Hi Sarah,
On Jul 25, 2009, at 8:25 AM, Buckmaster, Sarah wrote:
Hi everyone,
I have a question about calculating r-squared in R. I have tried
searching the archives and couldn't find what I was looking for -
but apologies if there is somewhere I can find this...
I carried out a droughting experiment to test plant competition
under limited water. I had:
- 7 different levels of watering treatment (1 -7 - from most watered
to least watered/)
- 15 replicates at each level.
Soil moisture readings were taken 4 times throughout the experiment
(so I have 105 readings for each of the 4 times) and I now want to
check that there was a significant decrease in soil moisture as I
decreased the watering frequency, i.e. watering level 7 showed lower
soil moisture units than level 1.
I have carried out a repeated measures anova as follows (where block
is which time the reading was taken: 1,2,3 or 4):
model1<-aov(soilmoisture~wateringlevel+Error(block/wateringlevel))
I then plotted (soilmoisture~wateringlevel) and fitted a regression
line:
lm1<-lm(soilmoisture~wateringlevel)
abline(lm1,lty=1)
Here are my questions:
1) Is the repeated measures anova I have entered correct to tell me if
there is a significant difference in my watering levels?
It seems like using anova here is reasonable -- I haven't used it in
R, though, so I can't comment on your *actual* use of it (looks right
-- can't u also just call aov on your lm1 object, too?)
2) How do I calculate r2 value to show much variation my watering
level explains? - and then put this figure on my plot?
I think this should be pretty straight forward -- you can find the
formula here:
http://en.wikipedia.org/wiki/Fraction_of_variance_unexplained
and R^2 = SSR / SST (on that page)
Using the formulas on that page, translating to R is pretty straight
forward. Let's take the example code at the bottom of ?lm help page
for reference and calculate the R^2:
ssr <- sum((predict(lm.D9, group) - weight)^2)
sst <- sum((weight - mean(weight))^2)
r2 <- ssr / sst
HTH,
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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