Ecological datasets for teaching statistics
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 at r-project.org] On Behalf Of Thierry Onkelinx
Sent: Thursday, June 18, 2020 9:07 PM
To: Manuel Sp?nola
Cc: r-sig-ecology at 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 at 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
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<https://www.inbo.be>
Op do 18 jun. 2020 om 19:58 schreef Manuel Sp?nola <mspinola10 at 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 at appl-ecosys.com
)
escribi?:
On Thu, 18 Jun 2020, Manuel Sp?nola 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
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-- *Manuel Sp?nola, Ph.D.* Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspinola at una.cr <mspinola at una.ac.cr> mspinola10 at gmail.com Tel?fono: (506) 8706 - 4662 Personal website: Lobito de r?o < https://sites.google.com/site/lobitoderio/> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> [[alternative HTML version deleted]]
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