### Name: anova.gls
### Title: Compare Likelihoods of Fitted Objects
### Aliases: anova.gls
### Keywords: models

### ** Examples

# AR(1) errors within each Mare
fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
           correlation = corAR1(form = ~ 1 | Mare))
anova(fm1)
# variance changes with a power of the absolute fitted values?
fm2 <- update(fm1, weights = varPower())
anova(fm1, fm2)

# Pinheiro and Bates, p. 251-252
fm1Orth.gls <- gls(distance ~ Sex * I(age - 11), Orthodont,
                correlation = corSymm(form = ~ 1 | Subject),
                weights = varIdent(form = ~ 1 | age))
fm2Orth.gls <- update(fm1Orth.gls,
                corr = corCompSymm(form = ~ 1 | Subject))
anova(fm1Orth.gls, fm2Orth.gls)

# Pinheiro and Bates, pp. 215-215, 255-260
#p. 215
fm1Dial.lme <-
  lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pressure^4))*QB,
      Dialyzer, ~ pressure + I(pressure^2))
# p. 216
fm2Dial.lme <- update(fm1Dial.lme,
                  weights = varPower(form = ~ pressure))
# p. 255
fm1Dial.gls <- gls(rate ~ (pressure +
     I(pressure^2) + I(pressure^3) + I(pressure^4))*QB,
        Dialyzer)
fm2Dial.gls <- update(fm1Dial.gls,
                 weights = varPower(form = ~ pressure))
anova(fm1Dial.gls, fm2Dial.gls)
fm3Dial.gls <- update(fm2Dial.gls,
                    corr = corAR1(0.771, form = ~ 1 | Subject))
anova(fm2Dial.gls, fm3Dial.gls)
# anova.gls to compare a gls and an lme fit 
anova(fm3Dial.gls, fm2Dial.lme, test = FALSE)

# Pinheiro and Bates, pp. 261-266
fm1Wheat2 <- gls(yield ~ variety - 1, Wheat2)
fm3Wheat2 <- update(fm1Wheat2,
      corr = corRatio(c(12.5, 0.2),
        form = ~ latitude + longitude, nugget = TRUE))
# Test a specific contrast 
anova(fm3Wheat2, L = c(-1, 0, 1))