ciecl: International Classification of Diseases ICD-10/ICD-11 for Chile

[Rodotasso]

Submitting Author Name: Rodolfo Tasso Suazo
Submitting Author Github Handle: @Rodotasso
Other Package Authors Github handles: (comma separated, delete if none)
Repository: https://github.com/Rodotasso/ciecl
Version submitted: 0.9.6
Submission type: Standard
Editor: TBD
Reviewers: TBD

Archive: TBD
Version accepted: TBD
Language: en

---

• Paste the full DESCRIPTION file inside a code block below:

Package: ciecl
Title: International Classification of Diseases 'ICD-10'/'ICD-11' for Chile
Version: 0.9.6
Authors@R:
    person("Rodolfo", "Tasso Suazo",
           email = "rtasso@uchile.cl",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-1264-4933"))
Description: Tools for working with the International Classification of
    Diseases ('ICD-10' Chile official 'MINSAL'/'DEIS' v2018). Includes
    optimized 'SQL' search with 'SQLite', fuzzy matching of medical terms
    ('Jaro-Winkler'), Charlson and Elixhauser comorbidity calculation,
    'WHO' 'ICD-11' 'API' integration, and hierarchical code validation.
    Data from Centro FIC Chile 'DEIS' <https://deis.minsal.cl/centrofic/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1.0)
Imports: DBI, RSQLite, stringdist, stringr, dplyr, tibble, tools, utils
Suggests: comorbidity, gt, httr2, readxl, usethis, withr, writexl,
    testthat (>= 3.1.5), knitr, litedown (>= 0.9), rmarkdown
URL: https://rodotasso.github.io/ciecl/,
    https://github.com/RodoTasso/ciecl
BugReports: https://github.com/RodoTasso/ciecl/issues

Scope

• data munging
• data validation and testing
• database software bindings

Explain how/why the package fits into these categories:

ciecl provides tools for working with Chile's official ICD-10 classification (MINSAL/DEIS v2018, 39,877 codes). It fits data munging (normalizing, expanding, and validating ICD-10 codes from messy clinical data), data validation (validating code format and existence against the official dataset), and database bindings (SQLite-backed search with FTS5 full-text indexing for fast lookups).

Target audience and scientific applications:

Health researchers, epidemiologists, biostatisticians, and public health analysts working with Chilean hospital discharge records, morbidity data, and clinical registries. The package is designed for the School of Public Health (Universidad de Chile) Data Science for Public Health group and the broader health informatics community in Chile and Latin America.

Are there other R packages that accomplish the same thing?

• icd (CRAN): US-focused ICD-9/10 comorbidity calculations. Does not include Chilean codes or MINSAL/DEIS classifications.
• comorbidity (CRAN): Comorbidity indices from ICD codes. ciecl uses it as optional backend and adds Chile-specific code search, fuzzy matching, and the complete MINSAL dataset.
• ICD10gm (CRAN): German ICD-10-GM modification. Country-specific like ciecl but for Germany.
• No existing R package provides the Chilean ICD-10 classification with Spanish-language fuzzy search and medical abbreviation support.

Ethics, data privacy, human subjects:

The package contains only publicly available classification codes from MINSAL/DEIS (government open data). No patient data is included or processed. The WHO ICD-11 API integration uses publicly available endpoints. No ethical concerns apply.

Pre-submission inquiry link: N/A

Explain any pkgcheck items which your package is unable to pass:

The goodpractice linter warnings are for line lengths >80 chars in test files (not in source code) and 95.6% coverage (vs 100%).

Technical checks

• I have read the rOpenSci packaging guide.

• I have read the author guide and I expect to maintain this package for at least 2 years.

• No Terms of Service violations

• CRAN and OSI accepted license (MIT)

• README with development installation instructions

• Roxygen2 documentation with examples for all exported functions

• Vignettes (5: English guide, Spanish guide, hospital discharge use case, language guide, installation)

• Test suite (1148 tests, 95.6% coverage)

• Continuous integration with coverage reporting (GitHub Actions: R-CMD-check, test-coverage)

Generative AI disclosure

• Generative AI tools were used in the development of this package.

AI tools (Claude Code / Claude Opus) were used to assist with: test suite expansion, documentation translation (Spanish - English), CI/CD workflow configuration, and code review. All AI-generated code was reviewed and validated by the author. The package repository is at https://github.com/Rodotasso/ciecl.

Publication options

• This package is currently on CRAN (v0.9.3).
• This package is on Bioconductor.
• This package is intended for submission to Methods in Ecology and Evolution.

Code of Conduct

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[ropensci-review-bot]

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

[emilyriederer]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for ciecl (v0.9.6)

git hash: 29bcc757

• ✔️ Package is already on CRAN.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 95.7%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	197
internal	ciecl	38
internal	graphics	1
internal	stats	1
imports	stringr	21
imports	dplyr	11
imports	DBI	10
imports	utils	6
imports	tibble	5
imports	RSQLite	2
imports	tools	2
imports	stringdist	1
suggests	httr2	7
suggests	usethis	2
suggests	comorbidity	1
suggests	gt	1
suggests	readxl	1
suggests	withr	NA
suggests	writexl	NA
suggests	testthat	NA
suggests	knitr	NA
suggests	litedown	NA
suggests	rmarkdown	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

list (91), character (17), vapply (12), paste0 (7), c (6), names (6), raw (6), is.na (4), tolower (4), ifelse (3), nchar (3), toupper (3), as.character (2), file.path (2), gsub (2), lapply (2), logical (2), paste (2), seq_along (2), sprintf (2), sum (2), unique (2), unlist (2), close (1), data.frame (1), emptyenv (1), file.exists (1), for (1), if (1), is.null (1), max (1), new.env (1), q (1), strsplit (1), switch (1), trimws (1)

ciecl

get_cie10_db (6), cie_lookup (3), get_siglas_medicas (3), cie_normalizar (2), cie_search (2), cie10_empty_tibble (2), normalizar_tildes (2), build_cache_atomic (1), build_fts (1), cache_is_current (1), cie_comorbid (1), cie_expand (1), cie_guia_busqueda (1), cie_lookup_single (1), cie_map_comorbid (1), cie_siglas (1), cie_table (1), cie_validate_vector (1), cie10_clear_cache (1), cie10_disconnect (1), cie10_sql (1), cie11_search (1), expandir_sigla (1), parsear_cie10_minsal (1), sigla_to_codigo (1)

stringr

str_detect (8), str_trim (7), str_split (3), str_extract (2), regex (1)

dplyr

any_of (3), all_of (2), matches (2), slice_head (2), everything (1), mutate (1)

DBI

dbGetQuery (7), dbConnect (2), dbWriteTable (1)

httr2

resp_body_json (3), req_perform (2), request (2)

utils

data (4), packageVersion (2)

tibble

tibble (4), as_tibble (1)

RSQLite

SQLite (2)

tools

R_user_dir (2)

usethis

use_data (2)

comorbidity

comorbidity (1)

graphics

title (1)

gt

fmt_markdown (1)

readxl

read_excel (1)

stats

weights (1)

stringdist

stringsim (1)

---

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in R (100% in 10 files) and
• 1 authors
• 5 vignettes
• 1 internal data file
• 8 imported packages
• 14 exported functions (median 23 lines of code)
• 17 non-exported functions in R (median 10 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	10	67.7
files_vignettes	5	96.6
files_tests	18	95.9
loc_R	1324	79.8
loc_vignettes	473	75.5
loc_tests	4337	97.3	TRUE
num_vignettes	5	96.8	TRUE
data_size_total	295860	81.4
data_size_median	295860	92.0
n_fns_r	31	73.5
n_fns_r_exported	14	65.2
n_fns_r_not_exported	17	79.9
n_fns_per_file_r	3	71.2
num_params_per_fn	2	28.7
loc_per_fn_r	18	64.7
loc_per_fn_r_exp	24	63.0
loc_per_fn_r_not_exp	10	71.1
doclines_per_fn_exp	21	35.2
doclines_per_fn_not_exp	5	88.3
fn_call_network_size	39	70.8

---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
23983557503	pkgdown	success	29bcc7	3	2026-04-04
23983557516	R-CMD-check	success	29bcc7	71	2026-04-04
23983557506	test-coverage	success	29bcc7	25	2026-04-04

---

3b. goodpractice results

Test coverage with covr

Package coverage: 95.69

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
cie_search	37
cie11_search	35
get_cie10_db	19
cie_lookup	17

Static code analyses with lintr

lintr found the following 91 potential issues:

message	number of times
Lines should not be more than 80 characters.	91

---

Package Versions

package	version
pkgstats	0.2.2.20
pkgcheck	0.1.2.276

---

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor.

This package has some noteworthy properties, see 'Package Statistics' details above.

[emilyriederer]

Hi @Rodotasso - thanks for the submission! Does this package have a documentation website? i didn't see one linked from GitHub.

[Rodotasso]

Hi @emilyriederer, thanks for the quick response! Yes, the pkgdown site is live at https://rodotasso.github.io/ciecl/. It's also listed in the DESCRIPTION URL field, but I notice the link might not be prominently visible from the GitHub repo page. I'll make sure it's easy to find. Thanks!

[emilyriederer]

Thank you, @Rodotasso ! Sorry I missed that

[Rodotasso]

Hi @emilyriederer !, idk if i have to let a msg for the pkgdown badge in the readme on repo, but i've done, sorry if i'm late. :)

[emilyriederer]

Thanks @Rodotasso and apologies for the slow reply! A few more initial questions:

• I notice the package has a very large amount of stored data. Did you consider having a function to let users download this versus shipping it inside of the package?
• I notice the main pkgdown website is bilingual English/Spanish (very nice!) but the function docs are in only Spanish. Is that true? I'm thinking what the best language for an editor would be

[Rodotasso]

Tyvm @emilyriederer for the reply and the questions!

On the stored data - I think you're referring to data/cie10_cl.rda? That file is just 289 KB zipped. The total number of codes (39,873) might give the impression of a large file, but the compressed .rda is quite small. The tarball on CRAN for v0.9.3 is around 2.6 MB in total. If you were referring to a different file, I'm happy to clarify.

One thing worth noting: in v0.9.3 I already removed a pre-built SQLite cache (~21 MB) that used to ship in inst/extdata/. It's now built on first use from the .rda into the user cache directory (tools::R_user_dir("ciecl", "data")), so the installed package stays lean.

On the bilingual question: yes, the pkgdown site and external documentation are bilingual, but the function docs are deliberately in Spanish because of the target users' context in Chile. The package is meant to support interoperability across real-world use cases - research, administrative, clinical, and even health-payment systems (GRD/DRG) - and in all of those domains the canonical CIE-10-CL terminology only exists in Spanish. Going English-first would create a gap between the code and the terminology users actually work with every day.

If it helps, I'm happy to consider adding English titles/descriptions in roxygen, or bilingual comments. Just let me know what works best on your end.