shinyTempSignal

0.0.8

Explore Temporal and Other Phylogenetic Signals

0packages depend

2.6Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Guangchuang YuFirst published 2022-04-147 releasesCRAN page ↗GitHub ↗

Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("shinyTempSignal", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("YuLab-SMU/shinyTempSignal")

Development version from YuLab-SMU/shinyTempSignal. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-shinytempsignal

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 4.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-08
3 OK · 11 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-07
3 OK · 10 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
3 OK · 11 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 180 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #16,478 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

20630 days

69790 days

2.6K1 year

Compare downloads with other packages →

Also on100 r2u

Repository

GitHub ↗ yulab-smu/shinytempsignal

9Stars

7Forks

1Open issues

0Open PRs

0Releases

152Commits

5Contributors

molecular-clockphylogeneticsshiny-app

152 commits · Last activity 2024-03-06

Stars over time

2024-03-28 · 92026-07-07 · 9

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/yulab-smu/shinytempsignal on 2026-07-19.

Reproducibility and dev environment (2)

data-raw/Makefile

CRAN release process (1)

CRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (2)

VS CodeRStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (15)

ape forecast ggplot2 ggprism ggpmisc ggtree golem (>= 0.3.1)shiny shinydashboard shinyjs shinyWidgetsstatstreeio yulab.utilsnlme

LinkingTo (0)

none

Suggests (10)

attempt conflicted config glue htmltools knitr prettydoc processx rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Guangchuang Yu

Author, Maintainer, Copyright holder

Authors (1)

Guangchuang Yu

Author, Maintainer, Copyright holder

Contributors (4)

Jianfeng Lin

Contributor

Xiao Luo

Contributor · added in 0.0.5

Li Zhan

Contributor · added in 0.0.5

Xuanan Zhu

Contributor

Guangchuang Yu

Author, Maintainer, Copyright holder

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.0.8Latest
2024-03-06 · current release · diff ↗
0.0.7
2024-02-21 · diff ↗
0.0.6
2024-01-22 · diff ↗
0.0.5
2023-12-12 · diff ↗
0.0.4
2023-11-26 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.0.3
2022-07-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.2
2022-04-14
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-04-14
Total releases: 7 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.3.0
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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