[R-sig-eco] Ecological datasets for teaching statistics

[Eduard Szöcs]

> 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, 11:33, um 11:33, Thierry Onkelinx <thierry.onkelinx using 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.onkelinx using 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 vr 19 jun. 2020 om 11:23 schreef Kanfra, Xorla <
>xorla.kanfra using 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.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> 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] On
>> Behalf Of Thierry Onkelinx
>> Sent: Thursday, June 18, 2020 9:07 PM
>> To: Manuel Spínola
>> Cc: 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
>> 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
><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
>> > >)
>> > 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
>> > > 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 <mspinola using una.ac.cr>
>> > 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/>
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > R-sig-ecology mailing list
>> > R-sig-ecology using r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology using 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 using r-project.org
>https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

	[[alternative HTML version deleted]]