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diskImageR

This R package analyzes photographs from disk diffusion disks to ascertain resistance parameters (resistance  = radius of inhibition, "RAD"; tolerance = fraction of growth achieved above RAD, "FoG"; sensitivity = rate of transition from low growth to full growth, "slope").

The package is available in a stable version on CRAN. New features are being continually added, and an updated package (that should be stable *most* of the time!) is available through github [github project page is here].

Major updates between the versions on github and CRAN:
- support for analysis of plates with 16 disks instead of just a single disk
- support for analysis of compounds that both inhibit growth and supply a required resource
- increased support for larger disks
- function to determine susceptible/intermediate/resistant (for known species x drug combination -- this database can be added to!)

Unfortunately a package vignette can not be automatically included since the scripts require ImageJ. Hence, a vignette (that I am continuing to work on) is provided here: 
diskImageR_vignette_v2
File Size: 4963 kb
File Type: html
Download File

Scripts for typical use of the package:
​Single disk, inhibitory drug (typical use)
Inhibitory/Growth compounds
Plates with 16 disks

Please don't hesitate to get in touch with me if you would like to explore whether we can adapt diskImageR for your own purposes, or whether you are already using diskImageR and it's working great (I'd love to know!) or it's not behaving the way you think it should (I can try and fix it!).
Updated April 16  2020
  • HOME
  • PEOPLE
    • Prospective students
  • RESEARCH
  • PUBLICATIONS
  • PROTOCOLS & SCRIPTS
    • diskImageR
  • COURSES
    • MBIO4030-SciComm
    • MBIO7040: Data analysis and visualization for microbiologists
    • STAT7350
  • COVID-19
  • VALUES
  • BLOG
  • LINKS