Description Usage Arguments Details Value Author(s) References See Also Examples

Returns information on the simultaneous construction of the treelet orthonormal basis and hierarchical tree, including which nodes were merged at each step and the basis at each specified step of the construction.

1 | ```
Run_JTree(X, maxlev, whichsave)
``` |

`X` |
the covariance matrix of the data. For example, if using this function on genetics data to improve estimates of heritability, as in the Crossett et al arXiv paper, this argument will be the estimated additive genetic relationship matrix |

`maxlev` |
the maximum height of the tree. This must be an integer between 1 and |

`whichsave` |
a vector containing the levels of the tree, specified as integers between 1 and |

This function serves as a wrapper for the functions `Build_JTree`

and `JTree_Basis`

, which build the hierarchical tree and calculate the basis and covariance matrix at each level, respectively.

a list with components

`basis` |
This is a list with |

`Zpos` |
A matrix of dimension |

`T` |
This is a list with |

`PCidx` |
A matrix of dimension |

`all_nodes` |
A matrix of dimension |

`TreeCovs` |
This is a list with |

Trent Gaugler [email protected]

Lee, AB, Nadler, B, Wasserman, L (2008). Treelets - an adaptive multi-scale basis for sparse unordered data. The Annals of Applied Statistics 2: 435-471. http://www.stat.cmu.edu/~annlee/AOAS137.pdf

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
data(Ahat)
out=Run_JTree(Ahat,49,49)
#The information in out$Zpos[1,] and out$all_nodes[1,]
#both show which two individuals were the first merged
#in the tree. The remaining rows give information
#on subsequent merges in the tree.
basis=out$basis[[49]]
cov=out$TreeCovs[[49]]
temp=basis
#This is how you can use the basis and cov output
#to reconstruct the estimated relationship matrix.
#See how close temp and the original Ahat are:
Ahat1=round(Ahat,14)
temp1=round(temp,14)
sum(Ahat1!=temp1)
#In this example, we do start seeing discrepancies in the 15th digit and beyond.
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.