[R-sig-eco] CALIBRATE program
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. 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:2010202...@njau.edu.cn ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] CALIBRATE program
Have a look at the bio.infer package Regards Mike -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Yong Zhang Sent: 14 March 2011 09:10 To: r-sig-ecology Subject: [R-sig-eco] CALIBRATE program 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. 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:2010202...@njau.edu.cn -- This message (and any attachments) is for the recipient only NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] CALIBRATE program
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:2010202...@njau.edu.cn ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] ecodist (MRM) error message
Hi Everyone, MRM is returning what seems to be a matrix singularity error: Error in solve.default(XX) : system is computationally singular: reciprocal condition number = 1.88323e-86 when running MRM(Dy~exp(Dx)). I would appreciate it if anyone could help me around this. Thanks, A -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/ecodist-MRM-error-message-tp6170910p6170910.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] nested factor for which i would like a parameter estimate
Thanks very much Mike. It clears things up immensely now that i'm not thinking
about nesting fixed effects inside random effects, and the model and dfs make
sense.
doug
On 13 Mar 2011, at 21:04, Dunbar, Michael J. wrote:
Hi Doug
Your first model can't be right, as AM/PM is clearly a fixed effect: it has
just two levels and you are only interested in making inferences about those
two levels. So you can't have AMPM on the right of the random part of the
model. Try not to think of nesting fixed effects in random effects. Think
about specifying the structure of the nesting with the random effects, then
the fixed effects are mapped onto the correct level automatically, lme is
clever like that. You can always check the degrees of freedom also.
The second model sounds more sensible although you probably need to tell it
explicitly that AM/PM corresponds to each measurement in your data, something
like:
Mod.lme3 - lme(bird_entropy ~ sound_entropy * landuse + AMPM, random = ~ 1 |
plot/subplot, data=Bird)
This treats subplot as a random effect nested within plot, and each subplot
has two measurements, AM and PM. This should handle the correlation between
AM/PM, and you can plot residuals to see if there is any further residual
correlation. If so, then you can perhaps consider one of the residual
correlation structure models. You could go further and fit a full bivariate
model between AM and PM, have a look at the paper by Doran and Lockwood 2006
for how to do this with lme.
regards
Mike
From: r-sig-ecology-boun...@r-project.org
[r-sig-ecology-boun...@r-project.org] On Behalf Of dougwyu [doug...@gmail.com]
Sent: 13 March 2011 07:29
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] nested factor for which i would like a parameter
estimate
Hello all,
I am trying to test whether sound diversity predicts bird diversity.
The question i have concerns how to deal with a factor that could be treated
either as a random or fixed factor.
Response: bird_entropy (continuous)
Fixed factors: landtype (factor), sound_entropy (continuous), AM/PM (factor)
Random factor: Plot
The problematic factor is AM/PM.
We have 29 total sampling plots, each of which is measured for
sound_diversity at five subplots, once in the AM (dawn) and again in the PM
(dusk), for a total 10 measurements per plot. (Each plot has only one,
overall measure of bird_diversity).
On the one hand, AMPM is nested within plot, but on the other hand, we would
like to estimate a parameter for AMPM, since we expect different suites of
sound producers (not just birds) at different times of the day. However, it's
reasonable to expect temporal correlation between AM and PM.
The first model seems uncontroversial to me (these are post-model-selection).
Mod.lme1 - lme(bird_entropy ~ sound_entropy * landuse, random = ~ 1 | plot /
AMPM, data=Bird)
But i'm curious to know if this second model is reasonable, and if so, how
would I code the plot variable?
Mod.lme2 - lme(bird_entropy ~ sound_entropy * landuse + AMPM, random = ~ 1 |
plot, data=Bird)
Thanks all,
Doug
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