# cghFLasso 0.2-1 (CRAN)

Detecting hot spot on CGH array data with fused lasso regression.

[Record of 0.2-1](/cran/cghFLasso/v/0.2-1.md) | Compare: [With 0.1-2](/cran/cghFLasso/compare/0.1-2...0.2-1.md), [With another package](/compare/cghFLasso.md#add), [Downloads](/downloads/compare/cghFLasso.md#add) | [Licences](/cran/cghFLasso/licences.md) | [SBOM](/cran/cghFLasso/sbom.md)

> **Archived on 17 Jun 2018**
>
> CRAN's reason "check problems were not corrected despite reminders" (Checks not fixed)
>
> Last release 0.2-1, 1 Jun 2009
>
> [All archived packages](/archived/left.md)

Install 0.2-1 from CRAN's archive:

```r
# Needs the pak package.
# install.packages("pak")
# Built from source, so it needs build tools.
pak::pak("cran::cghFLasso@0.2-1")
```

- CRAN checks: Not checked (archived 17 Jun 2018)
- Dependent packages: 0 (none suggest it)
- Advisories: None known

## About

[Method](/about/licenses.md)

Spatial smoothing and hot spot detection using the fused lasso regression

- Maintainer: Pei Wang
- Licence: [GPL (>= 2)](/cran/cghFLasso/licences.md)
- Latest release: 1 Jun 2009
- First release: 1 May 2007

- [CRAN page](https://cran.r-project.org/src/contrib/Archive/cghFLasso/)
- [Source of every release](https://github.com/cran/cghFLasso)

[Compare with another package](/compare/cghFLasso.md#add)

**More details**

- Releases: 2
- Date: 2009-06-01

**Cite**

#### Package

Run in R for the authors' preferred citation:

`citation("cghFLasso")`

APA: Johnson, N. A., Tibshirani, R., & Wang., P. (n.d.). cghFLasso: Detecting hot spot on CGH array data with fused lasso
regression. (Version 0.2-1) [Computer software]. Retrieved October 29, 2026, from https://CRAN.R-project.org/package=cghFLasso

BibTeX:

```
@Manual{cghFLasso,
  title  = {cghFLasso: Detecting hot spot on CGH array data with fused lasso
regression.},
  author = {Johnson, Nicholas Austin and Tibshirani, Robert and Wang., Pei},
  note   = {R package version 0.2-1},
  url    = {https://CRAN.R-project.org/package=cghFLasso}
}
```

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.

APA: Balamuta, J. J. (2026). R Observatory: Metrics for cghFLasso version 0.2-1 [Data set]. HJJB, LLC. Data release v2026-10-28. https://doi.org/10.5281/zenodo.21843040

BibTeX:

```
@misc{robservatorycghFLasso,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {cghFLasso} version 0.2-1},
  year      = {2026},
  publisher = {HJJB, LLC},
  doi       = {10.5281/zenodo.21843040},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/cghFLasso},
  note      = {Data set. Data release v2026-10-28}
}
```

From data release v2026-10-28, which the citation names so these numbers can be found later.

## Health

[Method](/about/checks-health.md)

CRAN checks only the packages on CRAN, and it archived this one on 17 Jun 2018.

## Downloads

[Method](/about/downloads.md)

- Downloads in the last 365 days: 42,173 (It is the sum of 2 channels: conda-forge and Bioconda.)

conda-forge alone: rank among conda-forge packages, last 365 days: 685 of 3,828.

| Channel | Downloads in the last 365 days | In the total | Rank in that channel | Change |
| --- | ---: | --- | --- | --- |
| conda-forge | 14,907 | yes | 685 of 3,828 |  |
| Bioconda | 27,266 | yes | 134 of 4,976 |  |

Other windows: [Last 30 days](/cran/cghFLasso.md#downloads), [Last 90 days](/cran/cghFLasso.md?win=90d#downloads), [All time](/cran/cghFLasso.md?win=all#downloads).

To leave channels out of the total, name them in the address, joined by dots: `?off=conda_forge.bioconda`.

#### Over time

Downloads over time, the last 12 whole months:

| Month | CRAN | conda-forge | Bioconda | Sum |
| --- | ---: | ---: | ---: | ---: |
| Oct 2025 | no figure | 1,070 | 2,817 | 3,887 |
| Nov 2025 | no figure | 1,156 | 2,709 | 3,865 |
| Dec 2025 | no figure | 1,310 | 2,731 | 4,041 |
| Jan 2026 | no figure | 997 | 2,718 | 3,715 |
| Feb 2026 | no figure | 1,215 | 2,280 | 3,495 |
| Mar 2026 | no figure | 1,879 | 2,459 | 4,338 |
| Apr 2026 | no figure | 1,131 | 1,978 | 3,109 |
| May 2026 | no figure | 1,226 | 1,598 | 2,824 |
| Jun 2026 | no figure | 1,305 | 1,131 | 2,436 |
| Jul 2026 | no figure | 1,233 | 1,683 | 2,916 |
| Aug 2026 | no figure | 1,018 | 2,375 | 3,393 |
| Sep 2026 | no figure | 1,367 | 2,787 | 4,154 |

First day on record: CRAN 6 Oct 2012, conda-forge 25 Aug 2017, Bioconda 1 Apr 2017.

Every channel here counts downloads, so the channels can be stacked and summed for one period. Each channel counts in its own way and covers a different span of years, so read a sum as a rough total, and read a rise where a channel begins as that channel starting, not as growth.

Weeks start on Monday. A first or last week or month that the channel does not cover in full is left out, so every point is a whole period.

Days with no record add nothing to their week or month. For a little-used package that is usually a day with no downloads, but it can also be a gap in collection.

[Compare downloads](/downloads/compare/cghFLasso.md#add)

## Dependencies

[Method](/about/reverse-dependencies.md)

- Needs: 0
- Dependent packages: 0
- Suggested by: 0

## Code

[Method](/about/code-metrics.md)

Selected function: `L2L1VitPath`

- Kind: Internal R function
- File: R/cghFLasso.R, line 96
- Lines: 29
- Complexity: 6

Called by 1: [`MatchPrimBd`](/cran/cghFLasso.md?fn=MatchPrimBd&view=focus#code)

Calls 7: [`L2L1VitFwd`](/cran/cghFLasso.md?fn=L2L1VitFwd&view=focus#code), [`soft_thresh`](/cran/cghFLasso.md?fn=soft_thresh&view=focus#code), [`GetNumeric`](/cran/cghFLasso.md?fn=GetNumeric&view=focus#code), [`GetInt`](/cran/cghFLasso.md?fn=GetInt&view=focus#code), [`AllocProtectInt`](/cran/cghFLasso.md?fn=AllocProtectInt&view=focus#code), [`AllocProtectReal`](/cran/cghFLasso.md?fn=AllocProtectReal&view=focus#code), [`L2L1GetNFused`](/cran/cghFLasso.md?fn=L2L1GetNFused&view=focus#code)

Paths: 2 steps each way.

Called by 1:

- [`MatchPrimBd`](/cran/cghFLasso.md?fn=MatchPrimBd&view=focus#code), called by 1
  - [`CGH.fused.lasso.one.fast`](/cran/cghFLasso.md?fn=CGH.fused.lasso.one.fast&view=focus#code), called by 1

Calls 7:

- [`L2L1VitFwd`](/cran/cghFLasso.md?fn=L2L1VitFwd&view=focus#code), calls 3
  - [`AddQuadPcwsQuad`](/cran/cghFLasso.md?fn=AddQuadPcwsQuad&view=focus#code)
  - [`L2L1VitArgmax`](/cran/cghFLasso.md?fn=L2L1VitArgmax&view=focus#code)
  - [`L2L1VitMsgMax`](/cran/cghFLasso.md?fn=L2L1VitMsgMax&view=focus#code)
- [`soft_thresh`](/cran/cghFLasso.md?fn=soft_thresh&view=focus#code)
- [`GetNumeric`](/cran/cghFLasso.md?fn=GetNumeric&view=focus#code)
- [`GetInt`](/cran/cghFLasso.md?fn=GetInt&view=focus#code)
- [`AllocProtectInt`](/cran/cghFLasso.md?fn=AllocProtectInt&view=focus#code)
- [`AllocProtectReal`](/cran/cghFLasso.md?fn=AllocProtectReal&view=focus#code)
- [`L2L1GetNFused`](/cran/cghFLasso.md?fn=L2L1GetNFused&view=focus#code)

The open file in the files map is `R/cghFLasso.R`.

- Functions: 26
- Lines: 824
- Calls that stay inside it: 13
- Calls to other files: 15, to 2
- Calls from other files: 0

It calls: `src/L2L1VitExact.c` (14 calls), `src/smooth.f90` (1 call)

| Function in cghFLasso.R | Calls in other files |
| --- | --- |
| [`L2L1VitPath`](/cran/cghFLasso.md?fn=L2L1VitPath&view=focus#code) selected | [`AllocProtectInt`](/cran/cghFLasso.md?fn=AllocProtectInt&view=focus#code), [`AllocProtectReal`](/cran/cghFLasso.md?fn=AllocProtectReal&view=focus#code), [`GetInt`](/cran/cghFLasso.md?fn=GetInt&view=focus#code), [`GetNumeric`](/cran/cghFLasso.md?fn=GetNumeric&view=focus#code) and 3 more |
| [`L2L1Vit`](/cran/cghFLasso.md?fn=L2L1Vit&view=focus#code) | [`GetInt`](/cran/cghFLasso.md?fn=GetInt&view=focus#code), [`GetNumeric`](/cran/cghFLasso.md?fn=GetNumeric&view=focus#code), [`L2L1BackTrace`](/cran/cghFLasso.md?fn=L2L1BackTrace&view=focus#code), [`L2L1VitFwd`](/cran/cghFLasso.md?fn=L2L1VitFwd&view=focus#code) |
| [`L2L1ExpandFit`](/cran/cghFLasso.md?fn=L2L1ExpandFit&view=focus#code) | [`GetNumeric`](/cran/cghFLasso.md?fn=GetNumeric&view=focus#code), [`soft_thresh`](/cran/cghFLasso.md?fn=soft_thresh&view=focus#code) |
| [`L2L1VitPathPrimBds`](/cran/cghFLasso.md?fn=L2L1VitPathPrimBds&view=focus#code) | [`L2L1GetPrimBds`](/cran/cghFLasso.md?fn=L2L1GetPrimBds&view=focus#code) |
| [`plugin.NA`](/cran/cghFLasso.md?fn=plugin.NA&view=focus#code) | [`avesmooth`](/cran/cghFLasso.md?fn=avesmooth&view=focus#code) |

**More functions (21)**

| Function in cghFLasso.R | Calls in other files |
| --- | --- |
| [`CGH.fused.lasso.one.fast`](/cran/cghFLasso.md?fn=CGH.fused.lasso.one.fast&view=focus#code) | nothing outside this file |
| [`CGH.FusedLasso.One`](/cran/cghFLasso.md?fn=CGH.FusedLasso.One&view=focus#code) | nothing outside this file |
| [`cghFLasso`](/cran/cghFLasso.md?fn=cghFLasso&view=focus#code) | nothing outside this file |
| [`cghFLasso.ref`](/cran/cghFLasso.md?fn=cghFLasso.ref&view=focus#code) | nothing outside this file |
| [`consensusFDR`](/cran/cghFLasso.md?fn=consensusFDR&view=focus#code) | nothing outside this file |
| [`countdf`](/cran/cghFLasso.md?fn=countdf&view=focus#code) | nothing outside this file |
| [`fdr.one`](/cran/cghFLasso.md?fn=fdr.one&view=focus#code) | nothing outside this file |
| [`fdr.seg`](/cran/cghFLasso.md?fn=fdr.seg&view=focus#code) | nothing outside this file |
| [`MatchPrimBd`](/cran/cghFLasso.md?fn=MatchPrimBd&view=focus#code) | nothing outside this file |
| [`my.mad`](/cran/cghFLasso.md?fn=my.mad&view=focus#code) | nothing outside this file |
| [`mystand`](/cran/cghFLasso.md?fn=mystand&view=focus#code) | nothing outside this file |
| [`output.cghFLasso`](/cran/cghFLasso.md?fn=output.cghFLasso&view=focus#code) | nothing outside this file |
| [`plot.CGH.FL.All`](/cran/cghFLasso.md?fn=plot.CGH.FL.All&view=focus#code) | nothing outside this file |
| [`plot.CGH.FL.Consensus`](/cran/cghFLasso.md?fn=plot.CGH.FL.Consensus&view=focus#code) | nothing outside this file |
| [`plot.CGH.FL.Single`](/cran/cghFLasso.md?fn=plot.CGH.FL.Single&view=focus#code) | nothing outside this file |
| [`plot.cghFLasso`](/cran/cghFLasso.md?fn=plot.cghFLasso&view=focus#code) | nothing outside this file |
| [`print.summary.cghFLasso`](/cran/cghFLasso.md?fn=print.summary.cghFLasso&view=focus#code) | nothing outside this file |
| [`segment.score`](/cran/cghFLasso.md?fn=segment.score&view=focus#code) | nothing outside this file |
| [`sumabs`](/cran/cghFLasso.md?fn=sumabs&view=focus#code) | nothing outside this file |
| [`sumabsd`](/cran/cghFLasso.md?fn=sumabsd&view=focus#code) | nothing outside this file |
| [`summary.cghFLasso`](/cran/cghFLasso.md?fn=summary.cghFLasso&view=focus#code) | nothing outside this file |


The whole package has 39 function names in 3 files and 33 calls between them. Most calls between files: `R/cghFLasso.R` and `src/L2L1VitExact.c` (14 calls), `R/cghFLasso.R` and `src/smooth.f90` (1 call).

Graph: the whole call graph has 31 function names that take part in a call and 33 calls between them, set out in 6 layers with callers before what they call. 8 function names have no calls and are left out. Called by the most functions: `soft_thresh` (4), `GetNumeric` (3), `GetInt` (2), `L2L1VitFwd` (2), `CGH.fused.lasso.one.fast` (1). Calling the most functions: `L2L1VitPath` (7), `L2L1Vit` (4), `MatchPrimBd` (3), `L2L1VitFwd` (3), `CGH.FusedLasso.One` (3).

Most connected functions: [`L2L1VitPath`](/cran/cghFLasso.md?fn=L2L1VitPath&view=focus#code) 8, [`L2L1Vit`](/cran/cghFLasso.md?fn=L2L1Vit&view=focus#code) 4, [`MatchPrimBd`](/cran/cghFLasso.md?fn=MatchPrimBd&view=focus#code) 4, [`CGH.fused.lasso.one.fast`](/cran/cghFLasso.md?fn=CGH.fused.lasso.one.fast&view=focus#code) 3, [`CGH.FusedLasso.One`](/cran/cghFLasso.md?fn=CGH.FusedLasso.One&view=focus#code) 3, [`L2L1ExpandFit`](/cran/cghFLasso.md?fn=L2L1ExpandFit&view=focus#code) 3

To select another function, add ?fn=NAME to this address.

The call graph also has an address of its own: /cran/cghFLasso/graph.md?fn=L2L1VitPath&view=focus

- Functions: 42
- Public exports: 6
- Lines of R code: 919
- Median complexity: 3.5

**Functions (42)**

| Function (sorted, low to high) | Kind | File | Lines | Complexity |
| --- | --- | --- | ---: | ---: |
| [`cghFLasso`](/cran/cghFLasso.md?fn=cghFLasso#code) | Public | R/cghFLasso.R | 40 | 5 |
| [`cghFLasso.ref`](/cran/cghFLasso.md?fn=cghFLasso.ref#code) | Public | R/cghFLasso.R | 23 | 3 |
| [`output.cghFLasso`](/cran/cghFLasso.md?fn=output.cghFLasso#code) | Public | R/cghFLasso.R | 14 | 3 |
| [`plot.cghFLasso`](/cran/cghFLasso.md?fn=plot.cghFLasso#code) | Public | R/cghFLasso.R | 56 | 7 |
| [`print.summary.cghFLasso`](/cran/cghFLasso.md?fn=print.summary.cghFLasso#code) | Public | R/cghFLasso.R | 20 | 4 |
| [`summary.cghFLasso`](/cran/cghFLasso.md?fn=summary.cghFLasso#code) | Public | R/cghFLasso.R | 41 | 3 |
| [`CGH.FusedLasso.One`](/cran/cghFLasso.md?fn=CGH.FusedLasso.One#code) | Internal | R/cghFLasso.R | 66 | 6 |
| [`CGH.fused.lasso.one.fast`](/cran/cghFLasso.md?fn=CGH.fused.lasso.one.fast#code) | Internal | R/cghFLasso.R | 32 | 1 |
| [`L2L1ExpandFit`](/cran/cghFLasso.md?fn=L2L1ExpandFit#code) | Internal | R/cghFLasso.R | 33 | 6 |
| [`L2L1Vit`](/cran/cghFLasso.md?fn=L2L1Vit#code) | Internal | R/cghFLasso.R | 29 | 5 |
| [`L2L1VitPath`](/cran/cghFLasso.md?fn=L2L1VitPath#code) | Internal | R/cghFLasso.R | 29 | 6 |
| [`L2L1VitPathPrimBds`](/cran/cghFLasso.md?fn=L2L1VitPathPrimBds#code) | Internal | R/cghFLasso.R | 25 | 6 |

This page lists 1 to 12 of 42 functions. [Next](/cran/cghFLasso.md?sort=name&order=asc&fpage=2#functions)

**Size and composition**

#### Lines by kind (2,245)

| Kind | Lines | Share |
| --- | ---: | ---: |
| R code | 919 | 41% |
| Documentation | 474 | 21% |
| Compiled code | 852 | 38% |

#### Lines by language

| Language | Lines | Share |
| --- | ---: | ---: |
| R | 919 | 41% |
| C | 820 | 37% |
| Rd | 474 | 21% |
| Fortran | 32 | 1% |

Languages are counted from file extensions.

- Files: 13
- R functions: 26
- Compiled functions: 16

**Complexity**

- Median: 3.5
- Mean: 4
- Highest: 15
- Median lines per function: 27

_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: 26
- Calls: 13
- Unconnected: 9
- Groups: 4

**Growth (2 releases)**

Total lines by release: from 1,654 (on 1 May 2007) to 2,245 (on 1 Jun 2009). The lowest is 1,654 and the highest is 2,245.

**Release changes**

[Both releases side by side](/cran/cghFLasso/compare/0.1-2...0.2-1.md)

**0.1-2 to 0.2-1**, 1 May 2007 to 1 Jun 2009

- Files changed: 18
- Lines added: 1,045
- Lines deleted: 2,193
- Exports: No change

**Changed measures (19)**

| Measure | Subject | Before | After |
| --- | --- | ---: | ---: |
| Internal functions | Structure | 16 | 20 |
| Total lines | Structure | 1,654 | 2,245 |
| Lines of R code | Structure | 833 | 919 |
| Lines of compiled code | Structure | 342 | 852 |
| R functions | Languages | 22 | 26 |
| C functions | Languages | 0 | 15 |
| Fortran functions | Languages | 9 | 1 |
| Compiled share | Languages | 21% | 38% |
| Lines of documentation | Documentation | 479 | 474 |
| Mean complexity | Complexity | 3.73 | 4 |
| Median complexity | Complexity | 3 | 3.5 |
| Lines per function (mean) | Complexity | 33.64 | 31.69 |
| Functions (nodes) | Call graph | 22 | 26 |
| Call edges | Call graph | 10 | 13 |
| Most connections on one function | Call graph | 3 | 4 |
| Mean connections | Call graph | 0.91 | 1 |
| Functions with no connections | Call graph | 8 | 9 |
| Calls into compiled code | Call graph | 2 | 5 |
| Licence is a standard identifier | Requirements | No | Yes |

**Most changed files (12 of 18)**

| File | Lines added | Lines deleted |
| --- | ---: | ---: |
| `configure` | 0 | 1,692 |
| `src/L2L1VitExact.c` | 821 | 0 |
| `src/CGH.FL.f90` | 0 | 342 |
| `R/cghFLasso.R` | 161 | 75 |
| `configure.in` | 0 | 40 |
| `src/smooth.f90` | 32 | 0 |
| `man/CGH.Rd` | 6 | 15 |
| `DESCRIPTION` | 13 | 7 |
| `configure.win` | 0 | 13 |
| `man/cghFLasso.ref.Rd` | 5 | 2 |
| `man/cghFLasso.Rd` | 3 | 2 |
| `man/summary.cghFLasso.Rd` | 2 | 2 |

## Tests

[Method](/about/coverage.md)

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

[Method](/about/code-metrics.md)

- Exports documented: 100%
- Arguments documented: 100%
- Return value documented: 100%
- Help pages with examples: 83.3%
- Examples run in checks: 100%

**Other documentation**

- README: No
- Release notes file: No
- Help pages: 6
- Lines of documentation: 474

## Datasets

[Method](/about/objects.md)

| Dataset | Size |
| --- | --- |
| [CGH](/cran/cghFLasso/data/CGH.md), Example CGH Array Data | length 5 |

## People

[Method](/about/author-identity.md)

- [Pei Wang](/people/Pei+Wang.md): Maintainer since 0.1-2 (2007)
- [Nicholas Austin Johnson](/people/Nicholas+Austin+Johnson.md)
- [Robert Tibshirani](/people/Robert+Tibshirani.md)
- [Pei Wang.](/people/Pei+Wang..md)

## Repository

[Method](/about/repo-signals.md#figures)

No repository on record

## History

[Method](/about/archive.md)

The line runs from the first release of cghFLasso on 1 May 2007 to 28 Oct 2026 and marks all 2 of its releases. CRAN archived it once, and it has not come back.

#### Archived

| Archived | Back | CRAN's reason | Kind |
| --- | --- | --- | --- |
| 17 Jun 2018 | not back | "check problems were not corrected despite reminders" | Checks not fixed |

| Version | Released | R | Events |
| --- | --- | ---: | --- |
| [0.2-1](/cran/cghFLasso/v/0.2-1.md) | 1 Jun 2009 | 2.9.0 | Archived 17 Jun 2018. “check problems were not corrected despite reminders” |
| [0.1-2](/cran/cghFLasso/v/0.1-2.md) | 1 May 2007 | 2.5.0 |  |

---

R Observatory is independent of the R Project, CRAN and Bioconductor. The same page for people is at /cran/cghFLasso?win=365d, and every address is listed at /llms.txt.