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MFPCA

Multivariate Functional Principal Component Analysis

https://github.com/clarahapp/mfpca

Science Score: 33.0%

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    Found 4 DOI reference(s) in README
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    Links to: ieee.org
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    1 of 3 committers (33.3%) from academic institutions
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    Low similarity (11.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Multivariate Functional Principal Component Analysis

Basic Info
  • Host: GitHub
  • Owner: ClaraHapp
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 737 KB
Statistics
  • Stars: 32
  • Watchers: 1
  • Forks: 13
  • Open Issues: 6
  • Releases: 0
Created over 10 years ago · Last pushed 11 months ago

https://github.com/ClaraHapp/MFPCA/blob/master/ 

# MFPCA

[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/MFPCA)](https://cran.r-project.org/package=MFPCA)



`MFPCA` is an `R`-package for calculating a PCA for multivariate functional data observed on different domains, that may also differ in dimension. The estimation algorithm relies on univariate basis expansions for each element of the multivariate functional data.

## Highlights ##

`MFPCA` allows to calculate a principal component analysis for multivariate (i.e. combined) functional data on up to three-dimensional domains:

* Standard functional data defined on a (one-dimensional) interval.
* Functional data with two-dimensional domains (images).
* Functional data with three-dimensional domains (3D images, e.g. brain scans).

It implements various univariate bases:

* Univariate functional PCA (only one-dimensional domains).
* Spline bases (one- and two-dimensional domains; with optional smoothing penalty).
* Cosine bases (two- and three-dimensional domains; fast implementation built on DCT).
* Tensor PCA (two-dimensional domains; UMPCA approach from [Lu et al. (2009)](https://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5272374) and FCP_TPA approach from [Allen (2013)](https://ieeexplore.ieee.org/document/6714047)).
* Given basis functions, e.g. from a previous univariate PCA.

The representation of the data is based on the object-oriented [`funData`](https://github.com/ClaraHapp/funData) package, hence all functionalities for plotting, arithmetics etc. included therein may be used.


## Installation ##

The `MFPCA` pacakge is available on [`CRAN`](https://CRAN.R-project.org/package=MFPCA). To install the latest version directly from GitHub, please use `devtools::install_github("ClaraHapp/MFPCA")` (install [`devtools`](https://cran.r-project.org/package=devtools) before).

If you would like to use the cosine bases make sure that the `C`-library [`fftw3`](http://www.fftw.org/) is installed on your computer before you install `MFPCA`. Otherwise, `MFPCA` is installed without the cosine bases and will throw an error if you attempt to use functions that need `fftw3`.

## Dependencies ##

The `MFPCA` package depends on the `R`-package [`funData`](https://CRAN.R-project.org/package=funData) for representing (multivariate) functional data. It uses functionalities from 
[`abind`](https://CRAN.R-project.org/package=abind), 
[`foreach`](https://CRAN.R-project.org/package=foreach), 
[`irlba`](https://CRAN.R-project.org/package=irlba), 
[`Matrix`](https://CRAN.R-project.org/package=Matrix), 
[`mgcv`](https://CRAN.R-project.org/package=mgcv) and
[`plyr`](https://CRAN.R-project.org/package=plyr).

## References ##

The theoretical foundations of multivariate functional principal component analysis are described in:

C. Happ, S. Greven (2018): [Multivariate Functional Principal Component Analysis for Data Observed on Different (Dimensional) Domains.](https://doi.org/10.1080/01621459.2016.1273115)
    *Journal of the American Statistical Association*, 113(522): 649-659 .
    
For more details on the implementation, which is based on the [`funData`](https://CRAN.R-project.org/package=funData) package, and a case study, see:

C. Happ-Kurz (2020): [Object-Oriented Software for Functional Data.](https://doi.org/10.18637/jss.v093.i05) *Journal of
Statistical Software*, 93(5): 1-38 .

## Bug reports ##

Please use [GitHub issues](https://github.com/ClaraHapp/MFPCA/issues) for reporting bugs or issues.

Owner

  • Name: Clara Happ-Kurz
  • Login: ClaraHapp
  • Kind: user
  • Location: Munich

GitHub Events

Total
  • Watch event: 1
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 1
Last Year
  • Watch event: 1
  • Delete event: 1
  • Push event: 2
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 478
  • Total Committers: 3
  • Avg Commits per committer: 159.333
  • Development Distribution Score (DDS): 0.019
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
ClaraHapp c****p@s****e 469
Clara Happ C****p 8
Katrin Leinweber k****i@p****e 1
Committer Domains (Top 20 + Academic)
posteo.de: 1 stat.uni-muenchen.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 8
  • Total pull requests: 21
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 6
  • Total pull request authors: 2
  • Average comments per issue: 1.13
  • Average comments per pull request: 0.48
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ClaraHapp (3)
  • jtfrench12 (1)
  • velcy (1)
  • TianshuFeng (1)
  • joseabernal (1)
  • crsgls (1)
Pull Request Authors
  • ClaraHapp (20)
  • katrinleinweber (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 519 last-month
  • Total docker downloads: 41,971
  • Total dependent packages: 4
  • Total dependent repositories: 1
  • Total versions: 16
  • Total maintainers: 1
cran.r-project.org: MFPCA

Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains

  • Versions: 16
  • Dependent Packages: 4
  • Dependent Repositories: 1
  • Downloads: 519 Last month
  • Docker Downloads: 41,971
Rankings
Docker downloads count: 0.6%
Forks count: 5.5%
Stargazers count: 9.9%
Dependent packages count: 10.9%
Average: 12.4%
Downloads: 23.7%
Dependent repos count: 24.0%
Maintainers (1)
chk_R@gmx.de
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • funData >= 1.3 depends
  • Matrix * imports
  • abind * imports
  • foreach * imports
  • irlba * imports
  • methods * imports
  • mgcv >= 1.8 imports
  • plyr * imports
  • stats * imports
  • covr * suggests
  • fda * suggests
  • testthat >= 2.0.0 suggests