R: Generalized Minimum Distance between a pair of distributions

gmdp {GMD} | R Documentation

## Generalized Minimum Distance between a pair of distributions

### Description

Generalized Minimum Distance between a pair of distributions

### Usage

    gmdp(v1, v2, labels=c("v1","v2"), pseudocount=0, sliding=TRUE,
    resolution=1)

    ## S3 method for class 'gmdp'
    print(x, mode=c("brief","detailed","full"),
    digits=3, ...)

    ## S3 method for class 'gmdp'
    summary(object, ...)

### Arguments

`v1` | a numeric vector, giving positional counts as a discrete distribution.
`v2` | a numeric vector, giving positional counts as a discrete distribution.
`labels` | a string vector of length 2, giving the names of v1 and v2 respectively.
`pseudocount` | a numeric value to be allocated for each position to reduce bias; by default `pseudocount = 0`.
`sliding` | logical, indicating whether sliding is allowed or not for an optimal solution; by default `sliding = TRUE`.
`resolution` | relative resolution, numeric (>=1), changing the size of the bin by multiplying the value. A larger value (lower resolution) is more computational efficiet but missing details.
`x` | an object of class `gmdp`.
`object` | an object of class `gmdp`.
`mode` | a string of the following: `c("brief","detailed","full")`, indicating whether to print in full mode (default).
`digits` | integer, indicating the number of decimal places to be printed.
`...` | arguments to be passed to method.

### Details

Generalized Minimum Distance between a pair of distributions

### Value

`gmdp` returns an object of class `gmdp`, a numeric with an attribute of meta in a list with components:

labels: a string vector, giving the names of distributions

v1.ori: a numeric vector, the first input distribution

v2.ori: a numeric vector, the second input distribution

v1: a numeric vector, the normalized version of the first input distribution

v2: a numeric vector, the normalized version of the second input distribution

distance: numeric, the GM-Distance (GMD)

sliding: logical, indicating whether sliding is performed

pseudocount: a numeric value that is allocated at each position in addition to original values

gap.pair: a numeric matrix, giving one gap pair per row: i.e. relative shifts between distributions of one optimal hit

n.hit: numeric, the number of (equally good) optimal hits

### References

See `citation("GMD")`

### See Also

`print.gmdp`, `summary.gmdp`, `plot.gmdp` `gmdm`

### Examples

    require(GMD)
    gmdp(c(4,1,1,0,0,0,3,1),c(2,1,1,0,0,0,3,3),sliding=FALSE)
    x <- gmdp(c(4,1,1,0,0,0,3,1), c(1,1,2,1,1,0,0,0,3,3,5,5),
    pseudocount=1, sliding=TRUE)
    print(x)
    print(x, "full")

[Package GMD version 0.3.3 Index]