plotVariofaces.data.frame {asremlPlus} | R Documentation |
Plots empirical variogram faces, including envelopes, from supplied residuals as described by Stefanova, Smith & Cullis (2009).
Description
Produces a plot for each face of an empirical 2D
variogram
based on supplied residuals from both an observed data set
and simulated data sets. Those from simulated data sets are used to
produce confidence envelopes If the data consists of sections, such as separate
experiments, the two variogram faces are produced for each section. This
function is less efficient in storage terms than variofaces.asreml
,
because here the residuals from all simulated data sets must be saved, in
addition to the values for the variogram faces; in
variofaces.asreml
, the residuals for each simulated data set are
discarded after the variogram has been calculated. On the other hand, the
present function is more flexible, because there is no restriction on how the
residuals are obtained.
Usage
## S3 method for class 'data.frame'
plotVariofaces(data, residuals, restype="Residuals", ...)
Arguments
data |
A |
residuals |
A |
restype |
A |
... |
Other arguments that are passed down to the function |
Details
For each set of residuals, asreml.variogram
is used to obtain the empirical
variogram, from which the values for its faces are obtained. Plots are produced for
each face and include the observed residuals and the 2.5%, 50% & 97.5% quantiles.
Value
A list
with the following components:
face1: a
data.frame
containing the variogram values on which the plot for the first dimension is based.face2: a
data.frame
containing the variogram values on which the plot for the second dimension is based.
Author(s)
Chris Brien
References
Stefanova, K. T., Smith, A. B. & Cullis, B. R. (2009) Enhanced diagnostics for the spatial analysis of field trials. Journal of Agricultural, Biological, and Environmental Statistics, 14, 392–410.
See Also
asremlPlus-package
, asreml
, asreml.variogram
,
variofaces.asreml
, simulate.asreml
.
Examples
## Not run:
data(Wheat.dat)
current.asr <- asreml(yield ~ Rep + WithinColPairs + Variety,
random = ~ Row + Column + units,
residual = ~ ar1(Row):ar1(Column),
data=Wheat.dat)
current.asrt <- as.asrtests(current.asr, NULL, NULL)
current.asrt <- rmboundary.asrtests(current.asrt)
# Form variance matrix based on estimated variance parameters
s2 <- current.asr$sigma2
gamma.Row <- current.asr$gammas[1]
gamma.unit <- current.asr$gammas[2]
rho.r <- current.asr$gammas[4]
rho.c <- current.asr$gammas[5]
row.ar1 <- mat.ar1(order=10, rho=rho.r)
col.ar1 <- mat.ar1(order=15, rho=rho.c)
V <- gamma.Row * fac.sumop(Wheat.dat$Row) +
gamma.unit * diag(1, nrow=150, ncol=150) +
mat.dirprod(col.ar1, row.ar1)
V <- s2*V
#Produce variogram faces plot (Stefanaova et al, 2009)
resid <- simulate(current.asr, V=V, which="residuals")
resid$residuals <- cbind(resid$observed[c("Row","Column")],
resid$residuals)
plotVariofaces(data=resid$observed[c("Row","Column","residuals")],
residuals=resid$residuals,
restype="Standardized conditional residuals")
## End(Not run)