R help - Feb 2014 - Help on best way to calculate and plot overall mean from dataset with two treatment groups

I am working on a dataset which has multiple species over several plots,
categorised into two treatment groups.

For example

group_xy group_op plot species value
x o 1 A 3
x o 1 A 5
x o 1 B 4
x o 2 A 3
x o 2 A 6
x o 2 A 3
y o 1 A 3
y o 1 A 5
y o 1 B 4
y o 2 A 3
y o 2 A 6
y o 2 A 3
x p 1 A 3
x p 1 A 5
x p 1 B 4
x p 2 A 3
x p 2 A 6
x p 2 A 3
y p 1 A 3
y p 1 A 5
y p 1 B 4
y p 2 A 3
y p 2 A 6
y p 2 A 3

What I would like to do is to take the mean of the species within each plot
in each treatment group, then generate the mean for the species based upon
the average of the values between plots.

Thus the intermediate output would be

group_xy group_op plot species mean_value standard_deviation
x o 1 A 3 sd
x o 1 B 4 sd
x o 2 A 4 sd
y o 1 A 3 sd
y o 1 B 4 sd
y o 2 A 4 sd
x p 1 A 3 sd
x p 1 B 4 sd
x p 2 A 4 sd
y p 1 A 3 sd
y p 1 B 4 sd
y p 2 A 4 sd

Then eventually
group_xy group_op species total_mean_value standard_deviation
x o A 3.5 sd
x o B 4 sd
y o A 3.5 sd
y o B 4 sd
x p A 3.5 sd
x p B 4 sd
y p A 3.5 sd
y p B 4 sd

I am looking for an elegant code which would allow me to do this and
generate plots. for all species for all treatment groups.

Any help would be appreciated!

	[[alternative HTML version deleted]]

Hi

Posting in HTML results in scrambled mail.

Maybe you want

?aggregate

Regards
Petr
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Rewarp
> Sent: Thursday, February 13, 2014 12:55 AM
> To: r-help at r-project.org
> Subject: [R] Help on best way to calculate and plot overall mean from
> dataset with two treatment groups
>
> I am working on a dataset which has multiple species over several
> plots, categorised into two treatment groups.
>
> For example
>
> group_xy group_op plot species value
> x o 1 A 3
> x o 1 A 5
> x o 1 B 4
> x o 2 A 3
> x o 2 A 6
> x o 2 A 3
> y o 1 A 3
> y o 1 A 5
> y o 1 B 4
> y o 2 A 3
> y o 2 A 6
> y o 2 A 3
> x p 1 A 3
> x p 1 A 5
> x p 1 B 4
> x p 2 A 3
> x p 2 A 6
> x p 2 A 3
> y p 1 A 3
> y p 1 A 5
> y p 1 B 4
> y p 2 A 3
> y p 2 A 6
> y p 2 A 3
>
> What I would like to do is to take the mean of the species within each
> plot in each treatment group, then generate the mean for the species
> based upon the average of the values between plots.
>
> Thus the intermediate output would be
>
> group_xy group_op plot species mean_value standard_deviation x o 1 A 3
> sd x o 1 B 4 sd x o 2 A 4 sd y o 1 A 3 sd y o 1 B 4 sd y o 2 A 4 sd x p
> 1 A 3 sd x p 1 B 4 sd x p 2 A 4 sd y p 1 A 3 sd y p 1 B 4 sd y p 2 A 4
> sd
>
> Then eventually
> group_xy group_op species total_mean_value standard_deviation x o A 3.5
> sd x o B 4 sd y o A 3.5 sd y o B 4 sd x p A 3.5 sd x p B 4 sd y p A 3.5
> sd y p B 4 sd
>
> I am looking for an elegant code which would allow me to do this and
> generate plots. for all species for all treatment groups.
>
> Any help would be appreciated!
>
>       [[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.
________________________________
Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny
pouze jeho adres?t?m.
Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho
odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho
syst?mu.
Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email
jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i
zpo?d?n?m p?enosu e-mailu.

V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
- vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a
to z jak?hokoliv d?vodu i bez uveden? d?vodu.
- a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout;
Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce
s dodatkem ?i odchylkou.
- trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m
dosa?en?m shody na v?ech jej?ch n?le?itostech.
- odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost
??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn?
pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn?
osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi
?i osob? j?m zastoupen? zn?m?.

This e-mail and any documents attached to it may be confidential and are
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender.
Delete the contents of this e-mail with all attachments and its copies from your
system.
If you are not the intended recipient of this e-mail, you are not authorized to
use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by
modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a
contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately
accept such offer; The sender of this e-mail (offer) excludes any acceptance of
the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an
express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into
any contracts on behalf of the company except for cases in which he/she is
expressly authorized to do so in writing, and such authorization or power of
attorney is submitted to the recipient or the person represented by the
recipient, or the existence of such authorization is known to the recipient of
the person represented by the recipient.