R help - Jan 2010 - using functions with multiple arguments in the "apply" family

typically, the apply family wants you to use vectors to run functions on. 
However, I have a function, kruskal.test, that requires 2 arguments.

kruskal.test(Herb.df$Score,Herb.df$Year)

This easily computes the KW ANOVA statistic for any difference across
years....

However, my data has multiple sites on which KW needs to be run...

here's the data:

Herb.df<-
data.frame(Score=rep(c(2,4,6,6,6,5,7,8,6,9),2),Year=rep(c(rep(1,5),rep(2,5)),2),Site=c(rep(3,10),rep(4,10)))

However, if I try this:

 tapply(Herb.df,Herb.df$Site,function(.data)
kruskal.test(.data$Indicator_Rating,.data$Year))

>Error in tapply(Herb.df, Herb.df$ID, function(.data)
kruskal.test(.data$Indicator_Rating,  : 
  arguments must have same length


How can I vectorize the kruskal.test() for all sites using tapply() in lieu
of a loop?




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chipmaney wrote:
> typically, the apply family wants you to use vectors to run functions on. 
> However, I have a function, kruskal.test, that requires 2 arguments.
> 
> kruskal.test(Herb.df$Score,Herb.df$Year)
> 
> This easily computes the KW ANOVA statistic for any difference across
> years....
> 
> However, my data has multiple sites on which KW needs to be run...
> 
> here's the data:
> 
> Herb.df<-
>
data.frame(Score=rep(c(2,4,6,6,6,5,7,8,6,9),2),Year=rep(c(rep(1,5),rep(2,5)),2),Site=c(rep(3,10),rep(4,10)))
> 
> However, if I try this:
> 
>  tapply(Herb.df,Herb.df$Site,function(.data)
> kruskal.test(.data$Indicator_Rating,.data$Year))
> 
> 
>> Error in tapply(Herb.df, Herb.df$ID, function(.data)
> kruskal.test(.data$Indicator_Rating,  : 
>   arguments must have same length
> 
> 
> How can I vectorize the kruskal.test() for all sites using tapply() in lieu
> of a loop?
Your example data makes little sense; you have precisely the
same data for both sites and you have only two sites (why do
kruskal.test on two sites?). Finally, you need to decide what
your response variable is: 'Score' or 'Indicator_Rating'.

So here's some made-up data and the use of by() to apply
the test to each site:

dat <- data.frame(y = rnorm(60), yr=gl(4,5,60), st=gl(3,20))
with(dat, by(dat, st, function(x) kruskal.test(y~yr, data=x)))

See the last example in ?by.

  -Peter Ehlers
> 
> 
> 
> 
-- 
Peter Ehlers
University of Calgary

I can actually answer this!!  I was trying to figure out how to use sapply
for a function I wrote with multiple arguments.
Suppose the function is called
FUN(a,b), where "a" is a number and "b" is a number
You can use mapply(FUN, a = VECTOR, b = VECTOR) where each vector is your
input arguments.  It will output a vector or a matrix (depending on the
output of your function).

This will also work:
mapply(FUN, a = VECTOR, b = NUMBER) and will apply your function with each
element of "a" but the same argument for "b" each time.

Let me know if it works!

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