pred.present.asreml {asreml3Plus} | R Documentation |
This function forms the predictions for each term in terms
using a supplied asreml
object and
predictparallel.asreml
.
Tables are produced using predictparallel.asreml
,
in conjunction with predictiondiffs.asreml
,
with the argument tables
specifying which tables are printed.
The argument plots
, along with transform.power
,
controls which plots are produced. The plots are
produced using predictionplot.asreml
, with
line plots produced when variables involving x.num
or x.fac
are involved in classify
for the predictions and bar charts
otherwise.
In order to get the correct predictions you may need to supply
additional arguments to predict through ...
e.g. present
.
pred.present.asreml(terms, asreml.obj = NULL, wald.tab = NULL, dDF.na = "residual", dDF.values = NULL, x.num = NULL, x.fac = NULL, nonx.fac.order = NULL, x.pred.values = NULL, x.plot.values = NULL, plots = "predictions", panels = "multiple", graphics.device = NULL, error.intervals = "Confidence", avsed.tolerance = 0.25, titles = NULL, colour.scheme = "colour", save.plots = FALSE, transform.power = 1, offset = 0, scale = 1, pairwise = TRUE, tables = "all", levels.length = NA, alpha = 0.05, inestimable.rm = TRUE, trace = FALSE, ggplotFuncs = NULL, ...)
terms |
a |
asreml.obj |
|
wald.tab |
a |
dDF.na |
the method to use to obtain approximate denominator degrees of freedom.
when the numeric or algebraic methods produce an |
dDF.values |
A |
x.num |
A character string giving the name of the numeric covariate that
corresponds to |
x.fac |
A |
nonx.fac.order |
A |
x.pred.values |
The values of |
x.plot.values |
The actual values to be plotted on the x axis or in the labels of
tables. They are
needed when values different to those in |
plots |
Possible values are |
panels |
Possible values are |
graphics.device |
A |
error.intervals |
A character string indicating the type of error interval, if any,
to calculate and plot in order to indicate uncertainty in the results.
Possible values are |
avsed.tolerance |
The values of the range of the SEDs divided by the average of the SEDs that, if exceeded, will cause calculations and plotting to revert to confidence intervals. It should be a value between 0 and 1. |
titles |
A |
colour.scheme |
A character string specifying the colour scheme for the plots.
The default is |
save.plots |
A |
transform.power |
A number specifying the power of a transformation, if one
has been applied to the response variable. Unless it is equal to 1, the default,
back-transforms of the predictions will be obtained and presented in tables
or graphs as appropriate. The back-transform will raise the predictions to the
power equal to the reciprocal of |
offset |
A number that has been added to each value of the response after any scaling
and before applying any power transformation. Unless it is equal to 0, the
default, back-transforms of the predictions will be obtained and presented in
tables or graphs as appropriate. The back-transform will, after backtransforming
for any power transformation and scaling for any scale transformation, subtract
the |
scale |
A number by which each value of the response has been multiply before adding
any offset and applying any power transformation. Unless it is equal to 1, the
default, back-transforms of the predictions will be obtained and presented in
tables or graphs as appropriate. The back-transform will, after backtransforming
for any power transformation, divide by the |
pairwise |
A logical indicating whether all pairise differences of the
|
tables |
The elements of the |
levels.length |
The maximum number of characters from the the levels of
factors to use in the row and column labels of the tables produced by
|
alpha |
the significance level for the test or 1 - alpha is the confidence level for confidence intervals. |
inestimable.rm |
A |
trace |
if TRUE then partial iteration details are displayed when ASReml-R functions are invoked; if FALSE then no output is displayed. |
ggplotFuncs |
A |
... |
further arguments passed to |
a list containing a alldiffs
object for each term
for
which tables are produced. The names of the components of this list are
the terms
with full-stops (.
) replacing colons (:
).
predictparallel.asreml
, predictiondiffs.asreml
,
predictionplot.asreml
,
print.alldiffs
,
as.Date
, Devices
## Not run: data(WaterRunoff.dat) titles <- list("Days since first observation", "Days since first observation", "pH", "Turbidity (NTU)") names(titles) <- names(WaterRunoff.dat)[c(5,7,11:12)] current.asr <- asreml(fixed = log.Turbidity ~ Benches + Sources + Type + Species + Sources:Type + Sources:Species + Sources:Species:xDay + Sources:Species:Date, data = WaterRunoff.dat, keep.order = TRUE) current.asrt <- asrtests(current.asr, NULL, NULL) diff.list <- pred.present.asreml("Date:Sources:Species", asreml.obj = current.asrt$asreml.obj, wald.tab = current.asrt$wald.tab, x.num = "xDay", x.fac = "Date", x.pred.values=sort(unique(WaterRunoff.dat$xDay)), x.plot.values=sort(unique(WaterRunoff.dat$Day)), plots = "predictions", error.intervals = "StandardError", titles = titles, transform.power = 0, present = c("Type","Species","Sources"), tables = "differences", levels.length = 6) ## End(Not run)