trio
2.1.1CRANTesting of SNPs and SNP Interactions in Case-Parent Trio Studies
Archived on 31 Aug 2013
- CRAN's reason
the request of the maintainer
Maintainer asked- Last release
- 2.1.1, 7 Aug 2013
The same name is also on Bioconductor.
# Needs the pak package.
# install.packages("pak")
pak::pak("cran::trio@2.1.1") - CRAN checks, method
Method
Checks and health
CRAN runs every current package through
R CMD checkon a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.- Problems
- Notes alone never count against a package, but a warning, an error or a failure on any platform is a problem. Open CRAN deadlines are a fact of their own, shown as a clock after the mark, so the mark always says what the checks found.
- Checks only
- Health reflects CRAN's check results and nothing else. Even a package with no tests, no coverage or no recent release can have every platform OK.
- Once a day
- Results are collected once a day from files CRAN publishes. Each platform is one machine set-up, named by its R version, operating system, architecture and compiler, such as r-devel-linux-x86_64-fedora-clang.
- Platforms counted
- The 13 in 3 of 13 is the number of platform rows CRAN published for that package on the day of collection. The set of machines changes over time, so the number is not fixed, and a package missing from a platform counts as neither passing nor failing there.
- Not checkedarchived 31 Aug 2013
- Dependent packages, method
Method
Reverse dependencies
Dependent packages are other packages that list this one under
Depends,ImportsorLinkingToin theirDESCRIPTIONfile. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.- As declared
- The counts follow the declarations as written, not whether a package uses the other one when it runs.
- Suggests apart
- Packages that list this one only under
Suggestsinstall and run without it, and use it for tests, examples or an optional feature. They are counted as Suggested by, never among the dependents, and a package that also lists it under one of the three fields is a dependent and is not counted again. - Zero
- Zero dependents means no current CRAN package declares a need for this one, though some may suggest it. On 28 Oct 2026, 19,572 of the 25,581 current CRAN packages had no dependent package.
- 0none suggest it
- Advisories, method
Method
Security advisories
Advisories come from the R Consortium advisory database, a community record of security problems in R packages, as OSV publishes it.
- The copy
- The record is read once a day. The data is published under the Apache License 2.0 and is credited on the advisories list.
- Box under the name
- Under the package's name, a box names any advisory that affects the current release, with its fix or that there is none.
- Ranges
- Advisories state ranges, such as from 0.9.12 up to but not including 1.8.8. Each range is checked against every version CRAN has published, using the version rules R itself uses, so a release that came out after the advisory was written is still caught by its range.
- Not the package
- The rating is for the library flaw itself, not for how exposed the R package is, and it is never added up into a figure for the package.
- None known
About
Method, About Method Licence figures come from the Licences
License field of each package's DESCRIPTION file, read the way R itself reads it. No licence file is opened.tools::analyze_license() and R's own licence database, as CRAN's checks read it.| is read, so one string can offer two families.
Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio ...
Full description
Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.
- Maintainer
- Holger Schwender
- Licence
- LGPL-2
- Latest release
- 7 Aug 2013
- First release
- 31 Jan 2010
More details
- Releases
- 43
- Needs R
- >= 3.0.1
- Date
- 2013-08-07
Cite
Package
Run in R for the authors' preferred citation:
citation("trio")Schwender, H., Li, Q., Neumann, C., Taub, M., & Ruczinski, I. (n.d.). trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies (Version 2.1.1) [Computer software]. Retrieved October 28, 2026, from https://CRAN.R-project.org/package=trio
About
This package has no citation file, so citation() returns this entry built from DESCRIPTION.
R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
Balamuta, J. J. (2026). R Observatory: Metrics for trio version 2.1.1 [Data set]. HJJB, LLC. Data release v2026-10-28. https://doi.org/10.5281/zenodo.21843040
About
From data release v2026-10-28, which the citation names so these numbers can be found later.
Health
CRAN checks only the packages on CRAN, and it archived this one on 31 Aug 2013.
Downloads
Method, Downloads Method Download figures count requests logged by each distribution channel. They are not counts of installs or of users, because each channel publishes its own totals and this site reads them.Downloads
All time
- Total downloads over all time
- 31,338It is the sum of 3 channels: CRAN, r2u and Bioconda.
The total is 31,338 downloads over all time. It is the sum of 3 channels: CRAN, r2u and Bioconda.
Over time
Dependencies
Code
Method, Code Method Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.Code metrics
README, vignettes, a NEWS file and the shares read from its help pages. Files kept only in the repository, such as a pkgdown configuration or CI files, are read by the repository scan instead.
- Functions
- 410
- Public exports
- 49
- Lines of R code
- 16,961
- Median complexity
- 4
Functions (410)
Size and composition
Lines by kind (29,556)
| Kind | Lines | Share |
|---|---|---|
| R code | 16,961 | 57% |
| Documentation | 3,300 | 11% |
| Guides | 9,295 | 31% |
Lines by language
| Language | Lines | Share |
|---|---|---|
| R | 16,961 | 57% |
| Other | 8,067 | 27% |
| Rd | 3,300 | 11% |
| Vignettes | 1,228 | 4% |
Languages are counted from file extensions.
- Files
- 84
- R functions
- 410
- Object systems
- S3: 28 methods
Complexity
- Median
- 4
- Mean
- 6.39
- Highest
- 43
- Median lines per function
- 24
About complexity
Cyclomatic complexity counts the independent paths through a function: 1 is a straight line, higher is harder to test. R functions only.
Call graph figures
- R functions
- 410
- Calls
- 437
- Unconnected
- 89
- Groups
- 25
Growth (43 releases)
Release changes
Tests
Method, Tests Method Test coverage is measured by downloading each CRAN package's current source file, installing its dependencies, building it and running its tests under covr.Test coverage
No coverage run is on record for this package.
- Lines of tests
- 0
- Exports named in tests
- 0%
- Has tests
- No
- Test frameworks
- No tests in this release
- Test lines per line of code
- 0
Documentation
- Exports documented
- 100%
- Arguments documented
- 99.2%
- Return value documented
- 96.2%
- Help pages with examples
- 100%
- Examples run in checks
- 56.3%
Other documentation
- README
- No
- Release notes file
- No
- Help pages
- 32
- Lines of documentation
- 3,300
Datasets
Method, Datasets Method The datasets inside packages are read from their R objects in datasets
data/ folders when the code is analysed. Each object is described by its class, its shape and its columns, and fingerprinted so the same data can be found in other packages.data() are listed, 76,161 on CRAN and 8,045 on Bioconductor, so the list is not every file in data/.
| Dataset | Size | Columns |
|---|---|---|
| LDdataCase-Parent Trio Dataalso in 1 other package | 500 × 50 | |
| freq. | 20 × 3 | key, hap, freq |
| mat. | 300 × 6 | |
| prob. | 334 × 180 | |
| simuBkMapCase-Parent Trio Dataalso in 1 other package | 66 × 3 | key, hap, freq |
| step3wayCase-Parent Trio Dataalso in 1 other package | length 4 | |
| trio. | 60 × 7 | famid, pid, snp1, snp2, snp3, snp4 and 1 more |
| trio. | 300 × 12 | famid, pid, snp1, snp2, snp3, snp4 and 6 more |
| trio. | 300 × 12 | famid, pid, snp1, snp2, snp3, snp4 and 6 more |
| trio. | 300 × 26 | famid, pid, fatid, motid, sex, affected and 20 more |
| trio. | 300 × 26 | famid, pid, fatid, motid, sex, affected and 20 more |
| trio. | 300 × 26 | famid, pid, fatid, motid, sex, affected and 20 more |
People
Method, People Method People on the site are the names packages give them in their Author and maintainer identity
DESCRIPTION files: authors from the author list, and the maintainer from the Maintainer field. Spellings of one name become one person only where the rules below allow it, and when in doubt the rules keep people apart.
Maintainer since 1.1.4 (2010), previously Qing Li (1.0.2 to 1.1.0)
Repository
Method, figures by host Method Repository signals are the figures read from the source repository a package links to: stars, forks, issues, commits, releases and the time issues take to close. They are read from GitHub, GitLab, Codeberg and Bitbucket.Repository signals
URL and BugReports fields of its DESCRIPTION file. Read-only mirrors, the cran and bioc accounts on GitHub and git.bioconductor.org, are left out.
No repository on record
History
Method, History Method Archived is built from CRAN's archive records, its list of check deadlines and Bioconductor's package records. Every figure is counted to 28 Oct 2026, the day the data was read.Packages leaving
- On CRAN
- Archived
- Release
Archived
| Archived | Back | CRAN's reason | Kind |
|---|---|---|---|
| 31 Aug 2013 | not back | the request of the maintainer | Maintainer asked |
| Version | Released | R | Events |
|---|---|---|---|
| 2.1.1 | 7 Aug 2013 | 3.0.1 | Archived 31 Aug 2013 “the request of the maintainer” |
| 2.0.2 | 1 Mar 2013 | 2.15.3 | |
| 2.0.1 | 27 Feb 2013 | 2.15.2 | |
| 1.9.3 | 4 Feb 2013 | 2.15.2 | |
| 1.7.1 | 3 Oct 2012 | 2.15.1 | |
| 1.7.0 | 29 Jul 2012 | 2.15.1 | |
| 1.5.0 | 20 Apr 2012 | 2.15.0 | |
| 1.4.26 | 18 Apr 2012 | 2.15.0 |
Earlier versions (35)
| Version | Released | R | Events |
|---|---|---|---|
| 1.4.24 | 9 Feb 2012 | 2.14.1 | |
| 1.4.23 | 7 Feb 2012 | 2.14.1 | |
| 1.4.18 | 6 Feb 2012 | 2.14.1 | |
| 1.4.12 | 11 Jan 2012 | 2.14.1 | |
| 1.2.9 | 14 Oct 2011 | 2.13.2 | |
| 1.2.8 | 23 Sep 2011 | 2.13.1 | |
| 1.2.7 | 13 Sep 2011 | 2.13.1 | |
| 1.2.6 | 10 Aug 2011 | 2.13.1 | |
| 1.2.3 | 5 Aug 2011 | 2.13.1 | |
| 1.2.2 | 3 Aug 2011 | 2.13.1 | |
| 1.2.1 | 3 Jul 2011 | 2.13.0 | |
| 1.2.0 | 22 Apr 2011 | 2.13.0 | |
| 1.1.22 | 4 Apr 2011 | 2.12.2 | |
| 1.1.17 | 29 Dec 2010 | 2.12.1 | |
| 1.1.16 | 20 Dec 2010 | 2.12.1 | |
| 1.1.15 | 29 Nov 2010 | 2.12.0 | |
| 1.1.13 | 14 Nov 2010 | 2.12.0 | |
| 1.1.12 | 29 Sep 2010 | 2.11.1 | |
| 1.1.10 | 11 Jun 2010 | 2.11.1 | |
| 1.1.8 | 10 Jun 2010 | 2.11.1 | |
| 1.1.5 | 27 May 2010 | 2.11.0 | |
| 1.1.4 | 19 May 2010 | 2.11.0 | Maintainer: Holger Schwender |
| 1.1.0 | 19 Apr 2010 first seen | 2.10.1 | |
| 1.0.19 | 19 Apr 2010 | 2.10.1 | |
| 1.0.16 | 17 Mar 2010 | 2.10.1 | |
| 1.0.15 | 10 Mar 2010 | 2.10.1 | |
| 1.0.14 | 8 Mar 2010 | 2.10.1 | |
| 1.0.13 | 3 Mar 2010 | 2.10.1 | |
| 1.0.12 | 1 Mar 2010 | 2.10.1 | |
| 1.0.2 | 26 Feb 2010 | 2.10.1 | |
| 1.0.11 | 25 Feb 2010 | 2.10.1 | |
| 1.0.9 | 17 Feb 2010 | 2.10.1 | |
| 1.0.7 | 4 Feb 2010 | 2.10.1 | |
| 1.0.4 | 2 Feb 2010 | 2.10.1 | |
| 1.0.3 | 31 Jan 2010 | 2.10.1 |