Author Topic: R statistics for plant breeding  (Read 69 times)

Ocimum

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R statistics for plant breeding
« on: 2019-12-01, 04:48:43 AM »
As William S. opened a thread on calculus for plant breeding, here another on R packages for plant breeding.

R is an open source statistics program, used increasingly around the world.
https://www.r-project.org

In R, many volunteers and projects create and share packages which are specific to certain domains.
For plant breeding, the package “agricolae” is useful, as you can analyze incomplete multi-location trials for example.
https://www.rdocumentation.org/packages/agricolae/versions/1.3-1/topics/agricolae-package

There is a new package in development “PPBstats” for statistical analyses of participatory plant breeding trials
https://priviere.github.io/PPBstats_web_site/

Having only played around a little with “agricolae”, but never worked on it with a breeding project, I think it can be very helpful to visualize the data for example. There is however a steep learning curve to get used to R.
Anyone worked on a breeding project with R?

William S.

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Re: R statistics for plant breeding
« Reply #1 on: 2019-12-01, 10:13:36 AM »
My relationship with R is a bit shaky. I used to work in a plant ecology lab where the post doc I was assigned to was the lab's R master. I downloaded R and tried to learn a few things. Then in my next job my boss had a small data set on some rare pine trees and asked me to learn R a bit and analyze it. I figured out how to do a few things with R for that, and then never used it again.

I have a small dataset from an experiment with insects not plant breeding to analyze and maybe will get some work done on it over Christmas break. Though there is an advanced statistics course I can take spring quarter to analyze it further. I have several R books from the last time I worked with it. I get a bit overambitious in my book purchases- some of them are already out in newer editions. I have one on ecological models in R and it does use Calculus a bit re: my calculus thread. I also have one on statistics in R and a large one that is simply the R book.

Interestingly one of the authors is also the author of a plant ecology text that is from the nutrient school of plant ecology which was the subdivision of plant ecology the lab I was in was focused on. I hadn't known prior that there were divisions within plant ecology.
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gmuller

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Re: R statistics for plant breeding
« Reply #2 on: 2019-12-01, 03:12:19 PM »
R?
Arrrrrggggghhhh!!! :'(
Gregg