Ecological datasets for teaching statistics

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.

Dear Manuel,
     Have a look at the Dryad data repository, datadryad.org.  You can
search around for many ecological data sets.  I have used this a lot for
similar classes.  You can also read the associated paper for the data sets
and give students as much background as you wish.
Sincerely,
Jeff


/*-----------------------------------------------------------------------------------------------------------------------------
Jeffrey D. Holland, Professor
jdhollan at purdue.edu
Dept. of Entomology, Purdue University                        765 /
494-7739
www.entm.purdue.edu/landscapeecology
Fellow of the Indiana Academy of Science
http://www.bugsmapsandmath.com

-------------------------------------------------------------------------------------------------------------------------------*/

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

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.

On Thu, 18 Jun 2020, Manuel Sp?nola wrote:

I teach mainly to wildlife ecology students.

Manuel,

I'm a stream ecologist/fluvial geomorphologist but have run my sole
environmental consulting practice for the past 27 years.

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.

I have fish and benthic macroinvertebate data and some terrestrial animal
data, but this might be a good resource for you:
<https://ecologicaldata.org/find-data>.

When the animal's population status or critical habitat is controversial,
as
most tend to be, it can be difficult to get good data sets from the
resource
agencies.

Let me know if I can help.

Regards,

Rich

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

--
*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]]

On 18Jun 2020, at 19:58, Manuel Sp?nola <mspinola10 at gmail.com> wrote:

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

-- 
*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]]

Allison Horst has packaged data on penguin species from the PAL-LTER
project at https://github.com/allisonhorst/palmerpenguins. This is a nice
dataset for basic instruction -- 344 observations and 7 variables, so
it's easily understandable but with enough complexity to at least introduce
most concepts.

Thanks,

Michael Mahoney
781-812-8842 | mike.mahoney.218 at gmail.com

Michael Mahoney
781-812-8842 | mike.mahoney.218 at gmail.com


On Thu, Jun 18, 2020 at 2:14 PM Manuel Sp?nola <mspinola10 at gmail.com>
wrote:

Thank you very much Rich.

Manuel

El jue., 18 jun. 2020 a las 12:11, Rich Shepard (<
rshepard at appl-ecosys.com>)
escribi?:

On Thu, 18 Jun 2020, Manuel Sp?nola wrote:

I teach mainly to wildlife ecology students.

Manuel,

I'm a stream ecologist/fluvial geomorphologist but have run my sole
environmental consulting practice for the past 27 years.

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.

I have fish and benthic macroinvertebate data and some terrestrial

animal

data, but this might be a good resource for you:
<https://ecologicaldata.org/find-data>.

When the animal's population status or critical habitat is

controversial,

as
most tend to be, it can be difficult to get good data sets from the
resource
agencies.

Let me know if I can help.

Regards,

Rich

--
*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]]

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

///////////////////////////////////////////////////////////////////////////////////////////

<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

--
*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]]

On 18Jun 2020, at 19:58, Manuel Sp?nola <mspinola10 at gmail.com> wrote:

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.


This specific example brings to mind?you could do presence/absence models
with 8 species of salamanders in the Salamanders data set
https://rdrr.io/cran/glmmTMB/man/Salamanders.html

Depending on class sizes, it might be enough for every student to get a
different species, or you could break it up even further into subsets of
data.

cheers,
Mollie


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

Thank you very much Rich.

Manuel

El jue., 18 jun. 2020 a las 12:11, Rich Shepard (<rshepard at appl-ecosys.com

)

escribi?:

On Thu, 18 Jun 2020, Manuel Sp?nola wrote:

I teach mainly to wildlife ecology students.

Manuel,

I'm a stream ecologist/fluvial geomorphologist but have run my sole
environmental consulting practice for the past 27 years.

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.

I have fish and benthic macroinvertebate data and some terrestrial animal
data, but this might be a good resource for you:
<https://ecologicaldata.org/find-data>.

When the animal's population status or critical habitat is controversial,
as
most tend to be, it can be difficult to get good data sets from the
resource
agencies.

Let me know if I can help.

Regards,

Rich

--
*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]]

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

--
*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]]

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

///////////////////////////////////////////////////////////////////////////////////////////

<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

--
*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]]

        [[alternative HTML version deleted]]

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<mailto: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

--
*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<mailto:mspinola at una.cr> <mspinola at una.ac.cr<mailto:mspinola at una.ac.cr>>
mspinola10 at gmail.com<mailto: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]]

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 Lu?trik [mailto:roman.lustrik at gmail.com]
*Sent:* Friday, June 19, 2020 8:40 AM
*To:* Kanfra, Xorla
*Cc:* Thierry Onkelinx; Manuel Sp?nola; r-sig-ecology at 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 at 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 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

///////////////////////////////////////////////////////////////////////////////////////////

<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

--
*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]]

        [[alternative HTML version deleted]]

but the p-values generated were

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 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
///////////////////////////////////////////////////////////////////////////////////////////

<https://www.inbo.be>


Op vr 19 jun. 2020 om 11:23 schreef Kanfra, Xorla <
xorla.kanfra at 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 Lu?trik [mailto:roman.lustrik at gmail.com]
*Sent:* Friday, June 19, 2020 8:40 AM
*To:* Kanfra, Xorla
*Cc:* Thierry Onkelinx; Manuel Sp?nola; r-sig-ecology at 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 at 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 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

///////////////////////////////////////////////////////////////////////////////////////////

<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

--
*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]]

        [[alternative HTML version deleted]]

[[alternative HTML version deleted]]

but the p-values generated were