[R-sig-eco] Data transformation prior to RDA

[Michael Denslow]

Hi Mariano,

> Dear all,
> I'm trying to do a redundancy analysis. I'm following Legendre & Legendre's
> (1998) tips to prepare the data prior to the analysis, and I惴 hoping to do
> the analysis using package 'vegan'.
> I've already centered and standardized my explanatory and response
> variables, but I'm having trouble at deciding whether or not (and how) data
> should be transformed "to linearise the relationships and make the
> distributions more symmetric". Is there a way to find the best possible
> transformation for each variable but considering at the same time its
> linearity to the other ones? Please tell me if I'm not even asking the right
> question here...


Have a look at the vegan function ?decostand with method =
'hellinger'. I believe that it is discussed and recommended in:

Legendre, P. & Gallagher, E.D. (2001) Ecologically meaningful
transformations for ordination of species data. Oecologia 129;
271–280.

Hope this helps,

Michael

> Here愀 my dataset. First 3 columns are my response variables. All the others
> are explanatory. I know this is a rather basic query, but any tips will be
> greatly appreciated.
>
>  -0.49350555 -0.37364383  0.70566360 -1.1180986 -1.14255167 -1.30234943
> -1.0812858 -0.4910362
> -1.02769104  0.21678178  1.11781073 -1.1123319 -0.88277150 -0.80445588
> -1.0638291  0.3241891
> -0.64335588 -2.07868376 -1.36782590 -1.0585453 -1.02709382 -1.07710897
> -0.2760976  1.4695121
> 0.25799225  0.82044015  1.02481726 -1.1114373 -0.94050043 -1.23089531
> -0.7064526 -0.5012921
> 0.56048832 -0.29655712 -0.07148828 -1.1099933 -1.17141614  1.54301771
> -1.0921962 -1.9517655
> -0.36443725 -1.49241963 -0.23840793 -1.1180554 -1.14255167 -1.24049362
> -1.0856499 -0.6977804
> -1.97959936  1.30035099 -1.18114614  1.0885061 -0.59412687 -0.21062037
> 1.7890870  0.5018224
> -0.24966043 -0.66228200  0.69101500 -0.8697510 -0.88277150 -0.83963955
> 0.1330428  1.3450534
> 0.24720930  0.35162548 -1.34252630  1.6571129 -0.59412687 -0.13708733
> 2.0090270  0.7553207
> -0.35385550  0.99058254 -1.14295716 -0.6801336 -0.76731365 -0.93148980
> 1.9120456  1.4084094
> -0.92880313  1.14039444  1.38922106 -0.9008538 -0.79617811 -0.96178699
> 0.6512872  1.2365340
> -0.24431565 -0.20947362  0.76084722 -0.8978493 -0.59412687 -0.56565825
> -0.4639991 -0.2045137
> -0.60428104  1.05108295 -0.68704030  1.1833813  0.41612935 -0.07054391
> 1.2816664  0.6181682
> 0.63837128  0.06672464  0.32041910  0.4154816  0.12748471  0.46057549
> -0.2488216  0.3867322
> 0.67144677  0.66889622  1.83857364  0.8375587  0.27180703  0.82551787
> -0.2488216 -0.5987399
> 2.53611774  1.45517653 -0.22337307  0.9253861  0.06975579 -0.22307224
> 1.6332240  0.5146235
> -0.13273765 -0.55628531  0.55154280 -0.2721408  0.99341861 -0.14553291
> -0.1669935  0.9976660
> -0.02043306 -1.52670601 -2.08967318  1.7138916  2.14799715  2.18006143
> -0.6034099 -0.9383742
> 0.80218610 -0.58481301  0.18945796  0.9761855  1.57070788  1.90295452
> -0.6579619 -1.3578423
> 1.32726744  0.64941495 -0.42596631  0.7975236  0.87796076  0.63986198
> -0.0760734 -1.0445683
> -1.53219503  0.57349823  1.03668089  0.5040093  1.05114754  0.83815684
> -0.3852017 -0.8672218
> 0.67016035  0.81036993  0.14519361  0.5065215  1.05114754  0.49360195
> -0.1124414 -0.7921778
> 1.53517131 -0.85469204 -0.12003248  0.3702800  1.02228308  0.66797133
> -0.3185269 -1.1538661
> -0.67154028 -1.45978251 -0.88080583 -0.7266479  0.93568969  0.18901542
> -0.8216180  1.0411473

> Thanks!
>
> Best wishes,
>
> Mariano
>
> --------------------------
>
> Mariano Devoto
> School of Biological Sciences
> University of Bristol
> Woodland Road
>
> Bristol, UK
> BS8 1UG
> Tel. +44 (0) 1179545960 (internal 45960)
> web: http://agro.uba.ar/~mdevoto <http://agro.uba.ar/%7Emdevoto>
>

-- 
Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
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Southeast Regional Network of Expertise and Collections
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