ggenealogy v1.0.0

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Visualization Tools for Genealogical Data

Methods for searching through genealogical data and displaying the results. Plotting algorithms assist with data exploration and publication-quality image generation. Includes interactive genealogy visualization tools. Provides parsing and calculation methods for variables in descendant branches of interest. Uses the Grammar of Graphics.

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ggenealogy

CRAN Downloads License: GPL v3 minimal R version CRAN_Status_Badge Maintenance

Motivation:

Genealogists wish to study the parent-child relationship between groups of organisms. Visual representations of genealogical relationships allow scientists to more effectively understand the historical changes that caused novel and desirable traits to arise in lineages. For example, in crops, desirable modifications could include an increase in protein yield or an increase in disease resistance. However, there are also times when lineages of detrimental traits can be viewed, such as to determine the origin of hazardous traits in rapidly-evolving viruses.

While there are visual methods available for genealogical data structures, there is a need for additional development of tools that are more customized to particular needs that arise when scientists want to make informed decisions while visualizing their data.

Description:

This package provides methods for searching through genealogical data and displaying the results. The available plotting algorithms can assist users in performing data exploration, as well as in generating publication-quality images. This package uses the Grammar of Graphics.

Some of the currently-available methods include:

  • Drawing genealogy trees from database of known lineage.
  • Selecting generation number of ancestors and descendants to show around a given variety.
  • Showing shortest path between two given varieties, and superimpose over full lineage structure.
  • Obtaining graph theory measures of the full lineage structure.
  • Producing color matrix plots of variables between a subset of varieties.
  • Interactively visualizing genealogical structure
  • Perform basic parsing and calculations on descendant branches of interest

Installation:

  • The latest released version: install.packages("ggenealogy")
  • The latest development version: install_github("lrutter/ggenealogy")

Resources:

Installation of the package will automatically download a vignette, which contains a more thorough explanation of the available methods, and example code.

License:

GPL

Functions in ggenealogy

Name Description
buildAncList Returns the ancestors of a particular variety (if they exist).
buildDesList Returns the descendants of a particular variety (if they exist).
getBranchQual Descendant branch calculations for quantitative variable
getBranchQuant Descendant branch calculations for quantitative variable
isParent Determine if a variety is a parent of another
nodeToDF Returns the data frame representation of all ancestors and descendants of a variety
plotVariableMatrix Returns the image object to show the heat map of dates between the inputted set of vertices
sbGeneal Soybean data
buildAncDesCoordDF Returns the coordinate positions of all ancestors and descendants of a variety.
buildEdgeTotalDF Build the edges in the genealogy graph.
buildMinusPathDF Process the genealogy graph
getDescendants Returns a list of the descendants of a particular variety (if they exist)
getEdges Returns edges (vertex names and edge weights) for the full genealogy
buildAncDesTotalDF Returns data frame with plot coordinates of all ancestors and descendants of a variety.
getPath Determine the path between two varieties
getNodes Returns the nodes for a full genealogy
getParent Returns the parents of a particular variety (if they exist)
getPathOnly Determine the path between two varieties
getVariable Determine the date of a variety
isChild Determine if a variety is a child of another
buildPathDF Build data frame for path representation
buildPlotTotalDF Build all labels in the graph
getAncestors Returns a list of the ancestors of a particular variety (if they exist)
statGeneal Academic statistics data
getBasicStatistics Determine basic statistics of the graph object
plotPath Construct the graphic object of the path
plotPathOnAll Plot a path between two vertices over the full genealogy
buildSpreadTotalDF Build a data frame where the varieties are spread so they do not overlap
getChild Returns the children of a particular variety (if they exist)
dfToIG Process the genealogy graph
getDegree Determine the degree between two varieties
plotDegMatrix Returns the image object to show the heat map of degrees between the inputted set of vertices
plotAncDes Returns the image object to show the ancestors and descendants of a variety
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Vignettes of ggenealogy

Name
dCox.png
ggenealogy.Rnw
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Details

License GPL
VignetteBuilder knitr
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2019-05-28 10:47:10 UTC; suzu
Repository CRAN
Date/Publication 2019-05-28 16:51:29 UTC

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