Hi,
Still no data.
>From your code, it looks like data is similar to this:
set.seed(25)
WrackMass<-
data.frame(Algae.Mass=sample(40:50,30,replace=TRUE),Seagrass.Mass=sample(30:70,30,replace=TRUE),Terrestrial.Mass=sample(80:100,30,replace=TRUE),Other.Mass=sample(40:60,30,replace=TRUE),Site.X.Treatment=rep(c("ALA1A","ALA1U","BLA1A","BLA1U","CLA1A","CLA1U"),each=5),stringsAsFactors=FALSE)
lst1<-split(WrackMass,substr(WrackMass$Site.X.Treatment,1,3))
res<-
lapply(lst1,function(x) do.call(cbind,lapply(x[,1:4],function(y)
{Site<-gsub(".*(\\d.*)","\\1",x$Site.X.Treatment);
t.test(y[Site=="1A"],y[Site=="1U"],paired=TRUE)$p.value } ) ))
res
#$ALA
# Algae.Mass Seagrass.Mass Terrestrial.Mass Other.Mass
#[1,] 1 0.7769256 0.3351745 0.6817365#
#
#$BLA
# Algae.Mass Seagrass.Mass Terrestrial.Mass Other.Mass
#[1,] 0.6482613 0.9411953 0.7927984 0.3027634
#
#$CLA
# Algae.Mass Seagrass.Mass Terrestrial.Mass Other.Mass
#[1,] 0.454294 0.02519427 0.5650988 0.2981702
A.K.
>Hello all,
>
>I have made some progress with the following code
>
>lapply(WrackMass[,8:11], function(x)
t.test(x[WrackMass$Site.X.Treatment=="ALA1A"],x[WrackMass$Site.X.Treatment=="ALA1U"])$p.value)
>
>this performs the paired t test for all four of my metrics
(WrackMass[,8:11]) for a defined site pair (ALA1A/ALA1U). My goal now
is repeat the >code so that is runs for all my pairs (28 of them). All
the pairs are named XXX1A paired with XXX1U (A and U are treatments).
As explained >above the pair names are broken down in separate columns
and concatenated in the Site.X.Treatment column. See below
>
> Site Treatment Site.X.Treatment
>ALA1 A ALA1A
>ALA1 U ALA1U
>
>for all pairs
>
>I guess my question now is how can I tell R that I want a
certain site (ALA1) paired by the treatment A or U for all sites.
Maybe something like
>t.test(x[WrackMass$Site=="ALA1" and Treatment=="A"],x[WrackMass$Site=="ALA"
>and Treatment=="U"])$p.value)
>
>Ideas?
----- Original Message -----
From: arun <smartpink...@yahoo.com>
To: R help <r-help@r-project.org>
Cc:
Sent: Thursday, May 2, 2013 1:58 PM
Subject: Re: Multiple Paired T test from large Data Set with multiple pairs
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))
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
A.K.
>Arun,
>
>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 <smartpink...@yahoo.com>
To: R help <r-help@r-project.org>
Cc:
Sent: Wednesday, May 1, 2013 5:43 PM
Subject: Re: Multiple Paired T test from large Data Set with multiple pairs
Hi,
Assuming that your dataset is similar to the one below:
set.seed(25)
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)
library(reshape2)
dat2<-melt(dat1,id.var="Site.X.Treatment")
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
#or
library(plyr)
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
A.K.
>Hey,
>
>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??
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
