[R-sig-eco] Ecological datasets for teaching statistics
Kanfra, Xorla
xor|@@k@n|r@ @end|ng |rom ju||u@-kuehn@de
Fri Jun 19 11:23:06 CEST 2020
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.lustrik using gmail.com]
Sent: Friday, June 19, 2020 8:40 AM
To: Kanfra, Xorla
Cc: Thierry Onkelinx; Manuel Spínola; r-sig-ecology using 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.kanfra using julius-kuehn.de<mailto:xorla.kanfra using 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-bounces using r-project.org<mailto:r-sig-ecology-bounces using r-project.org>] On Behalf Of Thierry Onkelinx
Sent: Thursday, June 18, 2020 9:07 PM
To: Manuel Spínola
Cc: r-sig-ecology using r-project.org<mailto:r-sig-ecology using 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.onkelinx using inbo.be<mailto:thierry.onkelinx using 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 <mspinola10 using gmail.com<mailto:mspinola10 using 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 (<rshepard using appl-ecosys.com<mailto:rshepard using 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 using r-project.org<mailto:R-sig-ecology using 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
> mspinola using una.cr<mailto:mspinola using una.cr> <mspinola using una.ac.cr<mailto:mspinola using una.ac.cr>>
> mspinola10 using gmail.com<mailto:mspinola10 using 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/>
>
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