STraTUS

Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

v1.1.2 · Apr 4, 2020 · GPL

Description

For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.

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14 NOTE

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	138.2s
r-devel-linux-x86_64-debian-gcc	NOTE	96.3s
r-devel-linux-x86_64-fedora-clang	NOTE	210.2s
r-devel-linux-x86_64-fedora-gcc	NOTE	198.6s
r-devel-macos-arm64	NOTE	32s
r-devel-windows-x86_64	NOTE	134s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	84s
r-oldrel-windows-x86_64	NOTE	162s
r-patched-linux-x86_64	NOTE	127.6s
r-release-linux-x86_64	NOTE	124s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	89s
r-release-windows-x86_64	NOTE	132s

Check details (14 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

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NOTE r-devel-macos-arm64

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checkRd: (-1) tt.generator.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:38: Lost braces in \itemize; \
...[truncated]...
r.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:43-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:38: Lost braces in \itemize; \
...[truncated]...
r.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:43-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:38: Lost braces in \itemize; \
...[truncated]...
r.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:43-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:38: Lost braces in \itemize; \
...[truncated]...
r.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:43-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in 
...[truncated]...
d:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

Dependency Network

Version History

new 1.1.2 Mar 10, 2026

updated 1.1.2 ← 1.1.1 diff Apr 3, 2020

updated 1.1.1 ← 1.1 diff May 20, 2019

new 1.1 Mar 17, 2019

Maintainer

Matthew Hall

Dependencies

Depends

R (>= 3.4)

Imports

ape phangorn igraph gmp ggplot2 ggtree (>= 2.0.0) RcppAlgos stats

Compilation

No compilation needed

First Published

Mar 17, 2019

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