Variogram.lme {nlme} | R Documentation |

This method function calculates the semi-variogram for the
within-group residuals from an `lme`

fit. The semi-variogram
values are calculated for pairs of residuals within the same group. If
`collapse`

is different from `"none"`

, the individual
semi-variogram values are collapsed using either a robust estimator
(`robust = TRUE`

) defined in Cressie (1993), or the average of
the values within the same distance interval. The semi-variogram is
useful for modeling the error term correlation structure.

## S3 method for class 'lme': Variogram(object, distance, form, resType, data, na.action, maxDist, length.out, collapse, nint, breaks, robust, metric, ...)

`object` |
an object inheriting from class `lme` , representing
a fitted linear mixed-effects model. |

`distance` |
an optional numeric vector with the distances between
residual pairs. If a grouping variable is present, only the
distances between residual pairs within the same group should be
given. If missing, the distances are calculated based on the
values of the arguments `form` , `data` , and
`metric` , unless `object` includes a `corSpatial`
element, in which case the associated covariate (obtained with the
`getCovariate` method) is used. |

`form` |
an optional one-sided formula specifying the covariate(s)
to be used for calculating the distances between residual pairs and,
optionally, a grouping factor for partitioning the residuals (which
must appear to the right of a `|` operator in
`form` ). Default is `~1` , implying that the observation
order within the groups is used to obtain the distances. |

`resType` |
an optional character string specifying the type of
residuals to be used. If `"response"` , the "raw" residuals
(observed - fitted) are used; else, if `"pearson"` , the
standardized residuals (raw residuals divided by the corresponding
standard errors) are used; else, if `"normalized"` , the
normalized residuals (standardized residuals pre-multiplied by the
inverse square-root factor of the estimated error correlation
matrix) are used. Partial matching of arguments is used, so only the
first character needs to be provided. Defaults to `"pearson"` . |

`data` |
an optional data frame in which to interpret the variables
in `form` . By default, the same data used to fit `object`
is used. |

`na.action` |
a function that indicates what should happen when the
data contain `NA` s. The default action (`na.fail` ) causes
an error message to be printed and the function to terminate, if there
are any incomplete observations. |

`maxDist` |
an optional numeric value for the maximum distance used for calculating the semi-variogram between two residuals. By default all residual pairs are included. |

`length.out` |
an optional integer value. When `object`
includes a `corSpatial` element, its semi-variogram values are
calculated and this argument is used as the `length.out`
argument to the corresponding `Variogram` method. Defaults to
`50` . |

`collapse` |
an optional character string specifying the type of
collapsing to be applied to the individual semi-variogram values. If
equal to `"quantiles"` , the semi-variogram values are split
according to quantiles of the distance distribution, with equal
number of observations per group, with possibly varying distance
interval lengths. Else, if `"fixed"` , the semi-variogram values
are divided according to distance intervals of equal lengths, with
possibly different number of observations per interval. Else, if
`"none"` , no collapsing is used and the individual
semi-variogram values are returned. Defaults to `"quantiles"` . |

`nint` |
an optional integer with the number of intervals to be
used when collapsing the semi-variogram values. Defaults to `20` . |

`robust` |
an optional logical value specifying if a robust
semi-variogram estimator should be used when collapsing the
individual values. If `TRUE` the robust estimator is
used. Defaults to `FALSE` . |

`breaks` |
an optional numeric vector with the breakpoints for the
distance intervals to be used in collapsing the semi-variogram
values. If not missing, the option specified in `collapse` is
ignored. |

`metric` |
an optional character string specifying the distance
metric to be used. The currently available options are
`"euclidean"` for the root sum-of-squares of distances;
`"maximum"` for the maximum difference; and `"manhattan"`
for the sum of the absolute differences. Partial matching of
arguments is used, so only the first three characters need to be
provided. Defaults to `"euclidean"` . |

`...` |
some methods for this generic require additional arguments. None are used in this method. |

a data frame with columns `variog`

and `dist`

representing,
respectively, the semi-variogram values and the corresponding
distances. If the semi-variogram values are collapsed, an extra
column, `n.pairs`

, with the number of residual pairs used in each
semi-variogram calculation, is included in the returned data frame. If
`object`

includes a `corSpatial`

element, a data frame with
its corresponding semi-variogram is included in the returned value, as
an attribute `"modelVariog"`

. The returned value inherits from
class `Variogram`

.

Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu

Cressie, N.A.C. (1993), "Statistics for Spatial Data", J. Wiley & Sons.

`lme`

, `Variogram.default`

,
`Variogram.gls`

, `plot.Variogram`

## Not run: fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat) Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE) ## End(Not run)

[Package *nlme* version 3.1-57 Index]