Description Usage Arguments Details Value Author(s) See Also Examples
The object class returned by bootMSD
and associated
print
, summary
, and plotting classes.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  ## 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 
height 
An object of class 
object 
An object of class 
p.adjust 
Multiple correction method for calculated pvalues, passed to

ylab 
Label for vertical axis, passed to 
names.arg 
Labels for individual bars in bar plot, passed to 
crit.vals 
If 
lty.crit, col.crit, lwd.crit 
Vectors of line style parameters for plotted critical values, passed to

digits 
integer; passed to 
signif.stars 
logical; if 
signif.legend 
logical; if 
... 
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, pvalues are initially calculated as the observed
proportion of simulated values exceeding the MSD value calculated by msd
. The
summary method additionally returns pvalues 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, dataspecific upper quantiles
(one column for each probability supplied to bootMSD
and the pvalues
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 pvalue 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.
pvalspvalues estimated as the observed proportion of
simulated values exceeding the MSD value calculated by msd
.
p.adjustCharacter value containing the name of the pvalue adjustment method used.
p.adj pvalues adjusted using the given pvalue 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  ## 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 pvalues. To
# avoid overinterpretation for the study as a whole,
# apply a sensible pvalue adjustment:
summary(boot.Pb, p.adjust="holm")
plot(boot.Pb, crit=TRUE)
## End(Not run)

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