Code hygiene: imports, deprecated ggplot2/scales APIs, loops, progress bars, roxygen

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Evaluación

Dificultad
3/5
Tiempo estimado
1-2 días
Aptitud para principiantes
40/100
Tipo de issue
Refactorización
Claridad
Bastante claro
Estado de actividad
Activo
Stack tecnológico
r
Área
tooling

Línea de trabajo

Start with the individual sites listed in R/psa.R, R/add_common_aes.R, R/owsa.R, and R/run_dsa.R, and check each against the ggplot2/scales/dplyr changes it describes. Begin with the simplest fix, adding @importFrom stats cor in R/psa.R and confirming the NAMESPACE update. Done means devtools::check() shows no new NOTEs and the tests pass with options(lifecycle_verbosity = "error") without deprecation warnings. Coordinate with #213 for the ggplot2 version bump before changing the trans arguments.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

bug good first issue

Suggested owner: Jorge Roa (or a newer contributor) · Plan: Phase 2b

Goal

Remove the deprecation warnings and latent errors that will break on future ggplot2 or R versions, and that JOSS and CRAN reviewers notice.

Scope

  • cor() is used but not imported (R/psa.R:215, R/psa.R:306). Add @importFrom stats cor. The NAMESPACE imports other stats functions but not cor.
  • trans =, soft-deprecated since ggplot2 3.5 (R/add_common_aes.R:208, R/add_common_aes.R:221): switch to transform =. This needs ggplot2 (>= 3.5.0) in DESCRIPTION; see #213.
  • scales::trans_new() is superseded (R/owsa.R:300-302, offset_trans): use scales::new_transform().
  • .groups = "drop_last" passed to group_by(), where it creates a dummy column (R/owsa.R:353, R/owsa.R:356, R/owsa.R:361). It belongs in summarize().
  • Loops of the form for (i in 1:n) that misbehave when n == 0: use seq_len() / seq_along(). The calculate_icers site is handled by #178.
    • R/ceac.R:79, R/ceac.R:289
    • R/create_sa.R:76
    • R/evpi.R:45, R/evppi.R:93, R/evsi.R:173
    • R/gen_psa_samp.R:147, R/gen_psa_samp.R:230, R/gen_psa_samp.R:358 (the last is 1:(n.params - 1))
    • R/icers.R:95
    • R/run_dsa.R:108, R/run_dsa.R:135, R/run_dsa.R:155, R/run_dsa.R:305, R/run_dsa.R:318
    • R/run_psa.R:106, R/run_psa.R:118
  • Progress bars are never closed (R/run_dsa.R:119, R/run_dsa.R:289): add on.exit(close(pb)).
  • rdirichlet() roxygen tags are indented and therefore ignored (R/gen_psa_samp.R:273-275, #' @importFrom / #' @return / #' @export). Reproduced: dampack::rdirichlet is "not an exported object". Decide whether to export it or mark it @keywords internal, then fix the indentation.

Acceptance

  • devtools::check() shows no new NOTEs.
  • Running the tests with options(lifecycle_verbosity = "error") raises no ggplot2/scales deprecation warnings.
  • seq_len() changes are covered by existing tests, plus at least one 0-length test where reachable.
Lenguaje dominante
R
Estrellas
43
Forks
14
Merge medio
4 h 44 min
PR fusionados (30 d)
15

Preparar el entorno

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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