R help - Oct 2023 - How to Calculate the Mean by Multiple Groups in R

Hello,
I have a data frame with different groups (Time, Target, Conc) and
each entry has a triplicate value of the measurements OD and ODnorm.
How can I merge the triplicates into a single mean value?
I tried the following:
```
df = data.frame(Time=rep(1, 9), Well=paste("A", 1:9,
sep=""),
                OD=c(666, 815, 815, 702, 739, 795, 657, 705, 663),
                Target=rep("BACT", 9),
                Conc=c(1,1,1,2,2,2,3,3,3),
                ODnorm=c(9, 158, 158,  45,  82, 138,   0,  48,   6),
                stringsAsFactors = FALSE)
aggregate(.~ODnorm, df, mean)
> aggregate(.~ODnorm, df, mean)
  ODnorm Time Well OD Target Conc
1      0   NA   NA NA     NA   NA
2      6   NA   NA NA     NA   NA
3      9   NA   NA NA     NA   NA
4     45   NA   NA NA     NA   NA
5     48   NA   NA NA     NA   NA
6     82   NA   NA NA     NA   NA
7    138   NA   NA NA     NA   NA
8    158   NA   NA NA     NA   NA

 aggregate(cbind(Time, Target, Conc) ~ ODnorm, df, mean)
  ODnorm Time Target Conc
1      0   NA     NA   NA
2      6   NA     NA   NA
3      9   NA     NA   NA
4     45   NA     NA   NA
5     48   NA     NA   NA
6     82   NA     NA   NA
7    138   NA     NA   NA
8    158   NA     NA   NA
```

Thank you.

Hi,

I think you're misunderstanding which set of variables go on either
side of the formula.

Is this what you're looking for?
> aggregate(OD ~ Time + Target + Conc, data = df, FUN = "mean")
  Time Target Conc       OD
1    1   BACT    1 765.3333
2    1   BACT    2 745.3333
3    1   BACT    3 675.0000
> aggregate(ODnorm ~ Time + Target + Conc, data = df, FUN = "mean")
  Time Target Conc    ODnorm
1    1   BACT    1 108.33333
2    1   BACT    2  88.33333
3    1   BACT    3  18.00000

Or using a different form, that might be more straightforward to you:
> aggregate(df[, c("OD", "ODnorm")], by = df[,
c("Time", "Target", "Conc")], data = df, FUN =
"mean")
  Time Target Conc       OD    ODnorm
1    1   BACT    1 765.3333 108.33333
2    1   BACT    2 745.3333  88.33333
3    1   BACT    3 675.0000  18.00000

Sarah

On Tue, Oct 24, 2023 at 8:31?AM Luigi Marongiu <marongiu.luigi at
gmail.com> wrote:
>
> Hello,
> I have a data frame with different groups (Time, Target, Conc) and
> each entry has a triplicate value of the measurements OD and ODnorm.
> How can I merge the triplicates into a single mean value?
> I tried the following:
> ```
> df = data.frame(Time=rep(1, 9), Well=paste("A", 1:9,
sep=""),
>                 OD=c(666, 815, 815, 702, 739, 795, 657, 705, 663),
>                 Target=rep("BACT", 9),
>                 Conc=c(1,1,1,2,2,2,3,3,3),
>                 ODnorm=c(9, 158, 158,  45,  82, 138,   0,  48,   6),
>                 stringsAsFactors = FALSE)
> aggregate(.~ODnorm, df, mean)
>
> > aggregate(.~ODnorm, df, mean)
>   ODnorm Time Well OD Target Conc
> 1      0   NA   NA NA     NA   NA
> 2      6   NA   NA NA     NA   NA
> 3      9   NA   NA NA     NA   NA
> 4     45   NA   NA NA     NA   NA
> 5     48   NA   NA NA     NA   NA
> 6     82   NA   NA NA     NA   NA
> 7    138   NA   NA NA     NA   NA
> 8    158   NA   NA NA     NA   NA
>
>  aggregate(cbind(Time, Target, Conc) ~ ODnorm, df, mean)
>   ODnorm Time Target Conc
> 1      0   NA     NA   NA
> 2      6   NA     NA   NA
> 3      9   NA     NA   NA
> 4     45   NA     NA   NA
> 5     48   NA     NA   NA
> 6     82   NA     NA   NA
> 7    138   NA     NA   NA
> 8    158   NA     NA   NA
> ```
>
> Thank you.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.


-- 
Sarah Goslee (she/her)
http://www.numberwright.com

A variation is to remove Well and then we can use dot to refer to the
remaining columns.

  aggregate(cbind(OD, ODnorm)  ~ . , subset(df, select = - Well), mean)


On Tue, Oct 24, 2023 at 8:32?AM Luigi Marongiu <marongiu.luigi at
gmail.com> wrote:
>
> Hello,
> I have a data frame with different groups (Time, Target, Conc) and
> each entry has a triplicate value of the measurements OD and ODnorm.
> How can I merge the triplicates into a single mean value?
> I tried the following:
> ```
> df = data.frame(Time=rep(1, 9), Well=paste("A", 1:9,
sep=""),
>                 OD=c(666, 815, 815, 702, 739, 795, 657, 705, 663),
>                 Target=rep("BACT", 9),
>                 Conc=c(1,1,1,2,2,2,3,3,3),
>                 ODnorm=c(9, 158, 158,  45,  82, 138,   0,  48,   6),
>                 stringsAsFactors = FALSE)
> aggregate(.~ODnorm, df, mean)
>
> > aggregate(.~ODnorm, df, mean)
>   ODnorm Time Well OD Target Conc
> 1      0   NA   NA NA     NA   NA
> 2      6   NA   NA NA     NA   NA
> 3      9   NA   NA NA     NA   NA
> 4     45   NA   NA NA     NA   NA
> 5     48   NA   NA NA     NA   NA
> 6     82   NA   NA NA     NA   NA
> 7    138   NA   NA NA     NA   NA
> 8    158   NA   NA NA     NA   NA
>
>  aggregate(cbind(Time, Target, Conc) ~ ODnorm, df, mean)
>   ODnorm Time Target Conc
> 1      0   NA     NA   NA
> 2      6   NA     NA   NA
> 3      9   NA     NA   NA
> 4     45   NA     NA   NA
> 5     48   NA     NA   NA
> 6     82   NA     NA   NA
> 7    138   NA     NA   NA
> 8    158   NA     NA   NA
> ```
>
> Thank you.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.


-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com