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Cheers, Roman On Fri, Jun 19, 2020 at 7:40 AM Kanfra, Xorla <xorla.kan...@julius-kuehn.de> wrote: > Dear All, > Sorry to use this thread for communication. I subscribed to this forum > just a few days ago but couldn’t manage to communicate across the board. > Please pardon me. If any of you can help me get around a statistical > challenge > I have just started using manyglm to analyze nematode with associated > microbial community data and I am really happy with how robust the > algorithm works. I have a question about the adjusted p- values. I run a > pairwise comparison for one of my factors but the p-values generated were > all the same for each pair of comparison. Is this output normal? besides, > are the p-values adjusted when running the pairwise comparison? Which > method does it use? ex Tukey, FDR, Holm, BH, etc. I am a bit confused as I > do not understand really what is going on behind the scripts. > Below is the script I used. > Thanks and hoping to hear from you soon > Xorla Kanfra > > mod_pairwise <-anova.manyglm(otutable.glm, nBoot=199, cor.type = "I", test > = "LR", p.uni="adjusted",pairwise.comp = ~envdata$soil) > > Analysis of Deviance Table > > Model: manyglm(formula = otutable.fv, family = "negative.binomial") > > Multivariate test: > Res.Df Df.diff Dev Pr(>Dev) > (Intercept) 88 > envdata$soil 81 7 42968 0.005 ** > envdata$response 80 1 4824 0.005 ** > envdata$soil:envdata$response 73 7 16066 0.005 ** > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > Pairwise comparison results: > Observed statistic Free Stepdown > Adjusted P-Value > envdata$soil:H vs envdata$soil:HH 6945 > 0.005 ** > envdata$soil:E vs envdata$soil:HH 6881 > 0.005 ** > envdata$soil:HH vs envdata$soil:R 6471 > 0.005 ** > envdata$soil:HH vs envdata$soil:M 6458 > 0.005 ** > envdata$soil:E vs envdata$soil:EE 6301 > 0.005 ** > envdata$soil:HH vs envdata$soil:K 6032 > 0.005 ** > envdata$soil:R vs envdata$soil:RR 5993 > 0.005 ** > envdata$soil:EE vs envdata$soil:RR 5855 > 0.005 ** > envdata$soil:EE vs envdata$soil:M 5835 > 0.005 ** > > > > -----Original Message----- > From: R-sig-ecology [mailto:r-sig-ecology-boun...@r-project.org] On > Behalf Of Thierry Onkelinx > Sent: Thursday, June 18, 2020 9:07 PM > To: Manuel Spínola > Cc: r-sig-ecology@r-project.org > Subject: Re: [R-sig-eco] Ecological datasets for teaching statistics > > Dear Manuel, > > Our institute has published 54 datasets under an open data licence at GBIF > ( > > https://www.gbif.org/dataset/search?publishing_org=1cd669d0-80ea-11de-a9d0-f1765f95f18b > ) > > You can look for local data on GBIF too. > > Best regards, > > ir. Thierry Onkelinx > Statisticus / Statistician > > Vlaamse Overheid / Government of Flanders > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND > FOREST > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance > thierry.onkel...@inbo.be > Havenlaan 88 bus 73, 1000 Brussel > www.inbo.be > > > /////////////////////////////////////////////////////////////////////////////////////////// > To call in the statistician after the experiment is done may be no more > than asking him to perform a post-mortem examination: he may be able to say > what the experiment died of. ~ Sir Ronald Aylmer Fisher > The plural of anecdote is not data. ~ Roger Brinner > The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > /////////////////////////////////////////////////////////////////////////////////////////// > > <https://www.inbo.be> > > > Op do 18 jun. 2020 om 19:58 schreef Manuel Spínola <mspinol...@gmail.com>: > > > Thank you very much Rich. > > > > Yes, you are right, is a very broad spectrum. > > > > I teach mainly to wildlife ecology students. > > > > I was using several datasets from different sources for homeworks and > > final projects, but some of the students were "sharing" the results of > the > > assignments so I decided to assign different datasets to each student for > > their homeworks. This means that I need several datasets for each > > assignment, and the data need to be similar in the structure, for > example, > > logistic regression, the response variable needs to be binary, and so on. > > > > Manuel > > > > > > > > El jue., 18 jun. 2020 a las 11:41, Rich Shepard (< > rshep...@appl-ecosys.com > > >) > > escribió: > > > > > On Thu, 18 Jun 2020, Manuel Spínola wrote: > > > > > > > I teach statistics to students in ecology and environmental sciences > > > > fields and I would like to know if you could point me in the right > > > > direction of sources of ecological/environmental datasets within and > > > > outside packages, especially for general/generalized linear models > and > > > > multivariate statistics. > > > > > > Manuel, > > > > > > Ecology, and it's applied focus Environmental science, are very broad. > > I've > > > been working with these data for several decades so I need to ask what > > > types > > > of data you want. > > > > > > I don't know what's available from Costa Rican agencies but I do know > > that > > > in the US you can get geochemical, biological, hydrologidal, and other > > data > > > from the US Geological Survay, Environmental Protection Agency (if > > they've > > > not removed them), Department of Agriculture's Forest Service and > Natural > > > Resources Conservation Service. > > > > > > You can also look at StreamNet run by the Pacific States Marine > Fisheries > > > Council, The Army Corps of Engineers for hydraulic, flow, and sediment > > > transport data. > > > > > > That's a start. > > > > > > Rich > > > > > > _______________________________________________ > > > R-sig-ecology mailing list > > > R-sig-ecology@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > > > > > -- > > *Manuel Spínola, Ph.D.* > > Instituto Internacional en Conservación y Manejo de Vida Silvestre > > Universidad Nacional > > Apartado 1350-3000 > > Heredia > > COSTA RICA > > mspin...@una.cr <mspin...@una.ac.cr> > > mspinol...@gmail.com > > Teléfono: (506) 8706 - 4662 > > Personal website: Lobito de río < > > https://sites.google.com/site/lobitoderio/> > > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > [[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 > -- In God we trust, all others bring data. 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