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

`logLik`

calculates the log likelihood and its gradient
for the vsn model. `plotVsnLogLik`

makes a false color plot for
a 2D section of the likelihood landscape.

1 2 3 4 5 6 7 8 9 10 11 | ```
## S4 method for signature 'vsnInput'
logLik(object, p, mu = numeric(0), sigsq=as.numeric(NA), calib="affine")
plotVsnLogLik(object,
p,
whichp = 1:2,
expand = 1,
ngrid = 31L,
fun = logLik,
main = "log likelihood",
...)
``` |

`object` |
A |

`p` |
For |

`mu` |
Numeric vector of length 0 or |

`sigsq` |
Numeric scalar. |

`calib` |
as in |

`whichp` |
Numeric vector of length 2, with the indices of those
two parameters in |

`expand` |
Numeric vector of length 1 or 2 with expansion factors for the plot range. The range is auto-calculated using a heuristic, but manual adjustment can be useful; see example. |

`ngrid` |
Integer scalar, the grid size. |

`fun` |
Function to use for log-likelihood calculation. This parameter is exposed only for testing purposes. |

`main` |
This parameter is passed on |

`...` |
Arguments that get passed on to |

`logLik`

is an R interface to the likelihood computations in vsn (which are done in C).

For `logLik`

, a numeric matrix of size `nrow(p)+1`

by `ncol(p)`

.
Its columns correspond to the columns of `p`

.
Its first row are the likelihood values, its rows `2...nrow(p)+1`

contain the gradients.
If `mu`

and `sigsq`

are
specified, the ordinary negative log likelihood is calculated using these
parameters as given. If they are not specified, the profile negative log likelihood
is calculated.

For `plotVsnLogLik`

, a dataframe with the 2D grid coordinates and
log likelihood values.

Wolfgang Huber

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
data("kidney")
v = new("vsnInput", x=exprs(kidney),
pstart=array(as.numeric(NA), dim=c(1, ncol(kidney), 2)))
fit = vsn2(kidney)
print(coef(fit))
p = sapply(seq(-1, 1, length=31), function(f) coef(fit)+c(0,0,f,0))
ll = logLik(v, p)
plot(p[3, ], ll[1, ], type="l", xlab=expression(b[1]), ylab=expression(-log(L)))
abline(v=coef(fit)[3], col="red")
plotVsnLogLik(v, coef(fit), whichp=c(1,3), expand=0.2)
``` |

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