Description Usage Arguments Value References Examples

View source: R/getBetaVcovDfList.R

This function returns a list with length equal to a `protLM`

object supplied as input.
Each element of this list corresponds to a model in the `protLM`

object and contains in itself a list holding the parameter estimates `beta`

, the variance-covariance matrix `vcov`

,
the residual degrees of freedom `df`

and the residual standard deviation `sigma`

for this model.
For mixed models, the variance covariance matrix is bias-adjusted, the degrees of freedom are calculated as the trace of the Hat matrix (Ruppert et al., 2003).

1 2 |

`protLM` |
An object of class |

`exp_unit` |
The effect that in all models corresponds to the experimental unit. Only needed when one would like to calculate a more conservative way of estimating the degrees of freedom.
The default way of estimating the degrees of freedom ( |

`pars_between` |
Only used if exp_unit is not |

`printProgress` |
A logical indicating whether the R should print a message before calculating the contrasts for each accession. Defaults to |

`shiny` |
A logical indicating whether this function is being used by a Shiny app. Setting this to |

`message` |
Only used when |

A list with length equal to the `models`

object containing list with four elements: (1) a named column matrix `beta`

containing the parameter estimates, (2) a named square variance-covariance matrix `vcov`

, (3) a numeric value `df`

equal to the residual degrees of freedom, (4) a numeric value `sigma`

equal to the residual standard deviation of the model and (5) `NULL`

if `exp_unit`

is left to its default value `NULL`

, else: a conservative estimate of the degrees of freedom based on the number of experimental units and the degrees of freedom lost due to between-treatment effects..

David Ruppert, M.P. Want and R.J. Carroll. Semiparametric Regression. Cambridge University Press, 2003.

1 2 3 4 | ```
#Load the protLM object protmodel:
data(modelRRCPTAC, package="MSqRob")
betaVcovDfList <- getBetaVcovDfList(getModels(modelRRCPTAC[1:10], simplify=FALSE))
betaVcovDfList
``` |

statOmics/MSqRob documentation built on Nov. 24, 2018, 6:52 a.m.

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.