[R] Multiple Paired T test from large Data Set with multiple pairs

arun smartpink111 at yahoo.com
Thu May 2 19:58:10 CEST 2013

My code was based on the assumption that your dataset was similar to the one I provided.  Please provide an example dataset (use dput(head(dataset),20))


>I have tried applying your suggestions to my data set but I 
cannot get it to work.  I think my lack of R skills may be a 
contributing factor.  I will keep >trying though. 

----- Original Message -----
From: arun <smartpink111 at yahoo.com>
To: R help <r-help at r-project.org>
Sent: Wednesday, May 1, 2013 5:43 PM
Subject: Re: Multiple Paired T test from large Data Set with multiple pairs

Assuming that your dataset is similar to the one below:
dat1<- data.frame(Algae.Mass=sample(40:50,10,replace=TRUE),Seagrass.Mass=sample(30:70,10,replace=TRUE),Terrestrial.Mass=sample(80:100,10,replace=TRUE),Other.Mass=sample(40:60,10,replace=TRUE),Site.X.Treatment=rep(c("ALA1A","ALA1U"),each=5),stringsAsFactors=FALSE)

sapply(split(dat2,dat2$variable),function(x) t.test(x[x$Site.X.Treatment=="ALA1A",3],x[x$Site.X.Treatment=="ALA1U",3],paired=TRUE)$p.value)
  #    Algae.Mass    Seagrass.Mass Terrestrial.Mass       Other.Mass 
  #     1.0000000        0.4624989        0.4388211        0.7521036 
 ddply(dat2,.(variable),function(x) summarize(x,Pvalue=t.test(value~Site.X.Treatment,data=x,na.rm=TRUE,paired=TRUE)$p.value))
#          variable    Pvalue
#1       Algae.Mass 1.0000000
#2    Seagrass.Mass 0.4624989
#3 Terrestrial.Mass 0.4388211
#4       Other.Mass 0.7521036


>I have a fairly large data set with multiple pairs of Sites. 
 Each site has two levels (the pairs) "A" and "U".  For each pair I want
to do a paired t test of >4 different metrics that exist as columns in 
my data set. 
>Here is the long version 
>t.test(Algae.Mass[Site.X.Treatment=="ALA1A"],Algae.Mass[Site.X.Treatment=="ALA1U"], paired=T) 
>t.test(Seagrass.Mass[Site.X.Treatment=="ALA1A"],Seagrass.Mass[Site.X.Treatment=="ALA1U"], paired=T) 
>t.test(Terrestrial.Mass[Site.X.Treatment=="ALA1A"],Terrestrial.Mass[Site.X.Treatment=="ALA1U"], paired=T) 
>t.test(Other.Mass[Site.X.Treatment=="ALA1A"],Other.Mass[Site.X.Treatment=="ALA1U"], paired=T) 
>How can I do this in one line of code?  I have tried lapply, 
tapply etc but keep running into issues.  It would also be great to not 
have to keep defining >"Site.X.Treatment".  I do have Site.X.Treatment 
broken down by just Site and Treatment in separate columns in the data 
set.  Any Ideas??

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