R help - Apr 2013 - Make barplot with error bars, anova out of a table

Helo everybody,
I'm new to R and have some issues with my data in R. 

My raw data look like that:

ID Day size 1 1 7 1 1 7.2 1 1 7.1 2 1 7.3 2 1 7.4 2 1 7.2 3 1 7 3 1 7.1 3 1
7.5 4 1 7.3 4 1 7.2 4 1 7.6 1 2 7 1 2 7.2 1 2 7.1 2 2 7.1 2 2 7.4 2 2 7.2 3
2 7.5 3 2 7.1 3 2 7.5 4 2 7.2 4 2 7.2 4 2 7.3 1 3 7.4 1 3 7.2 1 3 7.1 2 3
7.2 2 3 7.4 2 3 7.2 3 3 7.4 3 3 7.2 3 3 7.5 4 3 7.4 4 3 7.2 4 3 7.7

What I want to do is:
1) calculate the significant difference of the size for the 4 groups but
each day separately!)? E.g. difference in size between ID 1:2, 1:3, 1:4,
2:3, 2:4, 3:4 for each day.

I already tried lm() and anova() but just get the difference between day, ID
and size. I also tried to separate the data per hand but I think there
should be a way in "R" to do that automatically!? Moreover, I was
searching
the web for similar examples but couln't find anything useful so far.

2) to make a barplot with error bars of the standart error (from the mean).
So far I used: 
barplot(matrix(c(Rtest.dat$pH.mean),nr=3), beside=T,
col=c("black","grey","white"),
main="pH", names.arg=c("Green", "Yellow",
"Blue", "Red"), ylab="pH")
legend("topright", c("Day 1","Day 2","Day
3"),
cex=0.6, bty="n",
fill=c("black","grey","white"))
But I have problems to add the error bars. Also here I already searched the
web but couldn't manage to get a code working for my data.

3) and the last thing I would need is to add * or letters (a,b,...) to the
graph, indicating the significant difference between them.

Hope someone can help me!

Thanks for your help!!



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Hi

On Thu, Apr 11, 2013 at 6:43 AM, Simza <alex_steckbauer at gmx.at>
wrote:
> Helo everybody,
> I'm new to R and have some issues with my data in R.
>
> My raw data look like that:
>
> ID Day size 1 1 7 1 1 7.2 1 1 7.1 2 1 7.3 2 1 7.4 2 1 7.2 3 1 7 3 1 7.1 3 1
> 7.5 4 1 7.3 4 1 7.2 4 1 7.6 1 2 7 1 2 7.2 1 2 7.1 2 2 7.1 2 2 7.4 2 2 7.2 3
> 2 7.5 3 2 7.1 3 2 7.5 4 2 7.2 4 2 7.2 4 2 7.3 1 3 7.4 1 3 7.2 1 3 7.1 2 3
> 7.2 2 3 7.4 2 3 7.2 3 3 7.4 3 3 7.2 3 3 7.5 4 3 7.4 4 3 7.2 4 3 7.7
>
> What I want to do is:
> 1) calculate the significant difference of the size for the 4 groups but
> each day separately!)? E.g. difference in size between ID 1:2, 1:3, 1:4,
> 2:3, 2:4, 3:4 for each day.
>
> I already tried lm() and anova() but just get the difference between day,
ID
> and size. I also tried to separate the data per hand but I think there
> should be a way in "R" to do that automatically!? Moreover, I was
searching
> the web for similar examples but couln't find anything useful so far.
>
> 2) to make a barplot with error bars of the standart error (from the mean).
> So far I used:
> barplot(matrix(c(Rtest.dat$pH.mean),nr=3), beside=T,
> col=c("black","grey","white"),
main="pH", names.arg=c("Green", "Yellow",
> "Blue", "Red"), ylab="pH")
legend("topright", c("Day 1","Day 2","Day
3"),
> cex=0.6, bty="n",
fill=c("black","grey","white"))
> But I have problems to add the error bars. Also here I already searched the
> web but couldn't manage to get a code working for my data.
>
R has a function called "arrows" that we use to draw intervals like
that. You have to calculate the intervals, of course, that's up to
you, and then draw them on the plot.

As luck would have it, I've been working a vaguely similar type of plot,

http://pj.freefaculty.org/scraps/plot-factor-proto.pdf

and I'm going to upload the R code that produces that plot. It shows
how to do arrows and such. I'm calling this a WorkingExample

http://pj.freefaculty.org/R/WorkingExamples/plot-regression-factors-1.R
> 3) and the last thing I would need is to add * or letters (a,b,...) to the
> graph, indicating the significant difference between them.
>
Try text() to insert stuff on plots. * is writable by text.

> Hope someone can help me!
>
> Thanks for your help!!
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Make-barplot-with-error-bars-anova-out-of-a-table-tp4663979.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.


--
Paul E. Johnson
Professor, Political Science      Assoc. Director
1541 Lilac Lane, Room 504      Center for Research Methods
University of Kansas                 University of Kansas
http://pj.freefaculty.org               http://quant.ku.edu

On Apr 11, 2013, at 4:43 AM, Simza wrote:
> Helo everybody,
> I'm new to R and have some issues with my data in R. 
> 
> My raw data look like that:
> 
> ID Day size 1 1 7 1 1 7.2 1 1 7.1 2 1 7.3 2 1 7.4 2 1 7.2 3 1 7 3 1 7.1 3 1
> 7.5 4 1 7.3 4 1 7.2 4 1 7.6 1 2 7 1 2 7.2 1 2 7.1 2 2 7.1 2 2 7.4 2 2 7.2 3
> 2 7.5 3 2 7.1 3 2 7.5 4 2 7.2 4 2 7.2 4 2 7.3 1 3 7.4 1 3 7.2 1 3 7.1 2 3
> 7.2 2 3 7.4 2 3 7.2 3 3 7.4 3 3 7.2 3 3 7.5 4 3 7.4 4 3 7.2 4 3 7.7
> 
> What I want to do is:
> 1) calculate the significant difference of the size for the 4 groups but
> each day separately!)? E.g. difference in size between ID 1:2, 1:3, 1:4,
> 2:3, 2:4, 3:4 for each day.
> 
> I already tried lm() and anova() but just get the difference between day,
ID
> and size. I also tried to separate the data per hand but I think there
> should be a way in "R" to do that automatically!? Moreover, I was
searching
> the web for similar examples but couln't find anything useful so far.
I'm guessing this appeared as a three column data layout but using HTML
format has sabotaged your intent.
> 
> 2) to make a barplot with error bars of the standart error (from the mean).
> So far I used: 
> barplot(matrix(c(Rtest.dat$pH.mean),nr=3), beside=T,
> col=c("black","grey","white"),
main="pH", names.arg=c("Green", "Yellow",
> "Blue", "Red"), ylab="pH")
legend("topright", c("Day 1","Day 2","Day
3"),
> cex=0.6, bty="n",
fill=c("black","grey","white"))
> But I have problems to add the error bars. Also here I already searched the
> web but couldn't manage to get a code working for my data.
> 
> 3) and the last thing I would need is to add * or letters (a,b,...) to the
> graph, indicating the significant difference between them.
> 
> Hope someone can help me!
You might want to consider:

http://biostat.mc.vanderbilt.edu/wiki/Main/DynamitePlots

-- 

David Winsemius
Alameda, CA, USA