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:
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_v4.pdf |
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!).
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!).