Re: [ECOLOG-L] PDF of Sarmiento 1975
Dear friends, Thank you for your quick reply and the pdf I requested! My institution is temporarily out of connection with JSTOR. Best, Alexandre -- Forwarded message -- From: Alexandre F. Souza <alexsouza.cb.ufrn...@gmail.com> Date: 2017-08-22 16:28 GMT-03:00 Subject: PDF of Sarmiento 1975 To: "Ecological Society of America: grants, jobs, news" < ECOLOG-L@listserv.umd.edu> Hello all, Do someone have the pdf of the classic article on south american dry forest distribution Sarmiento G. 1975. The dry plant formations of South America and their floristic connections. J. Biogeogr. 2: 233–251. I could not reach it anywhere here. Sincerely, Alexandre
[ECOLOG-L] Willingness to review manuscript on Plant Functional Ecology
Dear Functional Ecology/Plant Ecology friends, I have written a manuscript on the relationships between plant traits in a harsh heath vegetation ecosystem in northeastern Brazil, using morphological, anatomical and biochemical traits, as well as establishing strategy gradients and their correspondence with the CSR scheme. I would like to have a second look to improve the manuscript before its publication. Are you willing to review the manuscript for me with a special eye to the writing (English is not my first language)? I am willing to review some text from you in exchange. My deadline is May 6th. Thank you very much in advance, Jose Luiz A. Silva Universidade Federal do Rio Grande do Norte
Re: [ECOLOG-L] Manuscript Review Exchange?
Dear friends, I would like to thank everybody for the quick response I got and for the help in revising my manuscript. I use this opportunity to let you know that I have already got some positive replies and I will not be able to manage any further reciprocal readings. Best wishes, Alexandre -- Forwarded message -- From: Alexandre F. Souza <alexsouza.cb.ufrn...@gmail.com> Date: 2017-02-04 8:12 GMT-03:00 Subject: Manuscript Review Exchange? To: "Ecological Society of America: grants, jobs, news" < ECOLOG-L@listserv.umd.edu> Dear Population Ecology/Plant Ecology friends, I have written a manuscript on the demography of the dominant conifer Araucaria angustifolia in a forest-grassland mosaic in southern Brazilian mixed conifer-hardwood ecoregion, using aerial photographs and satellite imagery as sampling techniques. I would like to have a second look to improve the manuscript before its publication. Are you willing to review the manuscript for me with a special eye to the writing (English is not my first language)? I am willing to review some text from you in exchange. My deadline is February 23th. Thank you very much in advance, Alexandre -- Dr. Alexandre F. Souza Professor Adjunto III Universidade Federal do Rio Grande do Norte CB, Departamento de Ecologia Campus Universitário - Lagoa Nova 59072-970 - Natal, RN - Brasil lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza -- Dr. Alexandre F. Souza Professor Adjunto III Universidade Federal do Rio Grande do Norte CB, Departamento de Ecologia Campus Universitário - Lagoa Nova 59072-970 - Natal, RN - Brasil lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza
[ECOLOG-L] Manuscript Review Exchange?
Dear Population Ecology/Plant Ecology friends, I have written a manuscript on the demography of the dominant conifer Araucaria angustifolia in a forest-grassland mosaic in southern Brazilian mixed conifer-hardwood ecoregion, using aerial photographs and satellite imagery as sampling techniques. I would like to have a second look to improve the manuscript before its publication. Are you willing to review the manuscript for me with a special eye to the writing (English is not my first language)? I am willing to review some text from you in exchange. My deadline is February 23th. Thank you very much in advance, Alexandre -- Dr. Alexandre F. Souza Professor Adjunto III Universidade Federal do Rio Grande do Norte CB, Departamento de Ecologia Campus Universitário - Lagoa Nova 59072-970 - Natal, RN - Brasil lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza
[ECOLOG-L] Grassland Article Review: Thank you
Dear friends, Yesterday I posted a message asking if someone was willing to review a manuscript I have written on the effects of afforestation on grassland ecology. I would like to thank the colleagues that wrote to me and tell you that I have already sent the ms to a number of colleagues that I believe will generate a good deal of work. All the best, Alexandre
[ECOLOG-L] Is someone willing to review a manuscript on grassland ecology?
Dear friends, I have just finished a manuscript on the effects of afforestation on the plant community composition and structure in southern Brazilian grasslands. They correspond to the northernmost part of the Pampas biome and are witnessing large-scale conversion to eucalypt plantations. I would like to know whether is someone willing to review this manuscript, so I have some input in order to improve it before submission. I am willing to review your manuscript in return. All the best, Alexandre
Re: [ECOLOG-L] Ecology What is it?
Hi Wayne,
It is possible that the manifesto has been caught in between three
worlds. In the world of ecology and conservation the article is not
citable in most research papers, which deal with very specialized
literature. I the world of sociology, which may study the phenomenon of
environmental activism, the journal Biodiversity is unlikely to be known
or read at all. Finally, in the world of activism itself, daily
activities do not include publishing articles and thus citation of the
manifesto, although it may have been read by people involved.
All the best,
Alexandre
Date:Wed, 9 Nov 2011 11:45:07 -0800
From:Wayne Tyson landr...@cox.net
Subject: Ecology What is it?
Honorable Forum:
A search on-line for precisely ecocentric on November 9, 2011 results =
in precisely THREE hits. ALL three are from ONE paper, A Manifesto for =
Earth ('Biodiversity' Volume 5, No. 1, pages 3 to 9, January/March =
2004) http://www.ecospherics.net/pages/EarthManifesto.html .=20
Can someone tell me why this paper has not been cited at all in almost =
eight years?=20
WT
Re: [ECOLOG-L] Neutral Theory Carried out to Physical Systems
Hi Mansour, Congratulations for your scientific initiative. Being out of the scientific community is an unfavourable position to do science but is by no means a final obstacle. See the recent example of a great contribution from Physics by Lou Jost on the calculation and interpretation of diversity and, to use an extreme example, by Einstein, who was working at a patent office when he developed his relativity theory. Generally speaking, I believe this to be a natural extension of the evolutionary theory to the molecular domain, and thus have potential to make a significant contribution. Since I do not work with neither evolution nor theoretical ecology, I am not able to discuss your theory directly. However, I disagree with your internet-based strategy. Note that both the researchers I mentioned before made a contribution to science because they published their ideas in scientific journals. These are the main forum in which researchers debate and exchange ideas, and these ideas become stronger when submitted to peer review and published criticism. Publish it in English, not in Arabian. Best wishes, Alexandre
[ECOLOG-L] Note on Video Explains Devastating Forest Bill in Brazil
Hello, As an obervation about my earlier message about the video that explains the proposed bill on the Brazilian forest code: the video was made a few months ago aiming at helping in the effort to better inform the Brazilian public opinion about the devastating consequences of the proppded bill. Because of that the video is in Portuguese. I added English subtitles to it hoping to make it available to English-speakers interested in the subject. Best wishes, Alexandre
[ECOLOG-L] Video Explains Devastating Forest Bill in Brazil
Dear friends, I have posted a video in Youtube http://www.youtube.com/watch?v=pf9TJiCj-jEfeature=related in which I explain the controversy of the new Forest Bill that the Brazilian Congress has approved and that is now being debated in the Senate. Click the cc button in the lower pane tool bar of the video to see English subtitles. If approved, the consequences for biodiversity conservation are devastanting. I invite you to take a look at it and consider talking about it with your friends and co-workers, maybe signing the AVAAZ electronic undersigned against the bill http://www.avaaz.org/po/salve_codigo_florestal Best regards, Alexandre
[ECOLOG-L] Is academic publishing a racket? Yes
Dear Julie, I fully agree with Monbiot's criticism of scientific publishing by academic publishers and believe it is far from paranoia. The main scape out are the open journals. For many of us third world researchers the main difficulty regarding open journals are page charges. I believe it can be partially staked round by including publication costs in advance in our projects. Personally I am beginning to do that. It is not a perfect solution because projects frequently ends before articles are published or even submitted. I am also not a fan of high-impact journals. In a web era like ours, articles are searched for easily and most people tends to pick them according to affinity to current interests and not so much by the importance of the vehicle. We should free ourselves from the largely psychological need to publish in famous journals. All the best, Alexandre
[ECOLOG-L] Ecological sensitivity of Australian rainforests to selective logging
Hello friends, Do anyone has the pdf of the review article ROSS HORNE and JOHN HICKEY 1991 Ecological sensitivity of Australian rainforests to selective logging. Australian Journal of Ecology Volume 16, Issue 1, pages 119129. It is online since 2006 but I do not have access in my university in Brazil and the library does not have the paper version of the journal. Thanks in advance, Alexandre
Re: [ECOLOG-L] ECOLOG-L Digest - 6 Apr 2011 to 7 Apr 2011 (#2011-97)
Dear Laura, Regarding the dissemination of scientific thought: Are scientists making scientific findings readily accessible to the general public? In general, no. Reader-friendly versions of regular research results are not commonly published in most cases. Results that reach the general public are mostly those choose by the mainstream press. Mainstream press in turn present a highly biased interest for technological results and bizarre natural findings. Most real understanding of Nature is not reaching society in general. What can scientists do to improve dissemination of scientific information to the general public? Actively prepare manuscripts targeted to the general public and send it to scientific divulgation journals and sites and newspapers in general. Roughly, for each paper, a divulgation article. Scientific societies should also create their own scientific divulgation journals. Do scientists need to be involved in teaching the public about the scientific method? Yes. Our participation is key to keep distortions at a minimum. Best regards, Alexandre Date:Thu, 7 Apr 2011 04:17:00 -0400 From:Laura S. lesla...@gmail.com Subject: Disseminating scientific thought to the general public: are scientists making science readily accessible? Dear all: I am interested in your thoughts. If needed, I can elaborate more on these questions. Are scientists making scientific findings readily accessible to the general public? What can scientists do to improve dissemination of scientific information to the general public? Do scientists need to be involved in teaching the public about the scientific method? Thank you, Laura
[ECOLOG-L] Defining Biodiversity
Hi Euan, I use the broad definition of biodiversity as senctioned by the US Congressional Biodiversity Act, HR1268 (1990), according to which biological diversity means the full range of variety and variability within and among living organisms and the ecological complexes in which they occur, and encompasses ecosystem or community diversity, species diversity, and genetic diversity. I think biodiversity should continue to have a broad and all-encompassing meaning, and the communication problem you mention arises much more from the use of the term in place of more specific ones, when we refer to specific issues. When communicating with the public, we should be more specific when speaking about specific issues, rather than abolishing a term that has a broad meaning, and that should be reserved for broad themes. The California Biodiversity Council has a compilation of scientific definitions of biodiverstiy (http://biodiversity.ca.gov/Biodiversity/biodiv_def2.html). Best whishes, Alexandre Date:Mon, 13 Dec 2010 15:05:31 -0800 From:Ritchie, Euan euan.ritc...@jcu.edu.au Subject: Defining biodiversity, and does the term capture the public's attention? Hi everyone, I have just returned from the Ecological Society of Australia meeting and a= mong other issues, there was much discussion about the term biodiversity. M= any people argue that this term is hard to define, and importantly, the pub= lic have no idea what it actually means and therefore they have less connec= tion/concern to preserve/conserve species and habitats. I thought it would = be interesting to hear how others define biodiversity, and if this term isn= 't helpful for conveying the importance of species diversity to the public,= what term(s) should we use? Over to you, Euan Dr. Euan G. Ritchie, Lecturer in Ecology, School of Life and Environmental = Sciences Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop
[ECOLOG-L] Help with Multiple Regression
Dear friends, It has been recently suggested by Legendre and co-authors that we include quadratic and product terms of our environmental variables in constrained ordinations. For instance, to include not only latitude but also latitude^2 and latitude*longitude, the same with physical and biotic variables aimed at being correlated with ordination axis in some way. I am following McCune and Grace's book (2002) suggestion of correlating environmental variables with NMDS axes. However common correlations of multiple variables x each nmds axis are not the best options because at each correlation they do not control for the other variables in the dataset. Those authors also state that multiple regression use partial correlation coefficients and thus would be a better methos for correlating several environmental variables with ordination axes. However, multiple regression suffers from multicolinearity, which is greatly enhanced when we use product or quadratic terms of the environmental variables. What do you think about that? Best whishes, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop
[ECOLOG-L] Post on How to Run a db-MRT
Dear Friends, Here are some replies I received on the above subject. Thank you for the help. Sincerely, Alexandre Dear Dr. Souza, I was advised to use regression trees, so you have solved one problem for me, what is the name of the package! For your question, I can suggest two ways which might work, based on their use in displaying results of non-metric multidimensional scaling (metaMDS in R): meta.x-metaMDS(x) plot(meta.x, display=sites, type=t) Here, the display command says to plot sites rather than species, and the type command specifies text (which should identify the plot) rather than points which would just put a symbol. Another possible solution is theidentify command: plot ( x, sites) identify (plot ( x,sites), sites) Using this command, you point to each symbol on the chart and click - causing the name of that plot to appear., but the result is not saved in the graphic by R until you have clicked o all of the points. I hope that this is helpful. I found the attached tutorial helpful. I believe that it addresses the question you posed regarding alternate distance matrices. Let me know if you have any further questions. http://www.ualberta.ca/~jspence/Spence_lab/MRT-r-package.html This tutorial presents how to actually implement db-MRT. Here is the information that you need to see species names (my previous message was probably of no use). Download the documentation for package (mvpart) at: http://bm2.genes.nig.ac.jp/RGM2/R_current/library/mvpart/man/mvpart.html In it you will find the different arguments with a brief comment about each, also an example, which is the most useful. These lines in the example produces two graphics, both of which identify and locate species. To see both of them open the graphics window in the R window (if you are using Windows) click on History in the Menu bar and click on Recording. Then you can use Previous and Next in that same menu. mvpart(data.matrix(spider[,1:12])~herbs+reft+moss+sand+twigs+water,spider,xv=p) # pick the tree size # pick cv size and do PCA fit - mvpart(data.matrix(spider[,1:12])~herbs+reft+moss+sand+twigs+water,spider,xv=1se,pca=TRUE) rpart.pca(fit,interact=TRUE,wgt.ave=TRUE) # interactive PCA plot of saved multivariate tree I modified he first line as follows mvpart(data.matrix(spider[,1:12])~herbs+reft+moss+twigs+water,spider,xadj=2, yadj=3,xv=min,pca=T) , using xadjand yadj to increase the size of the bar plots. I do not know how to move the legend out of the way of the tree diagram, though. Hi Alexandre, I don't think you can do it with mvpart since mvpart doesn't take the dissimilarity structure into account. There are other regression tree packages though, and you might want to look at randomForest which generally provides better results than classic CART analysis. In packagefunction 'rpart' there is a switch to select the dissimilarity measure. Depending on your dataset you may be able to change the dissimilarity measure by simply transforming the data, for example, a sqrt transform would give square-chord dissimilarity from euclidian distance. Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Post and New Question on Multivariate Regression Trees: how to identify sample units?
Dear friends, I have just posted a question on the identification of plots-sites in Multivariate Regression Trees produced by the mvpart package in R. However, I figured it out that it is just to sort the data according to the threshold values given by the resulting tree. Maybe there is a function in mvpart to give this information, but data sorting seems to work. Yet, another question arose. De'ath (2002, Ecology) states that MRT can be developed from other distance-based measures than the Euclidean distances. Do anyone knows how to implement it using mvpart? Best wishes, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] R: Multivariate Regression Trees: how to identify sample units?
Dear friends, I am sudying R's mvpart package, that implements Multivariate Regression Trees, aiming at applying it to a biogeographical dataset of tree speces in southern South America. My doubt is how to access plot identities after the tree is produced. For us it is rather important, but I could not find them with neither 'summary(fit)'[where fit is the object containing the mvpart(...) command] nor just 'fit'. This piece of information is likely to be somewhere in the package documentation (Package 'mvpart' or ?mvpart), but I did not succeed in finding it. Do anyone knows how to solve this? Thank you in advance and all the best, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Post on Obtaining Factor Loadings in Vegan's PCA
Dear friends, Here the solution for the question I posted some days ago about obtaining factor loadings when running a PCA with vegan package in R. The Question: Hi all, I am using the vegan package to run a prcincipal components analysis on forest structural variables (tree density, basal area, average height, regeneration density) in R. However, I could not find out how to extract factor loadings (correlations of each variable with each pca axis), as is straightforwar in princomp. Do anyone know how to do that? If ord is your fitted PCA ordination done using rda() from vegan, then we just need to extract the *unscaled* species scores to get the same things as is given by loadings() on a princomp ordination or the $rotation from a prcomp ordination require(vegan) foo - princomp(USArrests, cor = TRUE) FOO - prcomp(USArrests, scale = TRUE) bar - rda(USArrests, scale = TRUE) loadings(foo) with(FOO, rotation) scores(bar, choices = 1:4, display = species, scaling = 0) Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] PCA Factor Loadings in Vegan
Hi all, I am using vegan to run a pca on forest structural variables (tree density, basal area, average height, regeneration density) in R. However, I could not find out how to extract factor loadings (correlations of each variable with each pca axis). Do anyone know how to do that? Thanks a lot, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Post on Free Reference Manager
Dear friends, I have recently posted a question on open reference manager softwares (Indication of Free Reference Manager Software). Below I post the answers I got. Zotero and Mendeley were the most cited programs. Thanks to everybody who wrote. Best whishes, Alexandre *** I am also looking for similar software, and found this page on wikipedia: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software *** I like Bibdesk (http://bibdesk.sourceforge.net/) but it only works with Macs. I also use LaTeX, which BibDesk is designed for. *** I like zotero, see www.zotero.org I have had great luck with Zotero (www.Zotero.org) and it integrates into Word, OpenOffice and web browsers. Good luck and hope that helps. I use Zotero and highly recommend it. I stopped using EndNote as soon as this came out. The best part is that if the citation output format does not exist for a journal you are submitting to, you can modify and existing one easily as they are in an XML format. In addition, people post ones they create to the Zotero website all the time. I especially like the interface to Firefox. *** Try: http://jabref.sourceforge.net/ I've used it on linux and mac systems. Works great. *** Mendeley. It's great! ( http://www.mendeley.com/ ). It's a free program, although they plan on transitioning to a paid format some time in the future. However, my understanding is that the program itself will always be free; you will in future be able to pay for storage space online if you want to keep the pdfs from your library on their servers. Mendeley is great, free, and easy to use: it's an itunes-like reference manager that I prefer to EndNote. www.mendeley.com I use Mendeley. It is still a little glitchy and does crash a bit. But I like what it does and I hope it will only improve *** As a linux user I am all about the freeware :). I've never tried it but JabRef comes with the recommendation of some Ubuntu forum users. You can find it here: http://jabref.sourceforge.net/ I usually use JabRef, which provides similar functionalities to commercial software. However, it is not very user-friendly and it is not linkable to Microsoft applications. It works best with Latex. *** If you are familiar with the OpenOffice (free) alternative to Microsoft's Office suite (http://www.openoffice.org/), you might try looking into CiteProc (http://bibliographic.openoffice.org/citeproc/index.html). Although I haven't tried it yet, I have been meaning to. It looks like it will do all the things EndNote or RefWorks would, but it's free, open-source software. I use OpenOffice and have been very pleased with *** Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Indication of Free Reference Manager Software
Dear ECOLOG friends, I am in search of a bibliographic reference manager software that allows a researcher to do the most common tasks related to storing, searching and creating bibliographies and belongs to the growing community of open or free software. We have a problem here in Brazil when you purchase one of the most populat softwares (EndNote, Reference Manager) but most students do not. Thank you in advance, Sincerely, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Compositional Comparison with Different Sampling Efforts
Dear friends, I would like to know your opinion on an analytical issue I am facing. I am evaluating whether the main ideas found in the ecological literature regarding forest succession in tropical regions (a large part of which written or influenced by you) apply to intensively-logged subtropical mixed forests in southern Brazil. As some authors (Norden et al. 2009 is the most recent example), we also have plots of adult trees with subsamples of poles and saplings samples in subplots nested within the larger plots. When it comes to the calculation of compositional similarities between plots and across size classes through both NMDS ordinations and similarity indexes (e.g. the Chao-Jaccard), however, an important doubt arises: How to procceed with these calculations if size classes were sampled with different sample areas? I am inclined to simply use relativized or standardized abundances as input to Chao-Jaccard similarities and to NMDS. A second alternative would be to extrapolate species-specific abundances of poles and saplings to the scale of larger plots. How wouuld you handle with this problem? Thank you in advance for your attention, Best whishes, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] A solution to the problem of accessing envir matrices
Dear friends, I have recently posted a message questioning how could one discount the spatial variation in community species data (what has been increasingly done through canonical variation partitioning, e.g. varpart in Vegan) and still access the individual contribution of distinct environmental variables to variation in species data. I would like to tell the solution I found. Step 1. Proceed a PCNM analysis of the spatial aspect of the dataset. Step 2. Use the significant PCNM axis, taken as a group, as a covariate in a PERMANCOVA (Anderson, 2001). This can be done in vegan whith the code adonis(sp ~ . + as.matrix(pcnm), data = env) where sp means the rectangular matrix os species abundances, pcnm stands for the significant pcnm variables, and env stands for the rectangular environmental matrix. This yields a ANOVA-like output table, where the effect of the spatial structure is evaluated after removing the effect of the environmental variables, but individual environmental variables are still tested individually. I believe this partly alleviates the need for canonical partitioning several environmental matrices (i.e., subidiving the environmental matrix in subsets). Step 3. Proceed with a canonical variation partitioning of the data, to evaluate the overall % contribution of pure spatial, pure environmental, and spatially structured environmental matrices. What do you think? Best regards, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Distance-related puzzle
Dear Etienne, dear friends, Recently some of you have answered a message I posted in Ecolog. In that answer Etienne suggested I go through a tutorial written by Dr. Legendre. I went through that tutorial and would like to thank him for indicating that. Going through that, however, raised a few doubts that are between me and the final data analyses of my present work. I would like to hear the opinion some of you may have on that matter. Here is, briefly, the case. 1 - The Hellinger transformation allowed us to contour the difficult premises of classical RDA and CCA. 2 - Despite of this, these dbRDA and CCA still do not consider space explicitly 3 - Except from small-scale experiments and small organisms studied very locally, space is always a factor causing autocorrelation and confounding the effects of environmental factors 4 - We have 36 cacti communities, each on a rocky outcrop, scattered throug a seminatural grassland landscape. Eighteen of these communities are embedded in 2-years old eucalyptus plantations. In our database we have a total of 10 cacti species (gamma-diversity), the 36 sites per 10 species abundance species matrix, a matrix of environmental variables (eucalyptus (binary), outcrop size, distance to the nearest outcrop, size of the nearest outcrop, %shrub cover) and the spatial matrix (xy UTM coordinates). 5 - I permormed a PERMANCOVA in R taking management (eucalyptus or not) as the main factor and all the variables of the env matrix as covariates. Management was significant and almos all the covariates were not. A NMDS showed a weak division between outcrops in eucaliptus plantation and outcrops in grasslands (very scattered). 6 - This analysis was, however, flawed, because for obvious reasons these two groups of outcrops were clearly spatially apart in the landscape. Including the XY coordinates as covariates made the management to become not significant. 7 - However, the raw XY coordinates are not appropriate to include in the analysis. I performed a varpart (for short) in R, that showed that the environmental variables had only a small effect. And here comes the question. 8 - The environmental matrix contains very different variables, and management is one of them. How to consider those variables explicitly if the partitioning approach only attributes a % contribution to them as a group? For instance: the small effect the env matrix has is due to which variable? Management? Or those linked to shrub cover? This is important because there are large companies involved, and any outcome will push the destiny of this endemic and endangered cacti community. 9 - A possible solution would be to break the env matrix into a number of smaller matrices (management, physical properties, plant cover). But this would complicate the outpud and also management, for instance, has only one variable, which is binary. This cannot yield a distance-matrix in the analysis. Well, if you reached this point, thank you already. Any ideas are welcome. Best regards, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Space in Community Ecology
Dear friends, I am facing a problem that I am sure many of you have faced already. I am analyzing a cacti community dataset and want to partial out the spatial effects. So I ask: is there any reason for not including x and y UTM geographical coordinates as covariables in a perMANCOVA (main effect = management [eucalyptus x cattle grazing])? I am aware that another way round would be to carry a Mantel test on geographical distances, the perMANOVA separately, and perhaps Borcard's procedure to evaluate the % contribution of spatial and environmental matrices on the species dissimilarity matrix. This second approach, however, seems somewhat indirect and with too many analyses for me. What do you thinkw Kind regards, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
[ECOLOG-L] Constrained NMDS?
Hello All, Do anyone has ever performed a constrained NMDS with community data? I have read in McCune and Graces' Analysis of Ecological Communities that the theory of such analysis already exists (i.e., associating vectors of environmental variables to a NMDS ordination) but has seldon been used by ecologists. It would be a better alternative to CCA, which has stingent premises that ecological data does not match properly most of times. I suppose that this could be implemented in R, but I could not find it in Vegan or other packages. Thanks in advance, Alexandre Dr. Alexandre F. Souza Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida Silvestre Universidade do Vale do Rio dos Sinos (UNISINOS) Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil Telefone: (051)3590-8477 ramal 1263 Skype: alexfadigas afso...@unisinos.br http://www.unisinos.br/laboratorios/lecopop -- Esta mensagem foi verificada pelo sistema de antiv�rus e acredita-se estar livre de perigo.
