[R-sig-eco] how betadisper relates to traditional betadiversity
Im trying to figure out how betadisper {vegan}, and more specifically the
'average distance to median' relates to betadiversity, in my case calculated
using beta.multi (total=b.JAC or b.SOR) {betapart}. My distance matrix from
sequences and is calculated based on raw base-pair differences. I have
clustered these sequences to operational taxonomic units "OTU" (microbial
substitute for species) which gives me an presence-absence table for sites.
My first thought was that, a high value in betadiversity would mean a high
very different average distance values from betadisper, but so is not
necessarily the case. The average distances between sites can show very
similar low values although having a high betadiversity and vice versa. I
was thinking, maybe one could aggregate the "average distance to medan" for
the sites within a species in order to derive at a value reflecting
betadiversity calculated on the presence/absence of species between sites.
Any thoughts on this would be appreciated, thanks
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Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER
Gavin and Brandon, Yes, I am aware that betadisper() does not actually give you a test of differences between centroids, but the fact that it does calculate centroids is quite valuable for interpretation, in my opinion, especially when using non-euclidean distance matrices (e.g., Bray-Curtis) and also if you would prefer NOT to do additional pairwise tests between levels, but still would like to have some idea as to which pairwise differences between levels might be most responsible for the effect. When using bray-curtis distances, you can't get centroids by calculating averages of abundances among the observations of interest. If you just want to use a NMDS ordination with levels symbol-coded to make them distinct, that's fine. Sometimes folks calculate the average axis score per group or level of group and plot that. That's fine, too. The nice thing about obtaining centroids calculated using betadisper() is that they are based on a principal coordinates analysis that uses ALL the axes, not just the first two or three axes in the ordination. It is likely that if the first two or three axes of the NMDS explain most of the important variation, the average scores per level for those three axes will probably tell the same information as the centroids will. Even though it wasn't intended for this purpose, Sharon Graham and I, together, figured out that you could use the centroids calculated by betadisper() to analyze split-plot and repeated-measures designs using adonis. So, its value extends beyond what it was intended for. Steve J. Stephen Brewer Professor Department of Biology PO Box 1848 University of Mississippi University, Mississippi 38677-1848 Brewer web page - http://home.olemiss.edu/~jbrewer/ FAX - 662-915-5144 Phone - 662-915-1077 On 3/27/14 10:47 AM, "Gavin Simpson" wrote: >Note that `betadisper()` only considers statistically dispersions >about the group centroids. It might show the centroids and return >their values, but it doesn't consider differences in those centroids. >As far is `betadisper()` is concerned, the group centroids could all >be made exactly equal and it wouldn't change the results as it is only >the spread about the centroid that is used. > >HTH > >G > >On 27 March 2014 06:47, Brandon Gerig wrote: >> Hi Steve, >> >> Yes, this is precisely what I am interested in doing. It seems like >> betadisper might be a good way to visualize differences/similarities in >>the >> dispersion and examine differences among centroids for the levels >>within a >> factor. Am I correct in thinking that if I conduct additional PERMANOVA >> tests on a reduced data set, I could be evaluating differences between >>the >> levels of a main effect? >> >> Could anyone provide a citation for a paper that uses a similar >>procedure? >> >> >> On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer >>wrote: >> >>> Brandon, >>> >>> Are you asking if you can use betadisper as a substitute for post-anova >>> pairwise comparisons among levels? After using betadisper to obtain >>> dispersions, I believe you can plot the centroids for each level. In >>> addition to telling you if the dispersions differ among levels, you >>>could >>> see how the centroids differ from one another. Is this what you want to >>> know? If so, realize that it won't give you pairwise significance tests >>> for differences between levels. For that, you might want to do >>>additional >>> permanovas on reduced datasets containing only the two levels you want >>>to >>> compare. You could then adjust the p-values for multiple tests after >>>the >>> fact. >>> >>> Hope this helps, >>> >>> Steve >>> >>> >>> J. Stephen Brewer >>> Professor >>> Department of Biology >>> PO Box 1848 >>> University of Mississippi >>> University, Mississippi 38677-1848 >>> Brewer web page - http://home.olemiss.edu/~jbrewer/ >>> FAX - 662-915-5144 >>> Phone - 662-915-1077 >>> >>> >>> >>> >>> On 3/26/14 10:57 AM, "Brandon Gerig" wrote: >>> >>> >Thanks for the words of caution on simper. >>> > >>> >Am I completely off base in thinking that betadiver function >>>(analgous to >>> >Levene's test) could be used to examine variation between levels >>>within >>> >main effects? >>> > >>> >Cheers >>> > >>> > >>> >On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: >>> > >>> >> I am assessing the level of similarity between PCB congener >>>profiles in >>> >> spawning salmon and resident stream in stream reaches with and >>>without >>> >> salmon to determine if salmon are a significant vector for PCBs in >>> >> tributary foodwebs of the Great Lakes. >>> >> >>> >> My data set is arranged in a matrix where the columns represent the >>> >> congener of interest and the rows represent either a salmon >>>(migratory) >>> >>or >>> >> resident fish (non migratory) from different sites. You can think >>>of >>> >>this >>> >> in a manner analogous to columns representing species composition >>>and >>> >>rows >>> >> representing site. >>> >> >>> >> Currently, I am using the function
Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER
Thanks for the responses! Even if I reduced the size of my dataset and ran a separate Adonis model just on an individual factor, betadisper should not be used to infer pairwise differences between levels because betadisper is not measuring differences between centroids but differences in dispersion variance within a level. Would it be justifiable to then to run the Adonis model and use an NMDS plot to interpret differences and interactions among factors? I wish I were a gifted enough programmer to add a patch, but being a neophyte with multivariate statistics I think it best I not contribute :) On Thu, Mar 27, 2014 at 11:51 AM, Gavin Simpson wrote: > No, that will just consider the dispersions *about the centroids* not > location shifts of the centroids. The latter is what `adonis()` does, > but we don't have pairwise comparisons (with/without permutation test) > there or the Tukey post-hoc tests. I suppose we *could* automate the > process that Steve suggests, just as I automated it for > `betadisper()`, and I think this has been raised before, but it hasn't > risen to the top of anyone's TODO list yet to actually see it > implemented. Patches welcome :-) ! > > G > > On 27 March 2014 06:55, Johannes Björk wrote: > > Hi, > > > > For that I believe you can run TukeyHSD.betadisper... to getting > significant values between levels. see ?TukeyHSD.betadisper > > > > Cheers, > > On Mar 27, 2014, at 1:47 PM, Brandon Gerig wrote: > > > >> Hi Steve, > >> > >> Yes, this is precisely what I am interested in doing. It seems like > >> betadisper might be a good way to visualize differences/similarities in > the > >> dispersion and examine differences among centroids for the levels > within a > >> factor. Am I correct in thinking that if I conduct additional PERMANOVA > >> tests on a reduced data set, I could be evaluating differences between > the > >> levels of a main effect? > >> > >> Could anyone provide a citation for a paper that uses a similar > procedure? > >> > >> > >> On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer > wrote: > >> > >>> Brandon, > >>> > >>> Are you asking if you can use betadisper as a substitute for post-anova > >>> pairwise comparisons among levels? After using betadisper to obtain > >>> dispersions, I believe you can plot the centroids for each level. In > >>> addition to telling you if the dispersions differ among levels, you > could > >>> see how the centroids differ from one another. Is this what you want to > >>> know? If so, realize that it won't give you pairwise significance tests > >>> for differences between levels. For that, you might want to do > additional > >>> permanovas on reduced datasets containing only the two levels you want > to > >>> compare. You could then adjust the p-values for multiple tests after > the > >>> fact. > >>> > >>> Hope this helps, > >>> > >>> Steve > >>> > >>> > >>> J. Stephen Brewer > >>> Professor > >>> Department of Biology > >>> PO Box 1848 > >>> University of Mississippi > >>> University, Mississippi 38677-1848 > >>> Brewer web page - http://home.olemiss.edu/~jbrewer/ > >>> FAX - 662-915-5144 > >>> Phone - 662-915-1077 > >>> > >>> > >>> > >>> > >>> On 3/26/14 10:57 AM, "Brandon Gerig" wrote: > >>> > Thanks for the words of caution on simper. > > Am I completely off base in thinking that betadiver function > (analgous to > Levene's test) could be used to examine variation between levels > within > main effects? > > Cheers > > > On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: > > > I am assessing the level of similarity between PCB congener profiles > in > > spawning salmon and resident stream in stream reaches with and > without > > salmon to determine if salmon are a significant vector for PCBs in > > tributary foodwebs of the Great Lakes. > > > > My data set is arranged in a matrix where the columns represent the > > congener of interest and the rows represent either a salmon > (migratory) > > or > > resident fish (non migratory) from different sites. You can think of > > this > > in a manner analogous to columns representing species composition and > > rows > > representing site. > > > > Currently, I am using the function Adonis to test for dissimilarity > > between fish species, stream reaches (with and without salmon) and > lake > > basin (Superior, Huron, Michigan). > > The model statement is: > > > > > > > m1 > s=999) > > > > The output indicates significant main effects of FISH, REACH, and > BASIN > > and significant interactions between FISH and BASIN, and BASIN and > > REACH. > > > > Is it best to then interpret this output via an NMDS ordination plot > or > > use something like the betadiver function to examine variances > between > > main > > effect levels or both? > > > > Also, can anyone recommend a procedure to identify the congeners >
Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER
Patches welcome. It is best to use vegan in GitHub. Pairwise tests are not high on my TODO list, because they are so much against what I've learnt from statistical theory and I detest tests. Cheers, Jari Oksanen Sent from my iPad > On 27.3.2014, at 17.54, "Gavin Simpson" wrote: > > No, that will just consider the dispersions *about the centroids* not > location shifts of the centroids. The latter is what `adonis()` does, > but we don't have pairwise comparisons (with/without permutation test) > there or the Tukey post-hoc tests. I suppose we *could* automate the > process that Steve suggests, just as I automated it for > `betadisper()`, and I think this has been raised before, but it hasn't > risen to the top of anyone's TODO list yet to actually see it > implemented. Patches welcome :-) ! > > G > >> On 27 March 2014 06:55, Johannes Björk wrote: >> Hi, >> >> For that I believe you can run TukeyHSD.betadisper... to getting significant >> values between levels. see ?TukeyHSD.betadisper >> >> Cheers, >>> On Mar 27, 2014, at 1:47 PM, Brandon Gerig wrote: >>> >>> Hi Steve, >>> >>> Yes, this is precisely what I am interested in doing. It seems like >>> betadisper might be a good way to visualize differences/similarities in the >>> dispersion and examine differences among centroids for the levels within a >>> factor. Am I correct in thinking that if I conduct additional PERMANOVA >>> tests on a reduced data set, I could be evaluating differences between the >>> levels of a main effect? >>> >>> Could anyone provide a citation for a paper that uses a similar procedure? >>> >>> On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer wrote: Brandon, Are you asking if you can use betadisper as a substitute for post-anova pairwise comparisons among levels? After using betadisper to obtain dispersions, I believe you can plot the centroids for each level. In addition to telling you if the dispersions differ among levels, you could see how the centroids differ from one another. Is this what you want to know? If so, realize that it won't give you pairwise significance tests for differences between levels. For that, you might want to do additional permanovas on reduced datasets containing only the two levels you want to compare. You could then adjust the p-values for multiple tests after the fact. Hope this helps, Steve J. Stephen Brewer Professor Department of Biology PO Box 1848 University of Mississippi University, Mississippi 38677-1848 Brewer web page - http://home.olemiss.edu/~jbrewer/ FAX - 662-915-5144 Phone - 662-915-1077 > On 3/26/14 10:57 AM, "Brandon Gerig" wrote: > > Thanks for the words of caution on simper. > > Am I completely off base in thinking that betadiver function (analgous to > Levene's test) could be used to examine variation between levels within > main effects? > > Cheers > > >> On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: >> >> I am assessing the level of similarity between PCB congener profiles in >> spawning salmon and resident stream in stream reaches with and without >> salmon to determine if salmon are a significant vector for PCBs in >> tributary foodwebs of the Great Lakes. >> >> My data set is arranged in a matrix where the columns represent the >> congener of interest and the rows represent either a salmon (migratory) >> or >> resident fish (non migratory) from different sites. You can think of >> this >> in a manner analogous to columns representing species composition and >> rows >> representing site. >> >> Currently, I am using the function Adonis to test for dissimilarity >> between fish species, stream reaches (with and without salmon) and lake >> basin (Superior, Huron, Michigan). >> The model statement is: >> >> >> m1> s=999) >> >> The output indicates significant main effects of FISH, REACH, and BASIN >> and significant interactions between FISH and BASIN, and BASIN and >> REACH. >> >> Is it best to then interpret this output via an NMDS ordination plot or >> use something like the betadiver function to examine variances between >> main >> effect levels or both? >> >> Also, can anyone recommend a procedure to identify the congeners that >> contribute most to the dissimilarity between fish, reaches, and >> basins?. I >> was thinking the SIMPER procedure but am not yet sold. >> >> Any advice is appreciated! >> -- >> Brandon Gerig >> PhD Student >> Department of Biological Sciences >> University of Notre Dame > > > > -- > Brandon Gerig > PhD Student > Department of Biological Sciences > University of Notre Dame > >>>
Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER
No, that will just consider the dispersions *about the centroids* not location shifts of the centroids. The latter is what `adonis()` does, but we don't have pairwise comparisons (with/without permutation test) there or the Tukey post-hoc tests. I suppose we *could* automate the process that Steve suggests, just as I automated it for `betadisper()`, and I think this has been raised before, but it hasn't risen to the top of anyone's TODO list yet to actually see it implemented. Patches welcome :-) ! G On 27 March 2014 06:55, Johannes Björk wrote: > Hi, > > For that I believe you can run TukeyHSD.betadisper... to getting significant > values between levels. see ?TukeyHSD.betadisper > > Cheers, > On Mar 27, 2014, at 1:47 PM, Brandon Gerig wrote: > >> Hi Steve, >> >> Yes, this is precisely what I am interested in doing. It seems like >> betadisper might be a good way to visualize differences/similarities in the >> dispersion and examine differences among centroids for the levels within a >> factor. Am I correct in thinking that if I conduct additional PERMANOVA >> tests on a reduced data set, I could be evaluating differences between the >> levels of a main effect? >> >> Could anyone provide a citation for a paper that uses a similar procedure? >> >> >> On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer wrote: >> >>> Brandon, >>> >>> Are you asking if you can use betadisper as a substitute for post-anova >>> pairwise comparisons among levels? After using betadisper to obtain >>> dispersions, I believe you can plot the centroids for each level. In >>> addition to telling you if the dispersions differ among levels, you could >>> see how the centroids differ from one another. Is this what you want to >>> know? If so, realize that it won't give you pairwise significance tests >>> for differences between levels. For that, you might want to do additional >>> permanovas on reduced datasets containing only the two levels you want to >>> compare. You could then adjust the p-values for multiple tests after the >>> fact. >>> >>> Hope this helps, >>> >>> Steve >>> >>> >>> J. Stephen Brewer >>> Professor >>> Department of Biology >>> PO Box 1848 >>> University of Mississippi >>> University, Mississippi 38677-1848 >>> Brewer web page - http://home.olemiss.edu/~jbrewer/ >>> FAX - 662-915-5144 >>> Phone - 662-915-1077 >>> >>> >>> >>> >>> On 3/26/14 10:57 AM, "Brandon Gerig" wrote: >>> Thanks for the words of caution on simper. Am I completely off base in thinking that betadiver function (analgous to Levene's test) could be used to examine variation between levels within main effects? Cheers On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: > I am assessing the level of similarity between PCB congener profiles in > spawning salmon and resident stream in stream reaches with and without > salmon to determine if salmon are a significant vector for PCBs in > tributary foodwebs of the Great Lakes. > > My data set is arranged in a matrix where the columns represent the > congener of interest and the rows represent either a salmon (migratory) > or > resident fish (non migratory) from different sites. You can think of > this > in a manner analogous to columns representing species composition and > rows > representing site. > > Currently, I am using the function Adonis to test for dissimilarity > between fish species, stream reaches (with and without salmon) and lake > basin (Superior, Huron, Michigan). > The model statement is: > > > m1 s=999) > > The output indicates significant main effects of FISH, REACH, and BASIN > and significant interactions between FISH and BASIN, and BASIN and > REACH. > > Is it best to then interpret this output via an NMDS ordination plot or > use something like the betadiver function to examine variances between > main > effect levels or both? > > Also, can anyone recommend a procedure to identify the congeners that > contribute most to the dissimilarity between fish, reaches, and > basins?. I > was thinking the SIMPER procedure but am not yet sold. > > Any advice is appreciated! > -- > Brandon Gerig > PhD Student > Department of Biological Sciences > University of Notre Dame > -- Brandon Gerig PhD Student Department of Biological Sciences University of Notre Dame [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >>> >>> >>> >> >> >> -- >> Brandon Gerig >> PhD Student >> Department of Biological Sciences >> University of Notre Dame >> >> [[alternative HTML version deleted]] >> >> ___ >> R-sig-ecology mail
Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER
Note that `betadisper()` only considers statistically dispersions about the group centroids. It might show the centroids and return their values, but it doesn't consider differences in those centroids. As far is `betadisper()` is concerned, the group centroids could all be made exactly equal and it wouldn't change the results as it is only the spread about the centroid that is used. HTH G On 27 March 2014 06:47, Brandon Gerig wrote: > Hi Steve, > > Yes, this is precisely what I am interested in doing. It seems like > betadisper might be a good way to visualize differences/similarities in the > dispersion and examine differences among centroids for the levels within a > factor. Am I correct in thinking that if I conduct additional PERMANOVA > tests on a reduced data set, I could be evaluating differences between the > levels of a main effect? > > Could anyone provide a citation for a paper that uses a similar procedure? > > > On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer wrote: > >> Brandon, >> >> Are you asking if you can use betadisper as a substitute for post-anova >> pairwise comparisons among levels? After using betadisper to obtain >> dispersions, I believe you can plot the centroids for each level. In >> addition to telling you if the dispersions differ among levels, you could >> see how the centroids differ from one another. Is this what you want to >> know? If so, realize that it won't give you pairwise significance tests >> for differences between levels. For that, you might want to do additional >> permanovas on reduced datasets containing only the two levels you want to >> compare. You could then adjust the p-values for multiple tests after the >> fact. >> >> Hope this helps, >> >> Steve >> >> >> J. Stephen Brewer >> Professor >> Department of Biology >> PO Box 1848 >> University of Mississippi >> University, Mississippi 38677-1848 >> Brewer web page - http://home.olemiss.edu/~jbrewer/ >> FAX - 662-915-5144 >> Phone - 662-915-1077 >> >> >> >> >> On 3/26/14 10:57 AM, "Brandon Gerig" wrote: >> >> >Thanks for the words of caution on simper. >> > >> >Am I completely off base in thinking that betadiver function (analgous to >> >Levene's test) could be used to examine variation between levels within >> >main effects? >> > >> >Cheers >> > >> > >> >On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: >> > >> >> I am assessing the level of similarity between PCB congener profiles in >> >> spawning salmon and resident stream in stream reaches with and without >> >> salmon to determine if salmon are a significant vector for PCBs in >> >> tributary foodwebs of the Great Lakes. >> >> >> >> My data set is arranged in a matrix where the columns represent the >> >> congener of interest and the rows represent either a salmon (migratory) >> >>or >> >> resident fish (non migratory) from different sites. You can think of >> >>this >> >> in a manner analogous to columns representing species composition and >> >>rows >> >> representing site. >> >> >> >> Currently, I am using the function Adonis to test for dissimilarity >> >> between fish species, stream reaches (with and without salmon) and lake >> >> basin (Superior, Huron, Michigan). >> >> The model statement is: >> >> >> >> >> >>m1> >>s=999) >> >> >> >> The output indicates significant main effects of FISH, REACH, and BASIN >> >> and significant interactions between FISH and BASIN, and BASIN and >> >>REACH. >> >> >> >> Is it best to then interpret this output via an NMDS ordination plot or >> >> use something like the betadiver function to examine variances between >> >>main >> >> effect levels or both? >> >> >> >> Also, can anyone recommend a procedure to identify the congeners that >> >> contribute most to the dissimilarity between fish, reaches, and >> >>basins?. I >> >> was thinking the SIMPER procedure but am not yet sold. >> >> >> >> Any advice is appreciated! >> >> -- >> >> Brandon Gerig >> >> PhD Student >> >> Department of Biological Sciences >> >> University of Notre Dame >> >> >> > >> > >> > >> >-- >> >Brandon Gerig >> >PhD Student >> >Department of Biological Sciences >> >University of Notre Dame >> > >> > [[alternative HTML version deleted]] >> > >> >___ >> >R-sig-ecology mailing list >> >R-sig-ecology@r-project.org >> >https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> >> >> > > > -- > Brandon Gerig > PhD Student > Department of Biological Sciences > University of Notre Dame > > [[alternative HTML version deleted]] > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Error regarding to GDM function
Dear All I have been using my species data with corresponding lat and long and environmental variables with lat and long values for GDM testing. I have formatted my data table in the following way: >formatGDMData(EGS, bioFormat = 2, dist = "bray", abundance = F, siteColumn = Sites, XColumn=c(1:2), YColumn=c(1:2), sppColumn = Species, abundColumn = NULL, sppFilter = 0, predData=EGV, distPreds = NULL, weightType = "def", custWeightVect = NULL) >Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, : length of 'dimnames' [2] not equal to array extent In addition: Warning message: In formatGDMData(EGS, bioFormat = 2, dist = "bray", abundance = F, : * No abundance column specified, assuming all data is presence only* >formatGDMData(EGS, bioFormat = 2, dist = "bray", abundance = F, siteColumn = Sites, XColumn=c(1:2), YColumn=c(1:2), sppColumn = Species, abundColumn = NULL, sppFilter = 0, predData=EGV, distPreds = NULL, weightType = "def", custWeightVect = NULL) >Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, : length of 'dimnames' [2] not equal to array extent In addition: Warning message: In formatGDMData(EGS, bioFormat = 2, dist = "bray", abundance = F, : No abundance column specified, assuming all data is presence only > mymod <- gdm.fitfromtable(EGV, EGS, geo = TRUE) Error in gdm.fitfromtable(EGV, EGS, geo = TRUE) : *Response data has negative values* However, I have no negative entries in my data Your useful advise is highly appreciated With best Regards Rajendra M Panda School of Water Resources Indian Institute of Technology Kharagpur [[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] Vegan-Adonis-NMDS-SIMPER
Hi, For that I believe you can run TukeyHSD.betadisper... to getting significant values between levels. see ?TukeyHSD.betadisper Cheers, On Mar 27, 2014, at 1:47 PM, Brandon Gerig wrote: > Hi Steve, > > Yes, this is precisely what I am interested in doing. It seems like > betadisper might be a good way to visualize differences/similarities in the > dispersion and examine differences among centroids for the levels within a > factor. Am I correct in thinking that if I conduct additional PERMANOVA > tests on a reduced data set, I could be evaluating differences between the > levels of a main effect? > > Could anyone provide a citation for a paper that uses a similar procedure? > > > On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer wrote: > >> Brandon, >> >> Are you asking if you can use betadisper as a substitute for post-anova >> pairwise comparisons among levels? After using betadisper to obtain >> dispersions, I believe you can plot the centroids for each level. In >> addition to telling you if the dispersions differ among levels, you could >> see how the centroids differ from one another. Is this what you want to >> know? If so, realize that it won't give you pairwise significance tests >> for differences between levels. For that, you might want to do additional >> permanovas on reduced datasets containing only the two levels you want to >> compare. You could then adjust the p-values for multiple tests after the >> fact. >> >> Hope this helps, >> >> Steve >> >> >> J. Stephen Brewer >> Professor >> Department of Biology >> PO Box 1848 >> University of Mississippi >> University, Mississippi 38677-1848 >> Brewer web page - http://home.olemiss.edu/~jbrewer/ >> FAX - 662-915-5144 >> Phone - 662-915-1077 >> >> >> >> >> On 3/26/14 10:57 AM, "Brandon Gerig" wrote: >> >>> Thanks for the words of caution on simper. >>> >>> Am I completely off base in thinking that betadiver function (analgous to >>> Levene's test) could be used to examine variation between levels within >>> main effects? >>> >>> Cheers >>> >>> >>> On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: >>> I am assessing the level of similarity between PCB congener profiles in spawning salmon and resident stream in stream reaches with and without salmon to determine if salmon are a significant vector for PCBs in tributary foodwebs of the Great Lakes. My data set is arranged in a matrix where the columns represent the congener of interest and the rows represent either a salmon (migratory) or resident fish (non migratory) from different sites. You can think of this in a manner analogous to columns representing species composition and rows representing site. Currently, I am using the function Adonis to test for dissimilarity between fish species, stream reaches (with and without salmon) and lake basin (Superior, Huron, Michigan). The model statement is: m1>>> s=999) The output indicates significant main effects of FISH, REACH, and BASIN and significant interactions between FISH and BASIN, and BASIN and REACH. Is it best to then interpret this output via an NMDS ordination plot or use something like the betadiver function to examine variances between main effect levels or both? Also, can anyone recommend a procedure to identify the congeners that contribute most to the dissimilarity between fish, reaches, and basins?. I was thinking the SIMPER procedure but am not yet sold. Any advice is appreciated! -- Brandon Gerig PhD Student Department of Biological Sciences University of Notre Dame >>> >>> >>> >>> -- >>> Brandon Gerig >>> PhD Student >>> Department of Biological Sciences >>> University of Notre Dame >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> R-sig-ecology mailing list >>> R-sig-ecology@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> >> >> > > > -- > Brandon Gerig > PhD Student > Department of Biological Sciences > University of Notre Dame > > [[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
Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER
Brandon, Yes. Just remove the observations containing the levels you don't want to include and run permanova on the observations containing the levels of interest. Good luck, Steve J. Stephen Brewer Professor Department of Biology PO Box 1848 University of Mississippi University, Mississippi 38677-1848 Brewer web page - http://home.olemiss.edu/~jbrewer/ FAX - 662-915-5144 Phone - 662-915-1077 From: Brandon Gerig Date: Thu, 27 Mar 2014 08:47:58 -0400 To: Pyro Maniac , Subject: Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER Hi Steve, Yes, this is precisely what I am interested in doing. It seems like betadisper might be a good way to visualize differences/similarities in the dispersion and examine differences among centroids for the levels within a factor. Am I correct in thinking that if I conduct additional PERMANOVA tests on a reduced data set, I could be evaluating differences between the levels of a main effect? Could anyone provide a citation for a paper that uses a similar procedure? On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer wrote: > Brandon, > > Are you asking if you can use betadisper as a substitute for post-anova > pairwise comparisons among levels? After using betadisper to obtain > dispersions, I believe you can plot the centroids for each level. In > addition to telling you if the dispersions differ among levels, you could > see how the centroids differ from one another. Is this what you want to > know? If so, realize that it won't give you pairwise significance tests > for differences between levels. For that, you might want to do additional > permanovas on reduced datasets containing only the two levels you want to > compare. You could then adjust the p-values for multiple tests after the > fact. > > Hope this helps, > > Steve > > > J. Stephen Brewer > Professor > Department of Biology > PO Box 1848 > University of Mississippi > University, Mississippi 38677-1848 > Brewer web page - http://home.olemiss.edu/~jbrewer/ > FAX - 662-915-5144 > Phone - 662-915-1077 > > > > > On 3/26/14 10:57 AM, "Brandon Gerig" wrote: > >> >Thanks for the words of caution on simper. >> > >> >Am I completely off base in thinking that betadiver function (analgous to >> >Levene's test) could be used to examine variation between levels within >> >main effects? >> > >> >Cheers >> > >> > >> >On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: >> > >>> >> I am assessing the level of similarity between PCB congener profiles in >>> >> spawning salmon and resident stream in stream reaches with and without >>> >> salmon to determine if salmon are a significant vector for PCBs in >>> >> tributary foodwebs of the Great Lakes. >>> >> >>> >> My data set is arranged in a matrix where the columns represent the >>> >> congener of interest and the rows represent either a salmon (migratory) >>> >>or >>> >> resident fish (non migratory) from different sites. You can think of >>> >>this >>> >> in a manner analogous to columns representing species composition and >>> >>rows >>> >> representing site. >>> >> >>> >> Currently, I am using the function Adonis to test for dissimilarity >>> >> between fish species, stream reaches (with and without salmon) and lake >>> >> basin (Superior, Huron, Michigan). >>> >> The model statement is: >>> >> >>> >> >>> >>m1>> >>s=999) >>> >> >>> >> The output indicates significant main effects of FISH, REACH, and BASIN >>> >> and significant interactions between FISH and BASIN, and BASIN and >>> >>REACH. >>> >> >>> >> Is it best to then interpret this output via an NMDS ordination plot or >>> >> use something like the betadiver function to examine variances between >>> >>main >>> >> effect levels or both? >>> >> >>> >> Also, can anyone recommend a procedure to identify the congeners that >>> >> contribute most to the dissimilarity between fish, reaches, and >>> >>basins?. I >>> >> was thinking the SIMPER procedure but am not yet sold. >>> >> >>> >> Any advice is appreciated! >>> >> -- >>> >> Brandon Gerig >>> >> PhD Student >>> >> Department of Biological Sciences >>> >> University of Notre Dame >>> >> >> > >> > >> > >> >-- >> >Brandon Gerig >> >PhD Student >> >Department of Biological Sciences >> >University of Notre Dame >> > >> > [[alternative HTML version deleted]] >> > >> >___ >> >R-sig-ecology mailing list >> >R-sig-ecology@r-project.org >> >https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > -- Brandon Gerig PhD Student Department of Biological Sciences University of Notre Dame [[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] Vegan-Adonis-NMDS-SIMPER
Hi Steve, Yes, this is precisely what I am interested in doing. It seems like betadisper might be a good way to visualize differences/similarities in the dispersion and examine differences among centroids for the levels within a factor. Am I correct in thinking that if I conduct additional PERMANOVA tests on a reduced data set, I could be evaluating differences between the levels of a main effect? Could anyone provide a citation for a paper that uses a similar procedure? On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer wrote: > Brandon, > > Are you asking if you can use betadisper as a substitute for post-anova > pairwise comparisons among levels? After using betadisper to obtain > dispersions, I believe you can plot the centroids for each level. In > addition to telling you if the dispersions differ among levels, you could > see how the centroids differ from one another. Is this what you want to > know? If so, realize that it won't give you pairwise significance tests > for differences between levels. For that, you might want to do additional > permanovas on reduced datasets containing only the two levels you want to > compare. You could then adjust the p-values for multiple tests after the > fact. > > Hope this helps, > > Steve > > > J. Stephen Brewer > Professor > Department of Biology > PO Box 1848 > University of Mississippi > University, Mississippi 38677-1848 > Brewer web page - http://home.olemiss.edu/~jbrewer/ > FAX - 662-915-5144 > Phone - 662-915-1077 > > > > > On 3/26/14 10:57 AM, "Brandon Gerig" wrote: > > >Thanks for the words of caution on simper. > > > >Am I completely off base in thinking that betadiver function (analgous to > >Levene's test) could be used to examine variation between levels within > >main effects? > > > >Cheers > > > > > >On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig wrote: > > > >> I am assessing the level of similarity between PCB congener profiles in > >> spawning salmon and resident stream in stream reaches with and without > >> salmon to determine if salmon are a significant vector for PCBs in > >> tributary foodwebs of the Great Lakes. > >> > >> My data set is arranged in a matrix where the columns represent the > >> congener of interest and the rows represent either a salmon (migratory) > >>or > >> resident fish (non migratory) from different sites. You can think of > >>this > >> in a manner analogous to columns representing species composition and > >>rows > >> representing site. > >> > >> Currently, I am using the function Adonis to test for dissimilarity > >> between fish species, stream reaches (with and without salmon) and lake > >> basin (Superior, Huron, Michigan). > >> The model statement is: > >> > >> > >>m1 >>s=999) > >> > >> The output indicates significant main effects of FISH, REACH, and BASIN > >> and significant interactions between FISH and BASIN, and BASIN and > >>REACH. > >> > >> Is it best to then interpret this output via an NMDS ordination plot or > >> use something like the betadiver function to examine variances between > >>main > >> effect levels or both? > >> > >> Also, can anyone recommend a procedure to identify the congeners that > >> contribute most to the dissimilarity between fish, reaches, and > >>basins?. I > >> was thinking the SIMPER procedure but am not yet sold. > >> > >> Any advice is appreciated! > >> -- > >> Brandon Gerig > >> PhD Student > >> Department of Biological Sciences > >> University of Notre Dame > >> > > > > > > > >-- > >Brandon Gerig > >PhD Student > >Department of Biological Sciences > >University of Notre Dame > > > > [[alternative HTML version deleted]] > > > >___ > >R-sig-ecology mailing list > >R-sig-ecology@r-project.org > >https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > -- Brandon Gerig PhD Student Department of Biological Sciences University of Notre Dame [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
