cran-comments.md

In gherardovarando/stagedtrees: Staged Event Trees

stagedtrees 2.3.0

• Fix new package doc format.
• Carli et al. 2022 JSS citation added in DESCRIPTION.
• Added functions for random generation of staged trees: random_sevt and random_parentslist.
• Added new function depsubtree which build the dependency subtree.
• New functions to translate sevt and ceg objects to graphs (edge lists and igraph).
• Fix #98; fixed handling of NAs.
• fix bug on plot.sevt and on graph conversion methods when ignoring stage "1" which is assigned to root
• Fix #80; sevt_fit earns the scope argument, it is now possible to do partial re-fit of staged tree models. Moreover, with the compute_logLik argument, the user can decide if the log-likelihood should be computed when fitting the model.
• stages_hclust can now search the best cut of the hierarchical cluster with respect to some score function to be maximized.
• various minor fixes in colors specification for visualization functions.
• stages_simplebhc implements a new stage structure search by iterative joining of positions, thus searching in the space of simple staged trees.
• sevt_simplify return the simplified staged tree, that is a stage tree where positions and stages are equivalent.
• fix problem with positions computation in ceg when model has less than two variables.
• Fix #113; use cli package for errors and warnings.
• improve arguments checks in various functions.
• improve specific checks for sevt objects.
• fix minor coding style problems (some argument names have changed).
• improve test coverage.
• new return value of stages function and new indexing of stages via a new dedicated class sevt.stgs.
• use faster and unsafe functions internally, speedup in various functions (up to 10x).
• implemented stages_csbhc, a new stages learning algorithm which iteratively add context specific independencies. Additionally functions ci_matrices and join_all have been added.

Test environments

• local ubuntu 22.04.3 (64-bit) R 4.3.2
• github actions windows-latest (R release)
• github actions windows-latest (R 4.1)
• github actions windows-latest (R 3.6)
• github actions macOS-latest (R release)
• github actions ubuntu-latest (R release)
• github actions ubuntu-latest (R devel)
• github actions ubuntu-latest (R oldrel 1-4)
• win-builder (r-release)
• win-builder (r-oldrelease)
• win-builder (r-devel)
• mac-builder (r-release)
• R-hub windows-x86_64-devel (r-devel)
• R-hub ubuntu-gcc-release (r-release)
• R-hub fedora-clang-devel (r-devel)

R CMD Check results

local ubuntu 22.04.3 R 4.3.2

devtools::check()

── R CMD check results ─ stagedtrees 2.3.0 ──── Duration: 43s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

R CMD check succeeded

R CMD check --as-cran

Status: OK

github actions R-CMD-check

Status: OK

except ubuntu-latest (oldrel 1-4) Error: ! error in pak subprocess Caused by error: ! Could not solve package dependencies: * deps::.: Can't install dependency bnlearn * bnlearn: Needs R >= 4.3.0 * any::sessioninfo: dependency conflict * any::rcmdcheck: dependency conflict

The above is unrelated with the stagedtrees package. Package bnlearn is suggested for stagedtrees thus it should not be required.

win-builder

Status: 1 NOTE

Possibly misspelled words in DESCRIPTION: Carli (22:14) Leonelli (22:23) Varando (22:49)

The above words are the family names of the package authors and are correct.

macos-builder

Status: OK

• elapsed time (check, wall clock): 0:33

Rhub

❯ On windows-x86_64-devel (r-devel) checking CRAN incoming feasibility ... [14s] NOTE Maintainer: 'Gherardo Varando [e-mail]'

Possibly misspelled words in DESCRIPTION: Carli (22:14) Leonelli (22:23) Varando (22:49)

❯ On windows-x86_64-devel (r-devel) checking HTML version of manual ... [12s] NOTE Skipping checking math rendering: package 'V8' unavailable

❯ On windows-x86_64-devel (r-devel) checking for non-standard things in the check directory ... NOTE Found the following files/directories: ''NULL''

❯ On windows-x86_64-devel (r-devel) checking for detritus in the temp directory ... NOTE Found the following files/directories: 'lastMiKTeXException'

❯ On ubuntu-gcc-release (r-release) checking CRAN incoming feasibility ... [8s/32s] NOTE Maintainer: ‘Gherardo Varando [e-mail]’

Possibly misspelled words in DESCRIPTION: Carli (22:14) Leonelli (22:23) Varando (22:49)

❯ On ubuntu-gcc-release (r-release), fedora-clang-devel (r-devel) checking HTML version of manual ... NOTE Skipping checking HTML validation: no command 'tidy' found Skipping checking math rendering: package 'V8' unavailable

❯ On fedora-clang-devel (r-devel) checking CRAN incoming feasibility ... [9s/38s] NOTE Maintainer: ‘Gherardo Varando [e-mail]’

Possibly misspelled words in DESCRIPTION: Carli (22:14) Leonelli (22:23) Varando (22:49)

0 errors ✔ | 0 warnings ✔ | 7 notes ✖

gherardovarando/stagedtrees documentation built on July 5, 2025, 12:35 a.m.