Here's a quick R hint. (I had briefly forgotten how to do this, and the solution wasn't totally obvious online.) Say I have a vector of factors in memory in R and I want to get the frequency or relative frequency of the different levels of the factor, I can do this using the base generic function summary. Just to see how this works, consider a vector containing the best-fitting quantitative trait evolution model for a set of 100 trees:

> best.fit

[1] BM BM OU lambda BM BM OU BM

[9] BM BM BM lambda lambda BM OU BM

[17] BM BM OU BM BM BM lambda BM

[25] BM BM BM OU lambda BM BM BM

[33] BM OU BM BM lambda lambda lambda BM

[41] BM BM BM OU BM BM BM BM

[49] BM OU BM BM BM BM BM BM

[57] lambda lambda OU OU BM BM lambda BM

[65] BM BM BM BM lambda BM BM BM

[73] BM OU OU BM lambda BM lambda BM

[81] BM lambda BM BM BM OU BM BM

[89] BM BM OU OU lambda BM BM BM

[97] BM BM OU BM

Levels: BM lambda OU

We can count up the number or relative frequency of trees with each best fit model as follows:

> summary(best.fit)

BM lambda OU

68 16 16

> summary(best.fit)/sum(summary(best.fit))

BM lambda OU

0.68 0.16 0.16

That's it.

R trick 2 to follow.

ReplyDeleteNeat! I never use factors much, now I might!

ReplyDeletebut say i have a vector with numbers summary dosn't give me the frequencies it gives me the median, mean, min, max ect.

ReplyDeletehow do i get the Frequency?

say for simplicity i have this vector: c(1,2,1,4,1,5,6,5,6,5,7)

the frequencies are: [1] 3, [2] 1, [4] 1, [5] 3, [6] 2, [7] 1

But how do i get R to tell me this?

This is a hack:

Deletex<-c(1,2,1,4,1,5,6,5,6,5,7)

summary(as.factor(sort(x)))

Alternatively:

obj<-hist(x,breaks=min(x):(max(x)+1)-0.5)

f<-setNames(obj$counts,obj$mids)

f

The latter option also gives you any zeroes on the range of your integers.

There may (of course) be some better way to do this that I'm not aware of.

- Liam

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