ecogen2spagedi: Exporting an ecogen genetic data frame into SPAGeDi format

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Description

This function converts the genetic data of an ecogen object in a SPAGeDi input file. When distance classes are required, they can be constructed by combining the parameters "int", "smin", "smax", "nclass", "seqvec" and "size", as described in the function eco.lagweight. A distance matrix can also be included using the "distmat" parameter. Missing data must be coded as a single "NA" in the G data frame.

Usage

ecogen2spagedi(
  eco,
  pop = NULL,
  ndig = NULL,
  dir = "",
  outName = "infile.spagedi.txt",
  smin = 0,
  smax = NULL,
  int = NULL,
  nclass = NULL,
  seqvec = NULL,
  size = NULL,
  bin = c("sturges", "FD"),
  distmat = NULL,
  latlon = FALSE,
  to_numeric = FALSE,
  nout = 3,
  recode = c("all", "column", "paired"),
  replace_in = NULL,
  replace_out = NULL,
  ...
)

Arguments

eco	Object of class "ecogen".
pop	The name of the S slot column with the groups for the output data. The default option includes all the individuals into a single group.
ndig	Number of digits coding each allele in the output file (e.g., 1: x, 2: xx, or 3: xxx). If NULL, the vale will be deduced from the number of digits used for coding alleles in the ecogen object.
dir	output path. Default = "" (current directory).
outName	The name of the output file.
smin	Minimum class distance in the units of the XY slot data.
smax	Maximum class distance in the units of the XY slot data.
int	Distance interval in the units of the XY slot data.
nclass	Number of classes.
seqvec	Vector with breaks in the units of the XY slot data.
size	Number of individuals per class.
bin	Rule for constructing intervals when a partition parameter (int, nclass or size) is not given. Default is Sturge's rule (Sturges, 1926). Other option is Freedman-Diaconis method (Freedman and Diaconis, 1981).
distmat	Distance matrix to include (optional).
latlon	Are the coordinates in decimal degrees format? Defalut FALSE. If TRUE, the coordinates must be in a matrix/data frame with the longitude in the first column and latitude in the second. The position is projected onto a plane in meters with the function geoXY.
to_numeric	Recode the genetic data into numeric format? If TRUE, the functions performs the correction via eco.format. Additional formatting parameters can be passed to this function.
nout	Number of digits in the output when to_numeric = TRUE.
recode	Recode mode when to_numeric = TRUE: "all" for recoding the data considering all the individuals values at once (e.g., protein data), "column" for recoding the values by column (e.g., microsatellite data), "paired" for passing the values of allelic states and corresponding replacement values, using the replace_in and replace_out arguments (e.g. replace_in = c("A", "T", "C", "G"), replace_out = c(1,2,3,4)).
replace_in	vector with states of the data matrix to be replaced, when recode = "paired". This argument must be used in conjunction with the argument "replace_out".
replace_out	vector with states of the data matrix used for replacement, when recode = "paired". This argument must be used in conjunction with the argument "replace_in".
...	Additional parameters passed to eco.format when to_numeric = TRUE

Author(s)

Leandro Roser [e-mail]

References

Freedman D., and P. Diaconis. 1981. On the histogram as a density estimator: L 2 theory. Probability theory and related fields, 57: 453-476.

Hardy O. and X Vekemans. 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular ecology notes, 2: 18-620.

Sturges H. 1926. The choice of a class interval. Journal of the American Statistical Association, 21: 65-66.

Examples

## Not run: 

data(eco.test)
ecogen2spagedi(eco, dir = "", pop = "pop", ndig = 1,int=2, smax=6, outName="infile.spagedi.txt")


## End(Not run)

EcoGenetics documentation built on July 8, 2020, 5:46 p.m.