# 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.

## Readme

# ggenealogy

**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 | |

No Results! |

## Vignettes of ggenealogy

Name | ||

dCox.png | ||

ggenealogy.Rnw | ||

No Results! |

## Last month downloads

## 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 |

suggests | dplyr (>= 0.5.0) , knitr (>= 1.13) , roxygen2 (>= 3.0.0) , stringr (>= 0.6.2) |

imports | ggplot2 (>= 2.2.0) , igraph (>= 0.7.1) , plotly (>= 4.5.6) , plyr (>= 1.8.1) , reshape2 (>= 1.4) , tibble (>= 1.2) |

depends | R (>= 3.6.0) |

Contributors | Di Cook, Lindsay Rutter, Susan Vanderplas |

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