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metRology (version 0.9-28-1)

bootMSD-class : Object returned by bootMSD and associated methods.

Description

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

Usage

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

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

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

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

Arguments

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.

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.

Details

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.

See Also

msd, qmsd.

Examples

Run this code
# NOT RUN {
  
# }
# 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)

  
# }

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