Rogue
Identify Rogue Taxa in Sets of Phylogenetic Trees
Description
Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 25, 2026
ERROR 9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 25, 2026
package dependencies
Package required but not available: ‘TreeDist’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: ... --- re-building ‘Bayesian.Rmd’ using rmarkdown Quitting from Bayesian.Rmd:56-75 [load-trees] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `scan ...[truncated]... rror: processing vignette 'Bayesian.Rmd' failed with diagnostics: cannot read from connection --- failed re-building ‘Bayesian.Rmd’ SUMMARY: processing the following file failed: ‘Bayesian.Rmd’ Error: Vignette re-building failed. Execution halted
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 26, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used.