Multiple Comparisons Dialog Function

DESCRIPTION:

This function is used by the Multiple Comparisons dialog. The function calls multicomp and print.multicomp and plot.multicomp if necessary.

USAGE:

menuMulticomp(x, focus=NULL, adjust=NULL, lmat=NULL, 
              comparisons, conf.level, bounds, error.type, 
              method, crit.point=NULL, control=NULL, 
              simsize=NULL, plot, valid.check, est.check, 
              print.p, Srank = NULL, call.new.graphsheet = T) 

REQUIRED ARGUMENTS:

x
a model object that inherits from class "lm", typically this is created by a call to lm or aov.

OPTIONAL ARGUMENTS:

focus
the name of a factor in the lm model upon whose levels linear combinations will be computed; focus, adjust, and/or comparisons together specify the linear combinations. If focus, adjust and lmat are all NULL, the first factor in the specified model (if any) will be used as the focus factor.
adjust
a list of other factors and/or covariates in the model, and specified adjustment values for these. If NULL, the adjustment values will be the average over the levels of every (non- focus) factor in the model, and the grand average values of numeric covariates. Several combinations of values may be specified for each factor/covariate; adjusted means for the focus factor will be computed for every combination of values specified in the adjust list.
lmat
a matrix of coefficients specifying linear combinations. Each column of lmat specifies a linear combination to be estimated under the "textbook parametrization" of the linear model (see the details section in the multicomp help file). Warning: factor levels are ordered alphabetically within factors. Specifying lmat directly will override the focus and adjust arguments.
comparisons
a keyword specifying standard differences of the adjusted means specified by focus or adjust, or of the linear combinations specified by the columns of lmat. Available keywords at this time are the default "mca" for all pairwise differences of adjusted means; "mcc" for pairwise differences between a single adjusted mean of the focus factor or lmat column (the control) and the others; or "none", if the adjusted means or lmat columns themselves are of interest without further differencing. Any other value for comparisons will have the same effect as "none". If several adjustment combinations are specified by the adjust list, the differences specified by comparisons will be applied within each of these combinations.
conf.level
the desired joint confidence level ( error.type="fwe") or comparison-wise confidence level ( error.type="cwe").
bounds
a character string specifying the type of intervals to compute: bounds="both", the default, specifies two-sided intervals; bounds="lower" gives intervals with Inf for upper bounds (but sharper lower bounds than "both"); bounds="upper" will have an analogous effect. Mixed bounds can be achieved by specifying (e.g.) bounds="upper" and then providing in lmat the negative versions of combinations for which lower bounds are desired.
error.type
a character string specifying the type of error rate: error.type="fwe", the default, specifies family-wise error rate protection, so that the probability that all bounds hold is at least conf.level. error.type="cwe" specifies comparison-wise error rate protection, i.e. the probability that any one preselected bound holds is conf.level.
method
a character string that specifies the desired method for critical point calculation. The default is "best.fast". Available methods at this time are: "lsd", "tukey", "dunnett", "sidak", "bon", "scheffe" "sim", "best.fast", "best". See the multicomp help file for descriptions of the methods.
crit.point
if none of the above methods suits the user, a value for the critical point used in the intervals/bounds may be specified directly using crit.point. In this case, ensuring validity of the critical point is the user's responsibility. Method is changed to "user-specified", and alpha and error.type are merely labels in the output object, and may have no meaning.
control
when comparisons="mcc", this number specifies which column of the lmat matrix is to be treated as the control. The default is the last column of lmat.
simsize
optional specification of simulation size for the "sim" method. The default choice provides intervals or bounds whose actual family-wise error rate is within 10% of the nominal 1 - conf.level (with probability .99). This amounts to simulation sizes in the tens of thousands for most cases.
plot
a logical value, if TRUE, a plot of the calculated intervals will be created on the current graphics device. Alternately, the output object can be used as an argument to the generic function plot.
valid.check
a logical value, if TRUE, the default, validity of the specified critical point calculation method for the desired comparisons will be checked. If the condition for validity fails, the function will terminate with a message.
est.check
a logical value, if TRUE, estimability of the desired linear combinations will be checked. If the condition fails, the function will terminate with a message. Setting this to FALSE will disable the checking. Note that in certain cases, too much rounding of coefficients in a specified lmat can cause the estimability condition to fail.
print.p
a logical value; if TRUE, the results are printed, (by a call to print.multicomp).
Srank
Used when the method is "scheffe". If the rank of the covariance matrix of the estimators of the linear combinations of interest is Srank, the critical point will be sqrt(Srank*qf(1-alpha, Srank, df.residual)).
call.new.graphsheet
a logical value; if TRUE, the new.graphsheet function will be called before any plots are produced.

VALUE:

invisibly returns an object of class multicomp. See the multicomp help for its components.

SIDE EFFECTS:

A table of confidence bounds will be printed if print.p is TRUE. A plot of the confidence bounds will be drawn if requested.

SEE ALSO:

, , .