[R-sig-eco] Fwd: help

[Stephen Sefick]

Mahnaz,

We need this to be reproducible.  Assuming you can get this into R,  use 
dput and copy the results of that into an email.

#copy this into R
set.seed(1000)
x <- data.frame(a=rnorm(10), b=rnorm(10), c=rnorm(10))

dput(x)


#here is the output

x <- (structure(list(a = c(-0.445778264836677, -1.2058565689643, 
0.0411263138456899,
0.639388407571143, -0.786554355912735, -0.38548929809552, 
-0.475867884077706,
0.719750691474437, -0.018505622887574, -1.37311775893855), b = 
c(-0.982427827680338,
-0.554488701581856, 0.121381188657659, -0.120872315937481, 
-1.33604104855461,
0.170057481208407, 0.155078715940733, 0.0249318673672384, 
-2.04658541402115,
0.213154105608615), c = c(2.67007166431368, -1.22701600631211,
0.834247331947683, 0.532571747050487, -0.646824963186768, 
0.603161260832291,
-1.78384413571217, 0.334942167117471, 0.560975721885086, 1.22093565459939
)), .Names = c("a", "b", "c"), row.names = c(NA, -10L), class = 
"data.frame"))


notice that I have wrapped the output in x <-() to make it copy and 
paste ready.

Now we have something to work with.  If you can't get data into R then 
that is a different question.

Stephen Sefick





On 12/10/2011 12:57 PM, Mahnaz Rabbaniha wrote:
> ---------- Forwarded message ----------
> From: Mahnaz Rabbaniha<rab.mahnaz at gmail.com>
> Date: Sat, 10 Dec 2011 08:31:10 +0330
> Subject: Re: [R-sig-eco] help
> To: Sarah Goslee<sarah.goslee at gmail.com>
>
>   Dear Sarah
>
>
> thank you for your attention,
>
> I want to use PCA with supplementary variables due to correlation
> between the independent factor such as salinity ,temperature... with
> dependent variable ( fish larva ) therefore changed  dependent
> variable with log(x+1) and tested normality with shapiro test but data
> haven't changed and remained non normality then i decided to used the
> nonparametric analysis MDS   and found its order from net but it
> wasn't successfully and plot of matrix was empty.
>
> my question is: for using the MDS have to need the special form of
> excel ,
>
>
> thanks
>
> mahnaz
>
>
> On 12/9/11, Sarah Goslee<sarah.goslee at gmail.com>  wrote:
>> Hi,
>>
>> On Fri, Dec 9, 2011 at 7:13 AM, Mahnaz Rabbaniha<rab.mahnaz at gmail.com>
>> wrote:
>>> Hi
>>>
>>> in my project i collected its data in excel sheet that i attached,data
>>> were non normal then i transformed them and check the normality by
>>> shapiro.test that it showed again non-normality therefore i decided
>>> used the MDS analyses in r and download this site
>>>   ( http://www.statmethods.net/advstats/mds.html)
>>>
>>> but i haven't done it,  i think  the main problem is the form of excel
>>> matrix for doing it and also i want to know about different between
>>>   CLASSICAL
>>> MDS and isoMDS.
>> We need to know more about what you're donig to be able to help with
>> the excel matrix. What is the problem? How are you importing it into R?
>>
>> ?cmdscale
>> library(MASS)
>> ?isoMDS
>>
>> offers some information about the algorithms used in the two approaches,
>> as well as many references for more information
>>
>> Briefly and simplistically, the difference has to do with whether the
>> algorithm
>> attempts to preserve actual dissimilarities or rank-order dissimilarities.
>>
>>> please help me because this method is new in iran
>>>
>>> Thanks in advance
>>> --
>>> *Mahnaz Rabbaniha*
>>> *Senior expert of marine ecology *
>>> *Iranian Fisheries Research Organization (IFRO) *
>>> *P.O.Box: 14155-6116 , P.Code: 1411816618*
>>> Tehran, IRAN
>>> Phone:   +98 21 44580953
>>> *Fax:       +98 21 44580583*
>>> *Mobile:  +98 912 5790377*
>>> *Website: http://www.ifro.ir*
>>>
>> --
>> Sarah Goslee
>> http://www.functionaldiversity.org
>>
> _______________________________________________
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> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

-- 
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**************************************************
sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
**************************************************

Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods.  We are mammals, and have not exhausted the annoying little problems of being mammals.

                                 -K. Mullis

"A big computer, a complex algorithm and a long time does not equal science."

                               -Robert Gentleman