https://github.com/pdrhlik/phylomice

mice imputation methods using phylogenetic information
https://github.com/pdrhlik/phylomice

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mice imputation methods using phylogenetic information

• Host: GitHub
• URL: https://github.com/pdrhlik/phylomice
• Owner: pdrhlik
• Created: 2016-06-07T09:08:13.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-07-09T03:13:11.000Z (over 8 years ago)
• Last Synced: 2023-12-13T10:56:36.287Z (11 months ago)
• Language: R
• Homepage:
• Size: 15.6 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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README

        
# phylomice

Extension of R [mice](https://github.com/stefvanbuuren/mice) package adding new imputation methods that incorporate phylogenetic information.

You should be familiar with the mice package to use this one.

## Installation

You can install the package using [devtools](https://github.com/hadley/devtools):

```

devtools::install_github("pdrhlik/phylomice")

```

## Available methods

This is a list of methods that are available in the package. Each of these methods requires two additional arguments to the mice function: `psi` and `psiinv`.

* `psi` is a covariance matrix created from the phylogenetic tree,

* `psiinv` is the inverse of `psi`.

Both of these arguments need to be computed before running mice because of the computational cost.

### Creating `psi` and `psiinv`

Let's assume that you have your tree loaded in a `tree` variable. You can then create `psi` and `psiinv` using the `precomputePsi` helper function. You need to have the [ape](https://github.com/cran/ape) package installed.

```

prec <- precomputePsi(tree)

str(prec)

List of 2

 $ psi   : ...

 $ psiinv: ...

```

### phnorm

Imputes univariate continuous missing data using the generalized least square approach. It is based on the **mice.impute.norm** method in **mice** package.

```

library(phylomice)

imp <- mice(data, method = 'phnorm', psi = psi, psiinv = psiinv)

```

If you have precomputed `psi` and `psiinv` using `precomputePsi`, your call would look like this:

```

imp <- mice(data, method = 'phnorm', psi = prec$psi, psiinv = prec$psiinv)

```

### phpmm

This method is currently under development.

## Authors

* **Patrik Drhlik** - *Initial work* - [pdrhlik](https://github.com/pdrhlik)

* **Simon P. Blomberg** - *Theoretical background*

 

If you are interested in improving current or creating new imputation methods that use phylogenies, don't hesitate to contribute.

## License

This project is licensed under the GPL-3 License.

## Acknowledgments

This project wouldn't be possible without the following parties:

* The University of Queensland, Australia

* Technical University of Liberec, Czech Republic

* NESSIE Erasmus Mundus project