[R-sig-eco] CALIBRATE program

[Gavin Simpson]

On Mon, 2011-03-14 at 17:09 +0800, Yong Zhang wrote:
> Hi all,
> 
> Today, I noticed a C++ program named "CALIBRATE" when I looked into
> one paper. It is used for analysising and visualising
> species-environment relationships and for predicting environmental
> values from species assemblages, and it is developed by Juggins, S.,
> from department of geography, university of Newcastle, UK.
> 
> I really want to know if anyone has used this before? Or, if there is
> any package in R has the identical function as CALIBRATE?
> 
> Thanks very much in advance, and any of your reply will be greatly
> appreciated.

Wow, that is old. Steve Juggins has written a replacement package that
does what Calibrate did and more - it is called C2 and can be found
here:

http://www.staff.ncl.ac.uk/staff/stephen.juggins/software/C2Home.htm

C2 is free to use for 70 samples or fewer or for the data manipulations
between formats, but requires a paid-for licence for larger data sets.

There are several options available in R. The closest is probably Steve
Juggins' own package rioja which interfaces with the same numerical C++
code that is used in C2. Advantages are that it fits a wide range of
transfer function models. You *don't* need C2 to use rioja.

Another option is my own analogue package which focusses on the modern
analogue technique (MAT) and weighted averaging. analogue is better for
MAT, whilst rioja is arguably better for WA as it is implemented in
compiled code and things like bootstrapping are a bit faster there than
my R code implementations. analogue produces nicer stratigraphic plots,
IMHO, but you might need the version on R-forge to get the best out of
it.

Lest Yuan's bio.infer package implements the maximum likelihood method,
which is also available in rioja.

Finally there is Sven Adler's paltran package which likewise implements
a wide range of transfer functions including WA-PLS and ML, but last I
looked, WA-PLS gave different results to rioja and C2. It was also quite
a bit slower than rioja.

Yong, if you need further guidance, email back with exactly which
methods you wanted to use and I will try to point you in the right
direction. Seems like I should write this up for the Environmetrics Task
View...

HTH

G

> All the best
> 
> Yong
> 
> 
> 2011-03-14 
> 
> 
> Yong Zhang, Ph.D. 
> Lab of aquatic insects & stream ecology
> Dept.of Entonology, Nanjing Agricultural University
> Nanjing, 210095,China 
> Phone number:  (+86) -25-84395241
> E-mail:2010202035 at njau.edu.cn
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