truncated function

Truncated product methods

Implements two procedures for truncated versions of Fisher's method\loadmathjax

truncated(p, ptrunc = NULL, rtrunc = NULL, ...)
## S3 method for class 'truncated'
print(x, ...)
## S3 method for class 'truncated'
summary(object, ...)
## S3 method for class 'truncated'
plot(x, pparams = list(pchs = c(16, 1),
   pcols = c("black", "black")), ...)

Arguments

• p: A vector of significance values
• ptrunc: Value of \mjseqn p to truncate at. See Details
• rtrunc: Which rank \mjseqn p to truncate at. See Details
• x: An object of class ‘truncated’
• object: An object of class ‘truncated’
• ...: Other arguments to be passed through
• pparams: A list containing a vector pchs of plotting symbols and a vector pcols of colours

Details

Uses routines from TFisher to implement truncated Fisher \insertCite zaykin07,zhang18metap

and from mutoss to implement rank-truncated Fisher \insertCite dudbridge03metap

The print method prints the statistic and its associated \mjseqn p-value. The summary method also prints how many of the input values were actually used. The plot method provides an index plot of the \mjseqn p-values. By default used \mjseqn p-values are plotted with a black filled circle and those not used with a black unfilled circle. The colours and plotting symbols can be changed in pparams. The first element of each vector is for the used \mjseqn p-values and the second for the unused ones.

Returns

An object of class ‘truncated’

a list with entries - p: The resultant overall \mjseqn p-value

• stat: The test statistic

• validp: The input vector with illegal values removed

• ptrunc: The \mjseqn p-value used for truncation

• trunc: The rank value used for truncation

• n: A vector containing incl, the number of valid values included, excl, the number of valid values not used

• method: The method used

Note

Only one of ptrunc or rtrunc is returned as appropriate. If the function encounters an error it returns NA for the value of p and gives a warning message. The effect of specifying both ptrunc

and rtrunc is undefined.

References

\insertAllCited

Author(s)

Michael Dewey

See Also

ranktruncated, stat.tpm, and p.tpm

Examples

data(dat.metap)
validity <- dat.metap$validity
truncated(validity, ptrunc = 0.5)
truncated(validity, rtrunc = 5)