 FALSE FALSE FALSE
#> 6 Le, ~ 2020-07-03 FALSE FALSE FALSE
#> 7 Kang~ 2020-10-05 FALSE FALSE FALSE
#> 8 Shue~ 2020-07-04 FALSE FALSE FALSE
#> 9 Bouc~ 2020-12-10 FALSE FALSE TRUE
#> 10 Le, ~ 2020-11-14 FALSE FALSE FALSE
#> # ... with 90 more rows, and 20 more variables: cerebrovascular.disease <lgl>,
#> # dementia <lgl>, chronic.pulmonary.disease <lgl>, rheumatic.disease <lgl>,
#> # peptic.ulcer.disease <lgl>, mild.liver.disease <lgl>,
#> # diabetes.without.complication <lgl>, hemiplegia.or.paraplegia <lgl>,
#> # renal.disease <lgl>, diabetes.complication <lgl>, malignancy <lgl>,
#> # moderate.or.severe.liver.disease <lgl>, metastatic.solid.tumor <lgl>,
#> # AIDS.HIV <lgl>, charlson <dbl>, deyo_ramano <dbl>, dhoore <dbl>,
#> # ghali <dbl>, quan_original <dbl>, quan_updated <dbl>
How many patients were diagnosed with malignancy?
sum(ch$malignancy)
#> [1] 5
What is the distribution of the combined comorbidity index for each patient?
barplot(table(ch$charlson))
There are many versions of the Charlson comorbidity index, which might
be controlled by the index
argument. We might also be interested only
in diagnoses from 90 days before surgery as specified with an argument
list codify_args
as passed to codify()
:
ch <-
categorize(
ex_people, codedata = ex_icd10, cc = "charlson", id = "name", code = "icd10",
# Additional arguments
index = c("quan_original", "quan_updated"), # Indices
codify_args = list(
date = "surgery", # Name of column with index dates
code_date = "admission", # Name of column with code dates
days = c(-90, -1) # Time window
)
)
#> Classification based on: icd10
Number of malignancies during this period?
sum(ch$malignancy, na.rm = TRUE)
#> [1] 3
Distribution of the index as proposed by Quan et al 2011 during the 90 day period:
barplot(table(ch$quan_updated))
Classification schemes (classcodes
objects, see
vignette("classcodes")
) are based on regular expressions for
computational speed (see vignette("Interpret_regular_expressions")
),
but their content can be summarized and visualized for clarity.
Arbitrary classcodes
objects can also be specified by the user.
The package includes default classcodes
for medical patient data based
on the international classification of diseases version 8, 9 and 10
(ICD-8/9/10), as well as the Anatomical Therapeutic Chemical
Classification System (ATC) for medical prescription data.
Default classcades
are listed in the table. Each classification
(classcodes column) can be based on several code systems (regex column)
and have several alternative weighted indices (indices column). Those
might be combined freely.
coder::all_classcodes()
#> # A tibble: 7 x 3
#> classcodes regex indices
#> <chr> <chr> <chr>
#> 1 charlson icd10, icd9cm_deyo, icd9cm_enhan~ "charlson, deyo_ramano, dhoore~
#> 2 cps icd10 "only_ordinary"
#> 3 elixhauser icd10, icd10_short, icd9cm, icd9~ "sum_all, sum_all_ahrq, walrav~
#> 4 hip_ae icd10, kva, icd10_fracture ""
#> 5 hip_ae_hail~ icd10, kva ""
#> 6 knee_ae icd10, kva ""
#> 7 rxriskv atc_pratt, atc_caughey, atc_garl~ "pratt, sum_all"
coder
uses data.table
as a backend to increase computational speed
for large datasets. There are some R packages with a narrow focus on
Charlson and Elixhauser co-morbidity based on ICD-codes
(icd,
comorbidity,
medicalrisk,
comorbidities.icd10,
icdcoder). The coder
package
includes similar functionalities but has a wider scope.
Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.