DEMEtics (version 0.8.0)

H.out: Heterozygosities

Description

This function renders Hs, Ht, Hs.est and Ht.est values per locus. They are calculated according to the formulas given in Jost (2008)

Usage

H.out(filename, object=FALSE, format.table=FALSE, data.name=FALSE, v, h)

Arguments

filename

Its syntax depends on the setting of the argument 'object'. If 'object=FALSE', the filename has to be a combination of (1) the name of the data file ('.txt format') in which the raw data are saved and (2) the extension '.txt'. It has to be enclosed in q

object

This argument can be set as TRUE or FALSE, depending on the format of the argument 'filename'.

format.table

A logical argument either set as TRUE or FALSE (default '= TRUE') that defines if the format of the table has to be transformed before analysis (see details).

data.name

A logical argumet set as TRUE or FALSE (default), depending on whether you wish to name the data file specifically where the result table will be saved at. If set as TRUE, you can use the argument v and h. The mean part will always be: H.values, so

v

When data.name=TRUE, v determines the front part of the data file name where the result table will be saved. It has to be quoted: "v".

h

When data.name=TRUE, h determines the hind part of the data file name where the result table will be saved. It has to be quoted: "h".

Value

• A data table (space-delimited) and in '.txt'-format is returned and saved to the actual working directory. It lists Hs, Hs.est, Ht and Ht.est values for each locus. You will be informed about its filename.

  The location of the actual working directory can be requested by typing 'getwd()' and changed by using the function setwd.

Details

The data table comprising the raw data can be of two different formats. Format 1 equals the output of the function inputformat. Format 2 equals the input of the function inputformat. Please refer to this description file for details. If format 1 is used, the argument 'format.table' has to be set as FALSE. Using format 2, the argument 'format.table' has to be set as TRUE (default). In this case, the data table is automatically transformed to format 1 using the function inputformat.

In the data table that will be returned at the end, the loci will be sorted alphabetically and numerically if numbers are included in.

References

Jost, L. 2008 Gst and its relatives do not measure differentiation. Molecular Ecology 17, 18, p. 4015--4026.

See Also

all.pops.D, pair.pops.D

Examples

data(Example.transformed)
Example1 <- Example.transformed

data(Example.untransformed)
Example2 <- Example.untransformed

H.out("Example1", object=TRUE,format.table=FALSE,data.name=TRUE,v="Table.1.1",h="Jan.10.2010")
H.out("Example1", object=TRUE, format.table=FALSE)

H.out("Example2", object=TRUE,format.table=TRUE,data.name=TRUE,v="Table2.1",h="Feb.10.210")
H.out("Example2", object=TRUE, format.table=TRUE)