R/gstudio-package.R

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#' Routines used in spatial analysis of genetic marker data
#' 
#' gstudio is a suite of tools used in the spatial analysis
#'  of population genetic data created for the book 
#'  "Applied Landscape Genetics" by R.J. Dyer.   This version
#'  of the package (1.X) is a significant deviant from the 
#'  previous (versions 0.X) resulting from an entire re-write
#'  of the package to maximize ease of use and algorithm quickness.
#'  As such, previous scripts using gstudio (vers. 0.X) will need
#'  to be refactored a bit.  While this can be a bit of a pain, the
#'  larger utility of the new format will pay off in spades.
#'
#' \tabular{ll}{
#' Package: \tab gstudio\cr
#' Type: \tab Package\cr
#' Version: \tab 1.1\cr
#' Date: \tab 2013-06-07\cr
#' License: \tab GPL (>= 2)\cr
#' LazyLoad: \tab yes\cr
#' }
#'
#' There are some very good examples of the components of this package are used
#'	in the vignettes for this package.
#' @author Rodney J. Dyer \email{rjdyer@@vcu.edu}
#' @docType package
#' @keywords package
#' @import raster 
#' @import ggplot2 
#' @import ggmap
#' @import graphics
#' @importFrom graphics plot.default
#' @importFrom methods is
#' @importFrom stats pchisq
#' @importFrom utils read.csv
#' @importFrom utils read.table
#' @name gstudio-package
#' @rdname gstudio-package
#'
NULL

#' Data for Araptus attenuatus
#' 
#' This is a EPIC genetic dataset for the Sonoran desert
#'  beetle Araptus attenuatus
#' @name arapat
#' @docType data
#' @keywords data
NULL


#' AFLP example data set
#' 
#' This is an example of the AFLP data input types.
#' @name data_aflp
#' @docType data
#' @keywords data
NULL



#' Two Column Example Data
#' 
#' Example data for 2-column data types
#' @name data_2_column
#' @docType data
#' @keywords data
NULL



#' Separated Example Data
#' 
#' Example data for separated data types
#' @name data_separated
#' @docType data
#' @keywords data
NULL


#' SNP Example Data
#' 
#' Example data for SNP data types
#' @name data_snp
#' @docType data
#' @keywords data
NULL


#' Zyme-like Example Data
#' 
#' Example data like zyme genotypes
#' @name data_zymelike
#' @docType data
#' @keywords data
NULL

#' Cornus mom/offspring data set
#' 
#' Example data set for demonstrating parent/offspring data
#' @name cornus_florida
#' @docType data
#' @keywords data
NULL

#' Cornus adult data
#' 
#' Example data set with adult multilocus genotypes from
#' Cornus florida at the Rice Center
#' @name cornus
#' @docType data
#' @keywords data
NULL

#' CDPop Data
#' 
#' Example data set for CDPop input
#' @name grid.csv
#' @docType data
#' @keywords data
NULL

#' SNP probability data
#' 
#' Example data for probabilistically calling snps
#' @name snp_prob.csv
#' @docType data
#' @keywords data
NULL

#' AFLP Arapat data
#' 
#' A set of genotypes for arapat from an AFLP dataset
#' @name aflp_arapat
#' @docType data
#' @keywords data
NULL

#' Rice Canopy
#' 
#' A categorical raster of the rice center 
#' @name rice
#' @docType data
#' @keywords data
NULL
dyerlab/gstudio documentation built on Feb. 2, 2024, 8:24 p.m.