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Published August 26, 2019 | Version v3.0.0
Software Open

openplantpathology/hagis v3.0.0

Authors/Creators

  • 1. University of Southern Queensland
  • 2. Michigan State University
  • 3. Imperial College London

Description

hagis 3.0.0 Defunct functions
  • plot() is now defunct. Use autoplot() to plot hagis objects in place of plot(). This is to avoid the side-effect of generating and displaying a plot every time plot() is called, which can be troublesome when using ggplot2 themes since it created two plots, the original with the base theme and the new themed plot
Minor Changes

  • Rename output column N_susc to N_virulent_isolates

  • Don't round results from summarize_gene() or calculate_complexities() before returning values to user

  • Implement fix suggested by @zkamvar to ensure that the user-input data is not changed from a data.frame or tibble object to a data.table object in the R session

  • Add ability to sort graph x-axis in ascending or descending order based on the y-axis values rather than only by gene or complexity.

  • Move example data set into internal data and provide documentation for them

  • Provide documentation for how diversity indices are calculated along with mathematical notation where possible to display

  • Calculate Shannon and Simpson indices internally rather than rely on vegan to reduce number of Dependencies

  • Replace the term field with column in documentation

  • Test coverage now 100 %

  • Add funding agencies to DESCRIPTION Authors@R field

Files

openplantpathology/hagis-v3.0.0.zip

Files (119.7 kB)

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Additional details

Related works

Is supplement to
https://github.com/openplantpathology/hagis/tree/v3.0.0 (URL)