AltReg {MethComp}R Documentation

Estimate in a method comparison model with replicates

Description

Estimates in the general model for method comparison studies with replicate measurements by each method, allowing for a linear relationship between methods, using the method of alternating regressions.

Usage

  AltReg( data,
        linked = FALSE,
           IxR = linked,
           MxI = TRUE,
        varMxI = FALSE,
           eps = 0.001,
       maxiter = 50,
         trace = FALSE,
        sd.lim = 0.01,
     Transform = NULL,
     trans.tol = 1e-6 )

Arguments

data Data frame with the data in long format, (or a Meth object) i.e. it must have columns meth, item, repl and y
linked Logical. Are the replicates linked across methods? If true, a random item by repl is included in the model.
IxR Logical, alias for linked.
MxI Logical, should the method by item effect (matrix effect) be in the model?
varMxI Logical, should the method by item effect have method-specific variances. Ignored if only two methods are compared. See details.
eps Convergence criterion, the test is the max of the relative change since last iteration in both mean and variance parameters.
maxiter Maximal number of iterations.
trace Should a trace of the iterations be printed? If TRUE iteration number, convergence criterion and current estimates of means and sds are printed.
sd.lim Estimated standard deviations below sd.lim are disregarded in the evaluation of convergence. See details.
Transform Transformation of data before analysis. See choose.trans.
trans.tol The tolerance used to check whether the supplied transformation and its inverse combine to the identity.

Details

When fitting a model with both IxR and MxI interactions it may become very unstable to have different variances of the MxI random effects for each method, and hence the default option is to have a constant MxI variance across methods. On the other hand it may be grossly inadequate to assume these variances to be identical.

If only two methods are compared, it is not possible to separate different variances of the MxI effect, and hence the varMxI is ignored in this case.

The model fitted is formulated as:

y_mir = alpha_m + beta_m*(mu_i+a_{ir}+c_mi) + e_mir

and the relevant parameters to report are the estimates sds of a_{ir} and c_{mi} multiplied with the corresonidng beta_m. Therefore, different values of the variances for MxI and IxR are reported also when varMxI==FALSE. Note that varMxI==FALSE is the default and that this is the opposite of the default in BA.est.

Value

An object of class c("MethComp","AltReg"), which is a list with three elements:

Conv A 3-way array with the 2 first dimensions named "To:" and "From:", with methods as levels. The third dimension is classifed by the linear parameters "alpha", "beta", and "sd.pred".
VarComp A matrix with methods as rows and variance components as columns. Entries are the estimated standrd deviations.
data The orginal data used for the analysis. Needed for plotting purposes.

Moreover, if a transformation was applied before analysis, an attribute "Transform" is present; a list with two elements trans and inv, both of which are functions, the first the transform, the last the inverse.

Author(s)

Bendix Carstensen, bxc@steno.dk

References

B Carstensen: Comparing and predicting between several methods of measurement. Biostatistics (2004), 5, 3, pp. 399–413.

See Also

BA.est Meth.sim MethComp

Examples

dfr <- Meth.sim( Ni = 30,
                 Nm = 3,
               beta = c(0.9,0.8,1.1),
          sigma.mi  = c(4,5,8),
          sigma.ir  = 3,
          sigma.mir = c(5,4,3),
             m.thin = 1,
             i.thin = 1 )
levels(dfr$meth) <- paste( "m",1:3,sep="" )
str(dfr)
summary(dfr)
plot(dfr,var.names=TRUE)
# AltReg( dfr, linked=TRUE, trace=TRUE )
# AltReg( dfr, linked=TRUE, varMxI=TRUE, trace=TRUE )
data( sbp )
# AltReg( dfr, linked=TRUE, varMxI=TRUE, trace=TRUE )

[Package MethComp version 0.6.0 Index]