indelmiss

1.0.10

Insertion Deletion Analysis While Accounting for Possible Missing Data

0packages depend

2.4Kdownloads / year

71.6%test coverage

11/13checks pass

Overview

About

Maintained by Utkarsh J. DangFirst published 2016-08-224 releasesCRAN page ↗

Genome-wide gene insertion and deletion rates can be modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data using the models included within. These models simultaneously estimate insertion and deletion (indel) rates of gene families and proportions of "missing" data for (multiple) taxa of interest. The likelihood framework is utilized for parameter estimation. A phylogenetic tree of the taxa and gene presence/absence patterns (with data ordered by the tips of the tree) are required. See Dang et al. (2016) doi:10.1534/genetics.116.191973 for more details.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

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-indelmiss

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-indelmiss

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-indelmiss

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 3.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.39

71.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 30%

Downloads

2.4K

CRAN downloads in the past year

Rank #17,598 · ~7/day · ~200/mo

Releases R versions

Daily download trend is not available in this view yet.

22130 days

66590 days

2.4K1 year

Compare downloads with other packages →

Also on600 r2u18 autocran

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (4)

Rcpp ape numDeriv phangorn

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 693 (55%)Rd 452 (36%)C++ 104 (8%)

Code characteristics

Object systems

S32

Cyclomatic complexity: 3.0 median / 80 max
Test cases: 6 / 0.39 per code line

Test coverage

Line coverage

72%

Expression

70.2%

Tests / Examples

71.6% / 86% ex

Functions

14 6 exported

Complexity

11.9 avg / 80 max

Call network

14 nodes / 8 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

14 functions

Function	Cyclo	Coverage
plot.indelmiss exp	3	0%
plotp exp	4	0%
plotrates exp	3	0%
plottree exp	5	0%
print.indelmiss exp	7	0%
checkbglist	3	75%

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (2)

Utkarsh J. Dang

no longer listed · 1.0.7 to 1.0.10

G. Brian Golding

no longer listed · 1.0.7 to 1.0.10

Package Timeline

4 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
1.0.10Latest
2023-09-15 · current release · diff ↗
unarchivedReturned to CRAN
2023-09-15
archivedRemoved from CRAN
2023-08-19
email to the maintainer is undeliverable
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.9
2019-03-22 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.8
2018-01-30 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.7
2016-08-22

Show 1 earlier events

R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-08-22
Total releases: 4 / 10 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 14 KB / 3 files
Download size: 35 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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