bootMSD_class: Object returned by 'bootMSD' and associated methods.
In metRology: Support for Metrological Applications

Description Usage Arguments Details Value Author(s) See Also Examples

The object class returned by bootMSD and associated print, summary, and plotting classes.

       ## S3 method for class 'bootMSD'
print(x, ...)

       ## S3 method for class 'bootMSD'
plot(x, ...)

       ## S3 method for class 'bootMSD'
barplot(height, ylab="MSD", names.arg=height$labels, 
	crit.vals=TRUE, lty.crit=c(2,1), col.crit=2, lwd.crit=c(1,2), ... )

       ## S3 method for class 'bootMSD'
summary(object, p.adjust="none", ...) 

       ## S3 method for class 'summary.bootMSD'
print(x, digits=3, ..., 
		signif.stars = getOption("show.signif.stars"), 
		signif.legend=signif.stars)

`x`	An R object. For `print.bootMSD` and `plot.bootMSD`, an object of class `"bootMSD"`. For `print.summary.bootMSD`, an object of class `"summary.bootMSD"`.
`height`	An object of class `"bootMSD"`.
`object`	An object of class `"MSD"`.
`p.adjust`	Multiple correction method for calculated p-values, passed to `p.adjust`.
`ylab`	Label for vertical axis, passed to `barplot`
`names.arg`	Labels for individual bars in bar plot, passed to `barplot`. If `names(height)` is `NULL`, bars are numbered.
`crit.vals`	If `TRUE`, individual critical values based on observation-specific bootstrap quantiles are added to the plot. These are taken from `critical.values` in the supplied `bootMSD` object.
`lty.crit, col.crit, lwd.crit`	Vectors of line style parameters for plotted critical values, passed to `segments`. Recycled to the length of `critical.values` in the supplied `bootMSD` object.
`digits`	integer; passed to `print`. The minimum number of significant digits to be printed in values. Change to `NULL` for default.
`signif.stars`	logical; if `TRUE`, P-values are additionally encoded visually as ‘significance stars’ in order to help scanning of long coefficient tables. Defaults to the `show.signif.stars` slot of `options`.
`signif.legend`	logical; if `TRUE`, a legend for the ‘significance stars’ is printed provided `signif.stars == TRUE`.
`...`	Parameters passed to other methods.

The default plot method is an alias for the barplot method. For the plot methods, quantiles for each point are taken directly from the quantiles calulated by bootMSD and retained in the returned object.

For the summary method, p-values are initially calculated as the observed proportion of simulated values exceeding the MSD value calculated by msd. The summary method additionally returns p-values after adjustment for multiple comparisons using the adjustment method specified.

The print method for the summary.bootMSD object prints the summary as a data frame adjusted with columns for the calculated MSD values, data-specific upper quantiles (one column for each probability supplied to bootMSD and the p-values after adjustment for multiple comparisons based on the proportion of simulated values exceeding the observed MSD. Where that proportion is zero, the summary replaces the raw zero proportion with 1/B, corrects that proportion using the requested adjustment method, andreports the p-value as less than ("<") the resulting adjusted value.

The print method returns the object, invisibly.

The plot and barplot methods return the values at the midpoint of each bar.

The summary method returns an object of class "summary.bootMSD" which is a list with members:

msdCalculated MSD values from msd
labelscharacter vector of labels for individual data points
probsProbabilities used for quantiles
critical.valuesmatrix of quantiles. Each row corresponds to a probability in probs and each column to an individual data point.
pvalsp-values estimated as the observed proportion of simulated values exceeding the MSD value calculated by msd.
p.adjustCharacter value containing the name of the p-value adjustment method used.
p.adj p-values adjusted using the given p-value adjustment method specified by p.adjust.
BNumber of bootstrap replicates used.
methodThe sampling method used by the parametric bootstrap.

S. L. R. Ellison s.ellison@lgc.co.uk

msd, qmsd.

  ## Not run: 
  data(Pb)
  msd.Pb<-msd(Pb$value, Pb$u)  # Uses individual standard uncertainties

  set.seed(1023)
  boot.Pb <- bootMSD(msd.Pb)
  summary(boot.Pb)

  # The default summary gives individual observation p-values. To 
  # avoid over-interpretation for the study as a whole, 
  # apply a sensible p-value adjustment:
  summary(boot.Pb, p.adjust="holm")

  plot(boot.Pb, crit=TRUE)

  
## End(Not run)