nlme: corRatio – R documentation

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corRatio

Rational Quadratic Correlation Structure

Description

This function is a constructor for the corRatio class, representing a rational quadratic spatial correlation structure. Letting d denote the range and n denote the nugget effect, the correlation between two observations a distance r apart is 1/(1+(r/d)^2) when no nugget effect is present and (1-n)/(1+(r/d)^2) when a nugget effect is assumed. Objects created using this constructor need to be later initialized using the appropriate Initialize method.

Usage

corRatio(value, form, nugget, metric, fixed)

Arguments

`value`	an optional vector with the parameter values in constrained form. If `nugget` is `FALSE`, `value` can have only one element, corresponding to the "range" of the rational quadratic correlation structure, which must be greater than zero. If `nugget` is `TRUE`, meaning that a nugget effect is present, `value` can contain one or two elements, the first being the "range" and the second the "nugget effect" (one minus the correlation between two observations taken arbitrarily close together); the first must be greater than zero and the second must be between zero and one. Defaults to `numeric(0)`, which results in a range of 90% of the minimum distance and a nugget effect of 0.1 being assigned to the parameters when `object` is initialized.
`form`	a one sided formula of the form `~ S1+...+Sp`, or `~ S1+...+Sp \| g`, specifying spatial covariates `S1` through `Sp` and, optionally, a grouping factor `g`. When a grouping factor is present in `form`, the correlation structure is assumed to apply only to observations within the same grouping level; observations with different grouping levels are assumed to be uncorrelated. Defaults to `~ 1`, which corresponds to using the order of the observations in the data as a covariate, and no groups.
`nugget`	an optional logical value indicating whether a nugget effect is present. Defaults to `FALSE`.
`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"`.
`fixed`	an optional logical value indicating whether the coefficients should be allowed to vary in the optimization, or kept fixed at their initial value. Defaults to `FALSE`, in which case the coefficients are allowed to vary.

Value

an object of class corRatio, also inheriting from class corSpatial, representing a rational quadratic spatial correlation structure.

Author(s)

José Pinheiro and Douglas Bates bates@stat.wisc.edu

References

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

Venables, W.N. and Ripley, B.D. (2002) "Modern Applied Statistics with S", 4th Edition, Springer-Verlag.

Littel, Milliken, Stroup, and Wolfinger (1996) "SAS Systems for Mixed Models", SAS Institute.

Pinheiro, J.C., and Bates, D.M. (2000) "Mixed-Effects Models in S and S-PLUS", Springer.

Examples

sp1 <- corRatio(form = ~ x + y + z)

# example lme(..., corRatio ...)
# Pinheiro and Bates, pp. 222-249
fm1BW.lme <- lme(weight ~ Time * Diet, BodyWeight,
                   random = ~ Time)
# p. 223
fm2BW.lme <- update(fm1BW.lme, weights = varPower())
# p 246 
fm3BW.lme <- update(fm2BW.lme,
           correlation = corExp(form = ~ Time))
# p. 249
fm5BW.lme <- update(fm3BW.lme, correlation =
                   corRatio(form = ~ Time))

# example gls(..., corRatio ...)
# Pinheiro and Bates, pp. 261, 263
fm1Wheat2 <- gls(yield ~ variety - 1, Wheat2)
# p. 263 
fm3Wheat2 <- update(fm1Wheat2, corr = 
    corRatio(c(12.5, 0.2),
       form = ~ latitude + longitude,
             nugget = TRUE))

nlme

Linear and Nonlinear Mixed Effects Models

v3.1-152

GPL (>= 2) | file LICENCE

Authors

José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R-core [aut, cre]

Initial release

2021-02-03