Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
Standard Hypothesis statistical testing often starts with the null hypothesis that 2 things are identical, or that 2 population means are identical. The p value is then used to reject this null and accept the alternative, that they are indeed different. Practically we're actually asking if we have enough information to indeed say they are different. I do agree though that stopping there is a bit silly. If there is a statistical difference then we next need to look at the effect size or in other words the magnitude of the difference and decide if this is ecologically meaningful. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of David Valentim Dias Sent: Thursday, 26 April 2012 2:36 PM To: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu Hello Cichini, I cannot help with your code but seems like you have a silly hypothesis. Think about it: Probability of two communities to be identical? You need to restate it in some more useful way. We already know most things are different but with what magnitude? Which factors are causing these changes? How these changes matter from the environment and us? 2012/4/25 Chris Howden ch...@trickysolutions.com.au Why not try some type of ANOVA style glm? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. On 26/04/2012, at 7:19, Kay Cichini kay.cich...@gmail.com wrote: Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in Simpson-Diversity indices of collapsed abundances) - however, I am not quite sure if I oversee posssible pitfalls: library(vegan) data(dune) # a grouping variable: gr - gl(2, nrow(dune)/2) divdiff - function(x) abs(diversity(colSums(x[gr == 1, ]), simp) - diversity(colSums(x[gr == 2, ]), simp)) # testing function: divdiff(dune) oecosimu(dune, divdiff, r2dtable, nsimul = 1999) # oecosimu with 1999 simulations # simulation method r2dtable # alternative hypothesis: true mean is not equal to the statistic # statisticz 2.5% 50% 97.5% Pr(sim.) # statistic 0.00275 -0.20996 0.00013 0.00280 0.01 0.98 [[alternative HTML version deleted
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
@David, to ask for statistical *and* biological significance (effect size) is indeed essential and this statement does apply in general - but it does not contribute to a solution of my problem at all.. @Chris, as I want to test total diversity of each community (diversity calculated from samples collapsed over groups) I have only two values and thus ANOVA-like tests are not an option. Kind regards, Kay ps: Sorry Chris for double posting. 2012/4/26 Chris Howden ch...@trickysolutions.com.au Standard Hypothesis statistical testing often starts with the null hypothesis that 2 things are identical, or that 2 population means are identical. The p value is then used to reject this null and accept the alternative, that they are indeed different. Practically we're actually asking if we have enough information to indeed say they are different. I do agree though that stopping there is a bit silly. If there is a statistical difference then we next need to look at the effect size or in other words the magnitude of the difference and decide if this is ecologically meaningful. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of David Valentim Dias Sent: Thursday, 26 April 2012 2:36 PM To: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu Hello Cichini, I cannot help with your code but seems like you have a silly hypothesis. Think about it: Probability of two communities to be identical? You need to restate it in some more useful way. We already know most things are different but with what magnitude? Which factors are causing these changes? How these changes matter from the environment and us? 2012/4/25 Chris Howden ch...@trickysolutions.com.au Why not try some type of ANOVA style glm? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. On 26/04/2012, at 7:19, Kay Cichini kay.cich...@gmail.com wrote: Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in Simpson-Diversity indices of collapsed abundances) - however, I am not quite sure if I oversee posssible pitfalls: library(vegan) data(dune) # a grouping variable
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
Then use a t test, unless the underlying distribution is exceptionally skewed if they're means and the sample size is large enough u should be able to assume normality. If not the try a median test. However u may find a more accurate result if rather than collapsing over both communities u incorporate your study design via blocking or mixed modelling. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. On 26/04/2012, at 17:18, Kay Cichini kay.cich...@gmail.com wrote: @David, to ask for statistical *and* biological significance (effect size) is indeed essential and this statement does apply in general - but it does not contribute to a solution of my problem at all.. @Chris, as I want to test total diversity of each community (diversity calculated from samples collapsed over groups) I have only two values and thus ANOVA-like tests are not an option. Kind regards, Kay ps: Sorry Chris for double posting. 2012/4/26 Chris Howden ch...@trickysolutions.com.au Standard Hypothesis statistical testing often starts with the null hypothesis that 2 things are identical, or that 2 population means are identical. The p value is then used to reject this null and accept the alternative, that they are indeed different. Practically we're actually asking if we have enough information to indeed say they are different. I do agree though that stopping there is a bit silly. If there is a statistical difference then we next need to look at the effect size or in other words the magnitude of the difference and decide if this is ecologically meaningful. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of David Valentim Dias Sent: Thursday, 26 April 2012 2:36 PM To: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu Hello Cichini, I cannot help with your code but seems like you have a silly hypothesis. Think about it: Probability of two communities to be identical? You need to restate it in some more useful way. We already know most things are different but with what magnitude? Which factors are causing these changes? How these changes matter from the environment and us? 2012/4/25 Chris Howden ch...@trickysolutions.com.au Why not try some type of ANOVA style glm? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
On Thu, 2012-04-26 at 00:36 -0400, David Valentim Dias wrote: Hello Cichini, I cannot help with your code but seems like you have a silly hypothesis. Think about it: Probability of two communities to be identical? You need to restate it in some more useful way. We already know most things are different but with what magnitude? Which factors are causing these changes? How these changes matter from the environment and us? Surely if we knew the two things were different there would be no need to test if they were? Most statistics assumes a Null model as we can say something specific about the magnitude of the difference (it is zero) and we can then see if the observations are consistent with that model. I agree that subsequent analysis is required to understand why there are differences, but we still need a mechanism to say, given the data collected and the error processes, are the diversities of these two samples the same? G 2012/4/25 Chris Howden ch...@trickysolutions.com.au Why not try some type of ANOVA style glm? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. On 26/04/2012, at 7:19, Kay Cichini kay.cich...@gmail.com wrote: Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in Simpson-Diversity indices of collapsed abundances) - however, I am not quite sure if I oversee posssible pitfalls: library(vegan) data(dune) # a grouping variable: gr - gl(2, nrow(dune)/2) divdiff - function(x) abs(diversity(colSums(x[gr == 1, ]), simp) - diversity(colSums(x[gr == 2, ]), simp)) # testing function: divdiff(dune) oecosimu(dune, divdiff, r2dtable, nsimul = 1999) # oecosimu with 1999 simulations # simulation method r2dtable # alternative hypothesis: true mean is not equal to the statistic # statisticz 2.5% 50% 97.5% Pr(sim.) # statistic 0.00275 -0.20996 0.00013 0.00280 0.01 0.98 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ 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
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
On Thu, 2012-04-26 at 09:17 +0200, Kay Cichini wrote: @David, to ask for statistical *and* biological significance (effect size) is indeed essential and this statement does apply in general - but it does not contribute to a solution of my problem at all.. @Chris, as I want to test total diversity of each community (diversity calculated from samples collapsed over groups) I have only two values and thus ANOVA-like tests are not an option. So you have two numbers? Diversity in Comm1 computed by summing total number of unique species in Comm1 and the same but for Comm2. Hmm How about a null model that presupposes that Comm1 and Comm2 have the same diversity? Under that model can we reallocate the original samples (before you collapsed down to the two communities) to one or other of the communities, collapse to the community level, then compute the difference in diversity in permuted Comm1 and Comm2. Repeat a lot of times and look to see if the observed difference is extreme relative to the Null distribution? Would that make sense? If so you could cook that up with functions in vegan or the permute package. If you have the original counts, are they done to counts of species and you are just extracting diversity indices from that or do you only have the diversity indices? If the former then the multivariate dispersion of the species counts in samples for Comm1 and Comm2 will be equivalent if they are similarly diverse. I.e. they should have the same spread/variance. That can be tested using the work of Marti Anderson (her PERMDISP program) which is available as function betadisper() in vegan (though the method is biased with unbalanced sample designs - thanks to some excellent detective work that has just been brought to our attention - so do check out the R-forge version for changes to betadisper(). I'm not sure if the work has been done to add a correction in R-Forge or just in Jars' Github repo?). Alternatively, and perhaps more powerfully, see David Warton's mvabund package which has more formal glm-based tests of the distance-based methods Marti developed in NPMANOVA and PERMDISP. G Kind regards, Kay ps: Sorry Chris for double posting. 2012/4/26 Chris Howden ch...@trickysolutions.com.au Standard Hypothesis statistical testing often starts with the null hypothesis that 2 things are identical, or that 2 population means are identical. The p value is then used to reject this null and accept the alternative, that they are indeed different. Practically we're actually asking if we have enough information to indeed say they are different. I do agree though that stopping there is a bit silly. If there is a statistical difference then we next need to look at the effect size or in other words the magnitude of the difference and decide if this is ecologically meaningful. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of David Valentim Dias Sent: Thursday, 26 April 2012 2:36 PM To: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu Hello Cichini, I cannot help with your code but seems like you have a silly hypothesis. Think about it: Probability of two communities to be identical? You need to restate it in some more useful way. We already know most things are different but with what magnitude? Which factors are causing these changes? How these changes matter from the environment and us? 2012/4/25 Chris Howden ch...@trickysolutions.com.au Why not try some type of ANOVA style glm? Chris Howden Founding Partner
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
On Thu, Apr 26, 2012 at 12:17 AM, Kay Cichini kay.cich...@gmail.com wrote: Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in Simpson-Diversity indices of collapsed abundances) - however, I am not quite sure if I oversee posssible pitfalls: library(vegan) data(dune) # a grouping variable: gr - gl(2, nrow(dune)/2) divdiff - function(x) abs(diversity(colSums(x[gr == 1, ]), simp) - diversity(colSums(x[gr == 2, ]), simp)) # testing function: divdiff(dune) oecosimu(dune, divdiff, r2dtable, nsimul = 1999) # oecosimu with 1999 simulations # simulation method r2dtable # alternative hypothesis: true mean is not equal to the statistic # statistic z 2.5% 50% 97.5% Pr(sim.) # statistic 0.00275 -0.20996 0.00013 0.00280 0.01 0.98 Dear Kay, I am not sure about any possible pitfalls with your approach, but I have tested the same data using the randomisation functions of the rich library, and found that neither the Simpson diversity nor the simple species richness differ significantly among the defined groups. Here are the results following your example: library(rich) # prepare data one - as.data.frame(dune[gr == 1, ]) two - as.data.frame(dune[gr == 2, ]) data - list(one, two) # compare cumulative species richness c2cv(com1=data[[1]],com2=data[[2]],nrandom=1999) #$res # #cv1 27. #cv2 28. #cv1-cv2 -1. #p 0.4220 # N.S. #quantile 0.025 -4. #quantile 0.9754. #randomized cv1-cv20.0225 #nrandom1999. # compare the Simpson diversity simp.one - diversity(dune[gr == 1, ], simp) simp.two - diversity(dune[gr == 2, ], simp) c2m(pop1=simp.one,pop2=simp.two,nrandom=1999,verbose=FALSE) #done. #$res # #mv1 8.630e-01 #mv2 8.773e-01 #mv1-mv2-1.439e-02 #p 2.440e-01 # N.S. #quantile 0.025 -3.456e-02 #quantile 0.975 3.351e-02 #randomized mv1-mv2 3.899e-04 #nrandom 1.999e+03 # The possible pitfalls might be hidden under the different results ;-) Cheers, Ivailo -- UBUNTU: a person is a person through other persons. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
Hi, thanks a lot - things are much clearer now! Then I will take the one you and Gavin suggested. Kind regards, Kay Am 26.04.2012 17:47 schrieb Jari Oksanen jari.oksa...@oulu.fi: On 26 Apr 2012, at 0:19, Kay Cichini wrote: Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in Simpson-Diversity indices of collapsed abundances) - however, I am not quite sure if I oversee posssible pitfalls: library(vegan) data(dune) # a grouping variable: gr - gl(2, nrow(dune)/2) divdiff - function(x) abs(diversity(colSums(x[gr == 1, ]), simp) - diversity(colSums(x[gr == 2, ]), simp)) # testing function: divdiff(dune) oecosimu(dune, divdiff, r2dtable, nsimul = 1999) # oecosimu with 1999 simulations # simulation method r2dtable # alternative hypothesis: true mean is not equal to the statistic # statisticz 2.5% 50% 97.5% Pr(sim.) # statistic 0.00275 -0.20996 0.00013 0.00280 0.01 0.98 Kay, I think that Gav's suggestion is the most natural one: permute your classification vector and compare your observed difference to the permutation values. Null models can be problematic, and you must very carefully think what kind of null model you need and what is the null hypothesis under each null model. Quantitative null models are even trickier. I see the following possible problems with your idea: - You used r2dtable null model which fixes both row and column totals (but not frequencies). This means that for all simulations the overall gamma diversity is fixed: Simpson index is found from species totals, and these are fixed. When you also fix row totals, the generated null models can be too similar to each other, and this in turn gives too low P-values. I think that when analysing overall diversities from marginal sums, you should use a null model that allows those marginal sums to vary. This may not be possible with the release version of vegan, but the development version in R-Forge has a completely redesigned null model engine with several new quantitative null models and allows plugging in your own null models (which could even include permutation models). - If usual null models can be painful, the quantitative null models give you double trouble. One problem is that they produce too evenly distributed data. For r2dtable this holds in two ways: the method fixes marginal totals, but not marginal frequencies (= number of non-zero cells). Typically the number of zeros is much lower than in real data, and the variance of rows and columns is lower than in any real data. Moreover, the simulated samples are often much more similar to each other than real re-sampling of Nature. This is like using Poisson glm for abundance data: the data are regularly over-dispersed to Poisson, and therefore the P-values are too low. You have just the same danger with these null models: the simulation variation is too low, and therefore your P-values are too low. - The r2dtable method requires that your data are individuals: they are individuals that are swapped between cells. You used Dutch Dune meadow data in your example. Technically this works, since the data are integers, but they are cover class values and not individual, and therefore the swapping of integer pieces of cover classes has no meaning. If you want to consider null models, you should again switch to R-Forge version of vegan (currently there at version 2.1-15) which allows some models that apply to data that is not made of individuals, and also some methods that can retain the original marginal variances of the data. There are many things that you need to consider if you want to use null models. However, I think that permutation of classification vector saves a lot of trouble, and is more easily understood and communicated. Cheers, Jari Oksanen [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
Why not try some type of ANOVA style glm? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) ch...@trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information. If you are not the named or intended recipient, please delete this communication and contact us immediately. Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. On 26/04/2012, at 7:19, Kay Cichini kay.cich...@gmail.com wrote: Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in Simpson-Diversity indices of collapsed abundances) - however, I am not quite sure if I oversee posssible pitfalls: library(vegan) data(dune) # a grouping variable: gr - gl(2, nrow(dune)/2) divdiff - function(x) abs(diversity(colSums(x[gr == 1, ]), simp) - diversity(colSums(x[gr == 2, ]), simp)) # testing function: divdiff(dune) oecosimu(dune, divdiff, r2dtable, nsimul = 1999) # oecosimu with 1999 simulations # simulation method r2dtable # alternative hypothesis: true mean is not equal to the statistic # statisticz 2.5% 50% 97.5% Pr(sim.) # statistic 0.00275 -0.20996 0.00013 0.00280 0.01 0.98 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
