VGAM (version 1.1-14)

calibrate.qrrvglm.control: Control Function for CQO/CAO Calibration

Description

Algorithmic constants and parameters for running calibrate.qrrvglm are set using this function.

Usage

calibrate.qrrvglm.control(object, trace = FALSE, method.optim = "BFGS",
    gridSize = ifelse(Rank == 1, 21, 9), varI.latvar = FALSE, ...)

Value

A list which with the following components.

trace

Numeric (even though the input can be logical).

gridSize

Positive integer.

varI.latvar

Logical.

Details

Most CQO/CAO users will only need to make use of trace and gridSize. These arguments should be used inside their call to calibrate.qrrvglm, not this function directly.

References

Yee, T. W. (2020). On constrained and unconstrained quadratic ordination. Manuscript in preparation.

See Also

calibrate.qrrvglm, Coef.qrrvglm.

Examples

if (FALSE)  hspider[, 1:6] <- scale(hspider[, 1:6])  # Needed for I.tol=TRUE
set.seed(123)
p1 <- cqo(cbind(Alopacce, Alopcune, Pardlugu, Pardnigr,
                Pardpull, Trocterr, Zoraspin) ~
          WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
          family = poissonff, data = hspider, I.tol = TRUE)
sort(deviance(p1, history = TRUE))  # A history of all the iterations
siteNos <- 3:4  # Calibrate these sites
cp1 <- calibrate(p1, trace = TRUE,
                 new = data.frame(depvar(p1)[siteNos, ]))

if (FALSE) {
# Graphically compare the actual site scores with their calibrated values
persp(p1, main = "Site scores: solid=actual, dashed=calibrated",
      label = TRUE, col = "blue", las = 1)
abline(v = latvar(p1)[siteNos], col = seq(siteNos))  # Actual site scores
abline(v = cp1, lty = 2, col = seq(siteNos))  # Calibrated values
}