Dear Edward, You are right with your observation. I analyzed the data based on 999 nboots without pairwise comparison and it worked fine. However, I am not able to generate any output for the pairwise comparison at this high nboot (somehow the R could not output the results). I, therefore, reduced it to 199 to achieve these results. Thanks for your help. Xorla
From: Eduard Szöcs [mailto:szo...@uni-landau.de] Sent: Friday, June 19, 2020 1:01 PM Cc: Kanfra, Xorla; r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] Ecological datasets for teaching statistics > but the p-values generated were all the same for each pair of comparison. Is this output normal? With 199 bootstrap samples the smallest p you can get is 1/199=0,00502512... Hope this helps, Eduard Am 19. Juni 2020, um 11:33, Thierry Onkelinx <thierry.onkel...@inbo.be<mailto:thierry.onkel...@inbo.be>> schrieb: Try to send plain text mail without attachments. 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<http://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 vr 19 jun. 2020 om 11:23 schreef Kanfra, Xorla < xorla.kan...@julius-kuehn.de>: Dear Roman, Thank you for the suggestion. I tried a few minutes ago but go this response ‘’The message's content type was not explicitly allowed’’. Please can you advise? Kind regards Xorla *From:* Roman Luštrik [mailto:roman.lust...@gmail.com] *Sent:* Friday, June 19, 2020 8:40 AM *To:* Kanfra, Xorla *Cc:* Thierry Onkelinx; Manuel Spínola; r-sig-ecology@r-project.org *Subject:* Re: [R-sig-eco] Ecological datasets for teaching statistics Your question is likely to get lost in the debris. Try posting it as a new topic. 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<http://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. [[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
