Older releaseCRAN archived this package on 31 Aug 2013.
trio
‹1.0.7
- 2.1.17 Aug 2013
- 2.0.21 Mar 2013
- 2.0.127 Feb 2013
- 1.9.34 Feb 2013
- 1.7.13 Oct 2012
- 1.7.029 Jul 2012
- 1.5.020 Apr 2012
- 1.4.2618 Apr 2012
- 1.4.249 Feb 2012
- 1.4.237 Feb 2012
- 1.4.186 Feb 2012
- 1.4.1211 Jan 2012
- 1.2.914 Oct 2011
- 1.2.823 Sep 2011
- 1.2.713 Sep 2011
- 1.2.610 Aug 2011
- 1.2.35 Aug 2011
- 1.2.23 Aug 2011
- 1.2.13 Jul 2011
- 1.2.022 Apr 2011
- 1.1.224 Apr 2011
- 1.1.1729 Dec 2010
- 1.1.1620 Dec 2010
- 1.1.1529 Nov 2010
- 1.1.1314 Nov 2010
- 1.1.1229 Sep 2010
- 1.1.1011 Jun 2010
- 1.1.810 Jun 2010
- 1.1.527 May 2010
- 1.1.419 May 2010
- 1.1.019 Apr 2010
- 1.0.1919 Apr 2010
- 1.0.1617 Mar 2010
- 1.0.1510 Mar 2010
- 1.0.148 Mar 2010
- 1.0.133 Mar 2010
- 1.0.121 Mar 2010
- 1.0.226 Feb 2010
- 1.0.1125 Feb 2010
- 1.0.917 Feb 2010
- 1.0.74 Feb 2010
- 1.0.42 Feb 2010
- 1.0.331 Jan 2010
- Released
- 4 Feb 2010R 2.10.1 at the time
- 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 knownfor this release
- Test coverage, method
Method
Test coverage
Test coverage is measured by downloading each CRAN package's current source file, installing its dependencies, building it and running its tests under covr.
- Almost half of CRAN has no tests to run
- Only CRAN packages are measured. Many have no percentage, most often because the package has no tests, and that blank is a recorded outcome, not missing data.
- NOT_CRAN
- Tests run with NOT_CRAN=true, so tests that skip themselves on CRAN run here, and the figure can differ from what CRAN's own checks see.
- Current version only
- Only the current version is measured, and a new version on CRAN is measured again. Older rows are kept but never filled in later. This is one package's run.
- Never 0%
- On a package page three states stay apart: measured, no tests, and not measured. Neither of the last two is ever shown as 0%.
- –not measured for this release
- Public exports, method
Method
Code metrics
Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.
- One row a version
- Each analysed version gives one row of figures. The Code, Tests and Documentation sections, the pages of older releases and Release changes all read from those rows.
- CRAN
- CRAN versions are read from the github.com/cran mirror, which holds one commit for each released source file, and every version tag is analysed. Nothing is built, installed or run.
- Release, not repository
- Documentation describes what the analysed release holds: a
README, vignettes, aNEWSfile 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. - Zero
- Zero means the analysis looked and found none.
- 5none added or removed
Record made 28 Oct 2026, 23:09 UTC from data release v2026-10-28, merged 18:49 UTC. Project DOI 10.5281/zenodo.21843040.
https:/
This page reports what R Observatory measured for this release. It is not a validation, and it does not say whether the package is fit for your intended use.
Compare
Compared with 2.1.1, released 7 Aug 2013.
- Time between
- 1,280 days39 releases in between
- Advisories
- None knownfor either release
- Exports
- 1 removed45 added as well
- Files changed
- 316+29,926 −19,789 lines
Values that differ (15)
| Measure | Section | 1.0.7 | 2.1.1 |
|---|---|---|---|
| Maintainer | Release | Qing Li | Holger Schwender |
| Download size | Release | 331 KB | 722 KB |
| Authors | Release | Qing Li, Holger Schwender | Holger Schwender, Qing Li, Christoph Neumann, Margaret Taub, Ingo Ruczinski |
| Public exports | Code | 5 | 49 |
| Internal functions | Code | 9 | 165 |
| Lines of R code | Code | 10,947 | 16,961 |
| Complexity | Code | mean 7.7, highest 43 | mean 6.4, highest 43 |
| Help pages with running examples | Tests | 0 of 3 | 18 of 32 |
| Help pages | Documentation | 10 | 32 |
| Exports with examples | Documentation | 60% | 100% |
| Arguments documented | Documentation | 100% | 99.2% |
| Return value documented | Documentation | 100% | 96.2% |
| Vignettes | Documentation | 0 | 1 |
| Depends | Dependencies | survival, haplo.stats | R (>= 3.0.1) |
| Suggests | Dependencies | None | survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS (>= 1.28.1) |
Exports added (45)
allelicTDTcolGxEcolGxEPermscolGxGcolGxGPermscolMAFtriocolPOlrtcolTATcolTDTcolTDT2waycolTDTebamcolTDTinter2waycolTDTmaxStatcolTDTmaxTestcolTDTsamcompPermTDT2wayfastGxGfastGxGrecgetGxEstatsgetLDlargegetMatPseudogtdt.ebamgtdt.statlrControlorderSNPsped2genopoly4rootpoly4rootMatprobTDTread.pedfileremoveSNPsremoveTriosscoreGxEscoreGxGscoreMaxStatscoreTDTsplitBlockstdttdt2waytdtGxGtrio.permTesttrio.powertrio.preparetrioFStrioLR
Exports removed (1)
trio
Most changed files (12 of 316)
| File | Lines added | Lines deleted |
|---|---|---|
R/qingInternal.R | 11,056 | 526 |
src/generalLR.f | 3,477 | 3,477 |
inst/doc/trio.Rnw | 1,341 | 726 |
R/tdt.R | 987 | 409 |
src/trioExternal.f | 684 | 684 |
vignettes/trio.Rnw | 1,260 | 32 |
src/trioLR.f | 350 | 769 |
R/trioLR.R | 481 | 248 |
R/colGxE.R | 599 | 118 |
R/trio.power.R | 629 | 7 |
R/colTDTsam.R | 552 | 5 |
inst/plugin/My_own_scoring.f | 442 | 23 |
Release
- Published
- 4 Feb 2010
- Status
- Replaced by 1.0.9 on 17 Feb 2010
- Previous
- 1.0.4, 2 Feb 2010
- License
- LGPL-2, OSI approved
- Maintainer
- Qing Li
- Download size
- 331 KB
- Authors
- Qing Li, Holger Schwender
- Source code
- Not kept for this release
Advisories
- This release
- None known
CRAN checks
Method, CRAN checks Method CRAN runs every current package through Checks and health
R CMD check on a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.
- Results
- CRAN archived this package on 31 Aug 2013
Code
- Lines of R code
- 10,947
- Public exports
- 5
- Internal functions
- 9
- Mean complexity
- 7.7the most is 43
Lines by kind (11,688)
| Kind | Lines | Share |
|---|---|---|
| R code | 10,947 | 94% |
| Documentation | 741 | 6% |
Tests
- Test cases
- 0
- Lines of tests
- 0
- Exports named in tests
- 0%
- Tests
- No
- Test lines per line of code
- 0.00
- Coverage
- Not measured for this release
- Help pages with running examples
- 0 of 3
Documentation
- Exports documented
- 100%
- Arguments documented
- 100%
- Return value documented
- 100%
- Vignettes
- 0
- Help pages
- 10
- Exports with examples
- 60%
- NEWS
- No
- Citation file
- No
- Website
- Not kept for this release
Dependencies
Method, Dependencies Method Dependent packages are other packages that list this one under Reverse dependencies
Depends, Imports or LinkingTo in their DESCRIPTION file. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.Suggests install 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.
- Depends
- survival, haplo.stats
- Imports
- None
- LinkingTo
- None
- Suggests
- None
- Install tree
- Kept only for packages on CRAN
- Advisories in the install tree
- Kept only for packages on CRAN
Today
Checks, downloads, dependents, people and the repository describe the package as it is now, so they are on the package page.
Sources
| Part | From | As of |
|---|---|---|
| Release history | CRAN package versions | 28 Oct 2026 |
| Advisories | osv-advisories 1.0.0, R version 4.6.1 (2026-06-24) | 28 Oct 2026 |
| CRAN checks | CRAN check results | CRAN archived this package on 31 Aug 2013 |
| Tests, documentation, code | rpkg-analyzer 0.5.2 | 5 Oct 2026 |
| Coverage | covr | Not measured for this release |
| Use | CRAN downloads, reverse dependencies, repository | Not shown for this release |
Daily data releases are kept on GitHub, so the data behind this record can be fetched again from v2026-10-28 (merged 18:49 UTC). Values not kept for a release say so and are never filled in from another release.