R help - Sep 2012 - help with calculation from dataframe with multiple entries per sample

Hi 

I have a dataframe similar to:
>Sample<-c(1,1,1,2,2,2,3,3,3)
>Time<-c(1,2,3,1,2,3,1,2,3)
>Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
>mydata<-as.data.frame(cbind(Sample,Time,Mass))

  Sample Time Mass
1      1    1  3.0
2      1    2  3.1
3      1    3  3.4
4      2    1  4.0
5      2    2  4.3
6      2    3  4.4
7      3    1  3.0
8      3    2  3.2
9      3    3  3.5

where for each sample, I've measured mass at different points in time. 

I now want to calculate the difference between Mass at Time 2 and 3 for each
unique Sample and store this as a new variable called "Gain2-3". So in
my example three values of 0.3,0.1,0.3 would be calculated for my three unique
samples and these values would be repeated in the table according to Sample. I
am thus expecting:
>mydata #after adding new variable
  Sample Time MassGain2-3
1      1    1  3.00.3
2      1    2  3.1 0.3
3      1    3  3.4 0.3
4      2    1  4.0 0.1
5      2    2  4.3 0.1
6      2    3  4.4 0.1
7      3    1  3.0 0.3
8      3    2  3.2 0.3
9      3    3  3.5 0.3

Does anyone have any suggestions as to how to do this? I've looked at the
various apply functions but I can't seem to make anything work. I'm
fairly new to R and would appreciate specific suggestions. 

Thanks!
	[[alternative HTML version deleted]]

Julie -
    Since the apply functions operate on one row at a time, they
can't do what you want.  I think the easiest way to solve your 
problem is to reshape the data set, and merge it back with the 
original:
> dd = data.frame(Sample=c(1,1,1,2,2,2,3,3,3),
+                 Time=c(1,2,3,1,2,3,1,2,3),
+                 Mass=c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5))
> rdd =
reshape(dd,timevar='Time',idvar='Sample',direction='wide')
> rdd$"Gain2-3" = rdd$Mass.3 - rdd$Mass.2
> merge(dd,subset(rdd,select=c('Sample',"Gain2-3")))
   Sample Time Mass Gain2-3
1      1    1  3.0     0.3
2      1    2  3.1     0.3
3      1    3  3.4     0.3
4      2    1  4.0     0.1
5      2    2  4.3     0.1
6      2    3  4.4     0.1
7      3    1  3.0     0.3
8      3    2  3.2     0.3
9      3    3  3.5     0.3

You may want to avoid using special characters like dashes in variable
names.

Hope this helps.

 					- Phil Spector
 					 Statistical Computing Facility
 					 Department of Statistics
 					 UC Berkeley
 					 spector at stat.berkeley.edu




On Mon, 17 Sep 2012, Julie Lee-Yaw wrote:
> Hi?
>
> I have a dataframe similar to:
>
>> Sample<-c(1,1,1,2,2,2,3,3,3)
>
>> Time<-c(1,2,3,1,2,3,1,2,3)
>
>> Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
>
>> mydata<-as.data.frame(cbind(Sample,Time,Mass))
>
>
> ? Sample Time Mass
> 1 ? ? ?1 ? ?1 ?3.0
> 2 ? ? ?1 ? ?2 ?3.1
> 3 ? ? ?1 ? ?3 ?3.4
> 4 ? ? ?2 ? ?1 ?4.0
> 5 ? ? ?2 ? ?2 ?4.3
> 6 ? ? ?2 ? ?3 ?4.4
> 7 ? ? ?3 ? ?1 ?3.0
> 8 ? ? ?3 ? ?2 ?3.2
> 9 ? ? ?3 ? ?3 ?3.5
>
> where for each sample, I've measured mass at different points in time.?
>
> I now want to calculate the difference between Mass at Time 2 and 3 for
each unique Sample and store this as a new variable called "Gain2-3".
So in my example three values of 0.3,0.1,0.3 would be calculated for my three
unique samples and these values would be repeated in the table according to
Sample. I am thus expecting:
>
>> mydata #after adding new variable
>
> ? Sample Time MassGain2-3
> 1 ? ? ?1 ? ?1 ?3.00.3
> 2 ? ? ?1 ? ?2 ?3.1 0.3
> 3 ? ? ?1 ? ?3 ?3.4 0.3
> 4 ? ? ?2 ? ?1 ?4.0 0.1
> 5 ? ? ?2 ? ?2 ?4.3 0.1
> 6 ? ? ?2 ? ?3 ?4.4 0.1
> 7 ? ? ?3 ? ?1 ?3.0 0.3
> 8 ? ? ?3 ? ?2 ?3.2 0.3
> 9 ? ? ?3 ? ?3 ?3.5 0.3
>
> Does anyone have any suggestions as to how to do this? I've looked at
the various apply functions but I can't seem to make anything work. I'm
fairly new to R and would appreciate specific suggestions.?
>
> Thanks!
> 	[[alternative HTML version deleted]]
>
>

Hello,

Try the following.

sp <- split(mydata, mydata$Sample)
do.call(rbind, lapply(sp, function(x){x$Gain <- x$Mass[3] - x$Mass[2]; x}))

Hope this helps,

Rui Barradas
Em 18-09-2012 00:15, Julie Lee-Yaw escreveu:
> Hi
>
> I have a dataframe similar to:
>
>> Sample<-c(1,1,1,2,2,2,3,3,3)
>> Time<-c(1,2,3,1,2,3,1,2,3)
>> Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
>> mydata<-as.data.frame(cbind(Sample,Time,Mass))
>
>    Sample Time Mass
> 1      1    1  3.0
> 2      1    2  3.1
> 3      1    3  3.4
> 4      2    1  4.0
> 5      2    2  4.3
> 6      2    3  4.4
> 7      3    1  3.0
> 8      3    2  3.2
> 9      3    3  3.5
>
> where for each sample, I've measured mass at different points in time.
>
> I now want to calculate the difference between Mass at Time 2 and 3 for
each unique Sample and store this as a new variable called "Gain2-3".
So in my example three values of 0.3,0.1,0.3 would be calculated for my three
unique samples and these values would be repeated in the table according to
Sample. I am thus expecting:
>
>> mydata #after adding new variable
>    Sample Time MassGain2-3
> 1      1    1  3.00.3
> 2      1    2  3.1 0.3
> 3      1    3  3.4 0.3
> 4      2    1  4.0 0.1
> 5      2    2  4.3 0.1
> 6      2    3  4.4 0.1
> 7      3    1  3.0 0.3
> 8      3    2  3.2 0.3
> 9      3    3  3.5 0.3
>
> Does anyone have any suggestions as to how to do this? I've looked at
the various apply functions but I can't seem to make anything work. I'm
fairly new to R and would appreciate specific suggestions.
>
> Thanks!
> 	[[alternative HTML version deleted]]
>
>
>
> ______________________________________________
> 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.

	[[alternative HTML version deleted]]

On Sep 17, 2012, at 4:15 PM, Julie Lee-Yaw wrote:
> Hi 
> 
> I have a dataframe similar to:
> 
>> Sample<-c(1,1,1,2,2,2,3,3,3)
> 
>> Time<-c(1,2,3,1,2,3,1,2,3)
> 
>> Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
> 
>> mydata<-as.data.frame(cbind(Sample,Time,Mass))
> 
Please tell me where you learned that as.data.frame(cbind(.)) construction.
> (
>   Sample Time Mass
> 1      1    1  3.0
> 2      1    2  3.1
> 3      1    3  3.4
> 4      2    1  4.0
> 5      2    2  4.3
> 6      2    3  4.4
> 7      3    1  3.0
> 8      3    2  3.2
> 9      3    3  3.5
> 
> where for each sample, I've measured mass at different points in time. 
> 
> I now want to calculate the difference between Mass at Time 2 and 3 for
each unique Sample and store this as a new variable called "Gain2-3".
So in my example three values of 0.3,0.1,0.3 would be calculated for my three
unique samples and these values would be repeated in the table according to
Sample. I am thus expecting:
> 
>> mydata #after adding new variable
mydata$gain2.3 <- with( mydata, ave( Mass , Time, FUN=function(x)
diff(x[2],x[3]) ) )
> 
>   Sample Time MassGain2-3
> 1      1    1  3.00.3
> 2      1    2  3.1 0.3
> 3      1    3  3.4 0.3
> 4      2    1  4.0 0.1
> 5      2    2  4.3 0.1
> 6      2    3  4.4 0.1
> 7      3    1  3.0 0.3
> 8      3    2  3.2 0.3
> 9      3    3  3.5 0.3
> 
> mydata$gain2.3 <- with( mydata, ave( Mass , Sample, FUN=function(x)
(x[3]-x[2]) ) )
> mydata
  Sample Time Mass gain2.3
1      1    1  3.0     0.3
2      1    2  3.1     0.3
3      1    3  3.4     0.3
4      2    1  4.0     0.1
5      2    2  4.3     0.1
6      2    3  4.4     0.1
7      3    1  3.0     0.3
8      3    2  3.2     0.3
9      3    3  3.5     0.3
> Does anyone have any suggestions as to how to do this? I've looked at
the various apply functions but I can't seem to make anything work. I'm
fairly new to R and would appreciate specific suggestions.
-- 
David Winsemius, MD
Alameda, CA, USA

HI,
Try this:
?mydata$Gain<-rep(tapply(mydata$Mass,mydata$Sample,FUN=function(x)
(x[3]-x[2])),each=length(unique(mydata$Sample)))
?mydata
#? Sample Time Mass Gain
#1????? 1??? 1? 3.0? 0.3
#2????? 1??? 2? 3.1? 0.3
#3????? 1??? 3? 3.4? 0.3
#4????? 2??? 1? 4.0? 0.1
#5????? 2??? 2? 4.3? 0.1
#6????? 2??? 3? 4.4? 0.1
#7????? 3??? 1? 3.0? 0.3
#8????? 3??? 2? 3.2? 0.3
#9????? 3??? 3? 3.5? 0.3
A.K.




----- Original Message -----
From: Julie Lee-Yaw <julleeyaw at yahoo.ca>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Monday, September 17, 2012 7:15 PM
Subject: [R] help with calculation from dataframe with multiple entries per
sample

Hi?

I have a dataframe similar to:
>Sample<-c(1,1,1,2,2,2,3,3,3)
>Time<-c(1,2,3,1,2,3,1,2,3)
>Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
>mydata<-as.data.frame(cbind(Sample,Time,Mass))

? Sample Time Mass
1 ? ? ?1 ? ?1 ?3.0
2 ? ? ?1 ? ?2 ?3.1
3 ? ? ?1 ? ?3 ?3.4
4 ? ? ?2 ? ?1 ?4.0
5 ? ? ?2 ? ?2 ?4.3
6 ? ? ?2 ? ?3 ?4.4
7 ? ? ?3 ? ?1 ?3.0
8 ? ? ?3 ? ?2 ?3.2
9 ? ? ?3 ? ?3 ?3.5

where for each sample, I've measured mass at different points in time.?

I now want to calculate the difference between Mass at Time 2 and 3 for each
unique Sample and store this as a new variable called "Gain2-3". So in
my example three values of 0.3,0.1,0.3 would be calculated for my three unique
samples and these values would be repeated in the table according to Sample. I
am thus expecting:
>mydata #after adding new variable
? Sample Time MassGain2-3
1 ? ? ?1 ? ?1 ?3.00.3
2 ? ? ?1 ? ?2 ?3.1 0.3
3 ? ? ?1 ? ?3 ?3.4 0.3
4 ? ? ?2 ? ?1 ?4.0 0.1
5 ? ? ?2 ? ?2 ?4.3 0.1
6 ? ? ?2 ? ?3 ?4.4 0.1
7 ? ? ?3 ? ?1 ?3.0 0.3
8 ? ? ?3 ? ?2 ?3.2 0.3
9 ? ? ?3 ? ?3 ?3.5 0.3

Does anyone have any suggestions as to how to do this? I've looked at the
various apply functions but I can't seem to make anything work. I'm
fairly new to R and would appreciate specific suggestions.?

Thanks!
??? [[alternative HTML version deleted]]


______________________________________________
R-help at 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.

HI,
Modified version of my earlier solution:
res1<-tapply(mydata$Mass,mydata$Sample,FUN=function(x) (x[3]-x[2]))
res2<-data.frame(Sample=names(res1),Gain2_3=res1)
?merge(mydata,res2)

#Sample Time Mass Gain2_3
#1????? 1??? 1? 3.0???? 0.3
#2????? 1??? 2? 3.1???? 0.3
#3????? 1??? 3? 3.4???? 0.3
#4????? 2??? 1? 4.0???? 0.1
#5????? 2??? 2? 4.3???? 0.1
#6????? 2??? 3? 4.4???? 0.1
#7????? 3??? 1? 3.0???? 0.3
#8????? 3??? 2? 3.2???? 0.3
#9????? 3??? 3? 3.5???? 0.3
A.K.



----- Original Message -----
From: Julie Lee-Yaw <julleeyaw at yahoo.ca>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Monday, September 17, 2012 7:15 PM
Subject: [R] help with calculation from dataframe with multiple entries per
sample

Hi?

I have a dataframe similar to:
>Sample<-c(1,1,1,2,2,2,3,3,3)
>Time<-c(1,2,3,1,2,3,1,2,3)
>Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
>mydata<-as.data.frame(cbind(Sample,Time,Mass))

? Sample Time Mass
1 ? ? ?1 ? ?1 ?3.0
2 ? ? ?1 ? ?2 ?3.1
3 ? ? ?1 ? ?3 ?3.4
4 ? ? ?2 ? ?1 ?4.0
5 ? ? ?2 ? ?2 ?4.3
6 ? ? ?2 ? ?3 ?4.4
7 ? ? ?3 ? ?1 ?3.0
8 ? ? ?3 ? ?2 ?3.2
9 ? ? ?3 ? ?3 ?3.5

where for each sample, I've measured mass at different points in time.?

I now want to calculate the difference between Mass at Time 2 and 3 for each
unique Sample and store this as a new variable called "Gain2-3". So in
my example three values of 0.3,0.1,0.3 would be calculated for my three unique
samples and these values would be repeated in the table according to Sample. I
am thus expecting:
>mydata #after adding new variable
? Sample Time MassGain2-3
1 ? ? ?1 ? ?1 ?3.00.3
2 ? ? ?1 ? ?2 ?3.1 0.3
3 ? ? ?1 ? ?3 ?3.4 0.3
4 ? ? ?2 ? ?1 ?4.0 0.1
5 ? ? ?2 ? ?2 ?4.3 0.1
6 ? ? ?2 ? ?3 ?4.4 0.1
7 ? ? ?3 ? ?1 ?3.0 0.3
8 ? ? ?3 ? ?2 ?3.2 0.3
9 ? ? ?3 ? ?3 ?3.5 0.3

Does anyone have any suggestions as to how to do this? I've looked at the
various apply functions but I can't seem to make anything work. I'm
fairly new to R and would appreciate specific suggestions.?

Thanks!
??? [[alternative HTML version deleted]]


______________________________________________
R-help at 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.

Thanks everyone for the help! I pulled together a bunch of your suggestions
to get the result that I needed. I'm posting my final code below. Probably
not the most efficient way of doing things but gets the job done in a way
that a newbie can understand!

##Here again is the example dataset

Sample<-c(1,1,1,2,2,2,3,3,3)
Mass<-c(3,3.1,3.4,4,4.3,4.4,3,3.2,3.5)
Time<-c(1,2,3,1,2,3,1,2,3)
mydata<-as.data.frame(cbind(Sample,Time,Mass))

## I split the dataset by Sample and then calculate the difference between
mass at time 3 and mass at time 2 for each Sample; then use the merge
function to attach this data to my initial dataset

sp<-split(mydata,mydata$Sample)
y<-rbind(lapply(sp,function(x){Gain<-x$Mass[x$Time==3]-x$Mass[x$Time==2]}))

## note here that as I modification to some of the suggestions posted, I
wanted a way to specifically call "mass at time 3" etc. for each
sample
rather than relying on the position of such data within each split/Sample
(hence allowing me to deal with samples that may have the Time/Mass data
input in a different order

# some massaging of the results
u<-t(y)
s<-data.frame(Sample=row.names(u),Gain2_3=u)
fulldata<-merge(mydata,s)

## as I wished to export the data in the end using write.csv, I had to
covert "list" data into "numeric" in the final dataframe

fulldata$Gain<-as.numeric(fulldata$Gain2_3) 
fulldata$Gain2_3<-NULL

Thanks again everyone!




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