Hello:
I have created a dendrograms using hierarchical cluster analysis with the vegan package (function: hclust). By visually observing the dendrogram, I have determined that there are 3 main clusters if I "cut" the tree at the height 0.25 (please see the dendrogram from the code). I then created a new dataset, which is essentially the same as the original, but I have added the categorical variable Group to represent these 3 main clusters. ST0 is group a, AP0 and AP100 is group b, and AP200 AP300 ST100 ST200 ST 300 is group c. I want to now if they are significantly different from each other. I understand, from the output pasted below, that I can accept that there is a significant effect of Group. Is this the only thing I can say from Permanova? What would be the code for a follow up test to look at pair-wise significant differences? Thanks very much. Call: adonis(formula = species ~ Group, data = environ, permutations = 999) Permutation: free Number of permutations: 999 Terms added sequentially (first to last) Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Group 2 0.40244 0.201219 4.969 0.66528 0.007 ** Residuals 5 0.20248 0.040495 0.33472 Total 7 0.60492 1.00000 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Ansley Silva *"The clearest way into the Universe is through a forest wilderness." John Muir* *Graduate Research Assistant* *University of Georgia* *D.B. Warnell School of Forestry and Natural Resources* *180 East Green Street* *Athens, GA 30602* _______________________________________________ R-sig-ecology mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology Cluster.txt (7K) Download Attachment |
Dear Ansley,
I cannot answer your question, I hope someone else will answer. I'd rather point out a problem in your approach. Statistical tests were developed for testing difference between a priori groups, thus estimated Type I error rate is valid only for this situation. When you calculates Type I error rate for comparison of groups created by cluster analysis of the SAME data, the calculated error rate will be lower than the valid error rate. So you cannot use the term "significant" in this situation. Sorry for making you sadden by this information. Zoltan 2016.10.03. 21:52 keltez�ssel, Ansley Silva �rta: > Hello: > > I have created a dendrograms using hierarchical cluster analysis with the > vegan package (function: hclust). > > By visually observing the dendrogram, I have determined that there are 3 > main clusters if I "cut" the tree at the height 0.25 (please see the > dendrogram from the code). > I then created a new dataset, which is essentially the same as the > original, but I have added the categorical variable Group to represent > these 3 main clusters. > ST0 is group a, AP0 and AP100 is group b, and AP200 AP300 ST100 ST200 ST > 300 is group c. > I want to now if they are significantly different from each other. I > understand, from the output pasted below, that I can accept that there is a > significant effect of Group. Is this the only thing I can say from > Permanova? What would be the code for a follow up test to look at > pair-wise significant differences? > Thanks very much. > > Call: > adonis(formula = species ~ Group, data = environ, permutations = 999) > > Permutation: free > Number of permutations: 999 > > Terms added sequentially (first to last) > > Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) > Group 2 0.40244 0.201219 4.969 0.66528 0.007 ** > Residuals 5 0.20248 0.040495 0.33472 > Total 7 0.60492 1.00000 > --- > Signif. codes: 0 �***� 0.001 �**� 0.01 �*� 0.05 �.� 0.1 � � 1 > > > > > _______________________________________________ > R-sig-ecology mailing list > [hidden email] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Botta-Duk�t Zolt�n Zolt�n BOTTA-Duk�t ------------------------------------------------------------------------------------ �kol�giai �s Botanikai Int�zet Institute of Ecology and Botany Magyar Tudom�nyos Akad�mia Hungarian Academy of Sciences �kol�giai Kutat�k�zpont Centre for Ecological Research -------------------------------------------------------------------------------------------- 2163. V�cr�t�t, Alkotm�ny u. 2-4. H-2163 V�cr�t�t, Alkom�ny u. 2-4.,HUNGARY tel: +36 28 360122/157 Phone: +36 28 360122/157 fax: +36 28 360110 Fax +36 28 360110 [hidden email] [hidden email] http://okologia.mta.hu/Botta-Dukat.Zoltan http://okologia.mta.hu/en/Zoltan.BOTTA-DUKAT *New book:* Theory-Based Ecology; A Darwinian approach Authors: Liz P�sztor, Zolt�n Botta-Duk�t, Gabriella Magyar, Tam�s Cz�r�n, and G�za Mesz�na Available at Amazon <https://www.amazon.com/Theory-Based-Ecology-Darwinian-Liz-Pasztor/dp/0199577862/ref=sr_1_1?s=books&ie=UTF8&qid=1467644770&sr=1-1&refinements=p_27%3ATamas+Czaran>, in most major bookstores, or directly from Oxford University Press <https://global.oup.com/academic/product/theory-based-ecology-9780199577866?lang=en&cc=gb> Companion website: http://tbe.elte.hu/ [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology |
Dear Ansley,
I agree with Zoltan. I suggest SIMPROF test in package "clustsig". A complimentary package for use with hclust; simprof tests to see which (if any) clusters are statistically different. The null hypothesis is that there is no a priori group structure. See Clarke, K.R., Somerfield, P.J., and Gorley R.N. 2008. Testing of null hypothesis in exploratory community analyses: similarity profiles and biota-environment linkage. J. Exp. Mar. Biol. Ecol. 366, 56-69 HTH Pierre Le 04/10/2016 à 14:14, Zoltan Botta-Dukat a écrit : > Dear Ansley, > > I cannot answer your question, I hope someone else will answer. I'd > rather point out a problem in your approach. Statistical tests were > developed for testing difference between a priori groups, thus estimated > Type I error rate is valid only for this situation. When you calculates > Type I error rate for comparison of groups created by cluster analysis > of the SAME data, the calculated error rate will be lower than the valid > error rate. So you cannot use the term "significant" in this situation. > > Sorry for making you sadden by this information. > > Zoltan > > 2016.10.03. 21:52 keltez�ssel, Ansley Silva �rta: >> Hello: >> >> I have created a dendrograms using hierarchical cluster analysis with the >> vegan package (function: hclust). >> >> By visually observing the dendrogram, I have determined that there are 3 >> main clusters if I "cut" the tree at the height 0.25 (please see the >> dendrogram from the code). >> I then created a new dataset, which is essentially the same as the >> original, but I have added the categorical variable Group to represent >> these 3 main clusters. >> ST0 is group a, AP0 and AP100 is group b, and AP200 AP300 ST100 ST200 ST >> 300 is group c. >> I want to now if they are significantly different from each other. I >> understand, from the output pasted below, that I can accept that there is a >> significant effect of Group. Is this the only thing I can say from >> Permanova? What would be the code for a follow up test to look at >> pair-wise significant differences? >> Thanks very much. >> >> Call: >> adonis(formula = species ~ Group, data = environ, permutations = 999) >> >> Permutation: free >> Number of permutations: 999 >> >> Terms added sequentially (first to last) >> >> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) >> Group 2 0.40244 0.201219 4.969 0.66528 0.007 ** >> Residuals 5 0.20248 0.040495 0.33472 >> Total 7 0.60492 1.00000 >> --- >> Signif. codes: 0 �***� 0.001 �**� 0.01 �*� 0.05 �.� 0.1 � � 1 >> >> >> >> >> _______________________________________________ >> R-sig-ecology mailing list >> [hidden email] >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > _______________________________________________ > R-sig-ecology mailing list > [hidden email] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology |
pvclust is a good package to create and test significance of cluster groups.
2016-10-05 11:31 GMT-03:00 Pierre THIRIET <[hidden email]>: > Dear Ansley, > > I agree with Zoltan. > > I suggest SIMPROF test in package "clustsig". A complimentary package > for use with hclust; simprof tests to see which (if any) clusters are > statistically different. The null hypothesis is that there is no a > priori group structure. > See Clarke, K.R., Somerfield, P.J., and Gorley R.N. 2008. Testing of > null hypothesis in exploratory community analyses: similarity profiles > and biota-environment linkage. J. Exp. Mar. Biol. Ecol. 366, 56-69 > > HTH > Pierre > > Le 04/10/2016 à 14:14, Zoltan Botta-Dukat a écrit : > > Dear Ansley, > > > > I cannot answer your question, I hope someone else will answer. I'd > > rather point out a problem in your approach. Statistical tests were > > developed for testing difference between a priori groups, thus estimated > > Type I error rate is valid only for this situation. When you calculates > > Type I error rate for comparison of groups created by cluster analysis > > of the SAME data, the calculated error rate will be lower than the valid > > error rate. So you cannot use the term "significant" in this situation. > > > > Sorry for making you sadden by this information. > > > > Zoltan > > > > 2016.10.03. 21:52 keltez�ssel, Ansley Silva �rta: > >> Hello: > >> > >> I have created a dendrograms using hierarchical cluster analysis with > the > >> vegan package (function: hclust). > >> > >> By visually observing the dendrogram, I have determined that there are 3 > >> main clusters if I "cut" the tree at the height 0.25 (please see the > >> dendrogram from the code). > >> I then created a new dataset, which is essentially the same as the > >> original, but I have added the categorical variable Group to represent > >> these 3 main clusters. > >> ST0 is group a, AP0 and AP100 is group b, and AP200 AP300 ST100 ST200 ST > >> 300 is group c. > >> I want to now if they are significantly different from each other. I > >> understand, from the output pasted below, that I can accept that there > is a > >> significant effect of Group. Is this the only thing I can say from > >> Permanova? What would be the code for a follow up test to look at > >> pair-wise significant differences? > >> Thanks very much. > >> > >> Call: > >> adonis(formula = species ~ Group, data = environ, permutations = 999) > >> > >> Permutation: free > >> Number of permutations: 999 > >> > >> Terms added sequentially (first to last) > >> > >> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) > >> Group 2 0.40244 0.201219 4.969 0.66528 0.007 ** > >> Residuals 5 0.20248 0.040495 0.33472 > >> Total 7 0.60492 1.00000 > >> --- > >> Signif. codes: 0 �***� 0.001 �**� 0.01 �*� 0.05 �.� 0.1 � � 1 > >> > >> > >> > >> > >> _______________________________________________ > >> R-sig-ecology mailing list > >> [hidden email] > >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > > > > _______________________________________________ > > R-sig-ecology mailing list > > [hidden email] > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > [hidden email] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Graciliano Galdino A. dos Santos Biólogo Doutorando em Ciências Florestais - PPGCF Universidade Federal Rural da Amazônia - UFRA [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology |
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