Posts by Category

BIOMAT

Beta diversity

Disentangling the Drivers of beta Diversity Along Latitudinal and Elevational Gradients (updated)

1 minute read

Published:

Roughly, this science paper suggest that gamma diversity can explain the latitudinal/altitudinal variations in beta diversity so there is no need to invoke different local assembly mechanisms, they use two extensive data sets (One of them is here ). It seems to me that almost the same thing is formulated in the Hubbell’s neutral theory, local alfa diversity is determined by metacommunity (regional or gamma) diversity so beta diversity will also be determined by gamma diversity. In fact an expression for beta diversity under the neutral model was derived and it was found inconsistent with data. But different measures of beta diversity were used… Read more

Course

Ecological theory

Percolation and scaling in ecology

5 minute read

Published:

Scaling is a central theme in ecology, well this is my opinion, but there are others that think like me, for example Brian Enquist, that organized a symposium for the 100th anniversary of the Ecological Society of America Scaling in Ecology. He mentioned that two of the most influential papers from ESA were about scaling: Simon Levin The Problem of Pattern and Scale in Ecology and J.H. Brown The Metabolic Theory of Ecology. But why some processes permeate through scales and others do not; scaling is important because it implies something that crosses scales, did you ever heard the phrase: think globally act locally. Our new preprint analyzes what happens when one species percolates through the landscape Read more

Ecology

Percolation and scaling in ecology

5 minute read

Published:

Scaling is a central theme in ecology, well this is my opinion, but there are others that think like me, for example Brian Enquist, that organized a symposium for the 100th anniversary of the Ecological Society of America Scaling in Ecology. He mentioned that two of the most influential papers from ESA were about scaling: Simon Levin The Problem of Pattern and Scale in Ecology and J.H. Brown The Metabolic Theory of Ecology. But why some processes permeate through scales and others do not; scaling is important because it implies something that crosses scales, did you ever heard the phrase: think globally act locally. Our new preprint analyzes what happens when one species percolates through the landscape Read more

Metacommunity theory

Metacommunities or self organization principles

3 minute read

Published:

I am thinking of writing in Spanish, because Spanish is my mother language, but there seem to be not much people writing about ecological science in Spanish. At the end I started to think in English and then write in English, so the next one should be in Spanish, who knows. Read more

Neutral theory

Disentangling the Drivers of beta Diversity Along Latitudinal and Elevational Gradients (updated)

1 minute read

Published:

Roughly, this science paper suggest that gamma diversity can explain the latitudinal/altitudinal variations in beta diversity so there is no need to invoke different local assembly mechanisms, they use two extensive data sets (One of them is here ). It seems to me that almost the same thing is formulated in the Hubbell’s neutral theory, local alfa diversity is determined by metacommunity (regional or gamma) diversity so beta diversity will also be determined by gamma diversity. In fact an expression for beta diversity under the neutral model was derived and it was found inconsistent with data. But different measures of beta diversity were used… Read more

Percolation

Percolation and scaling in ecology

5 minute read

Published:

Scaling is a central theme in ecology, well this is my opinion, but there are others that think like me, for example Brian Enquist, that organized a symposium for the 100th anniversary of the Ecological Society of America Scaling in Ecology. He mentioned that two of the most influential papers from ESA were about scaling: Simon Levin The Problem of Pattern and Scale in Ecology and J.H. Brown The Metabolic Theory of Ecology. But why some processes permeate through scales and others do not; scaling is important because it implies something that crosses scales, did you ever heard the phrase: think globally act locally. Our new preprint analyzes what happens when one species percolates through the landscape Read more

Posters

A poster like a flower

1 minute read

Published:

These are my ideas about self-publishing a poster. There are tons of places on the Internet about how to write the best poster, but I think that most of them don’t apply their guidelines for it’s own publication, I mean the web page where the guidelines are published.\ Read more

Scaling

Percolation and scaling in ecology

5 minute read

Published:

Scaling is a central theme in ecology, well this is my opinion, but there are others that think like me, for example Brian Enquist, that organized a symposium for the 100th anniversary of the Ecological Society of America Scaling in Ecology. He mentioned that two of the most influential papers from ESA were about scaling: Simon Levin The Problem of Pattern and Scale in Ecology and J.H. Brown The Metabolic Theory of Ecology. But why some processes permeate through scales and others do not; scaling is important because it implies something that crosses scales, did you ever heard the phrase: think globally act locally. Our new preprint analyzes what happens when one species percolates through the landscape Read more

community ecology

Metacommunities or self organization principles

3 minute read

Published:

I am thinking of writing in Spanish, because Spanish is my mother language, but there seem to be not much people writing about ecological science in Spanish. At the end I started to think in English and then write in English, so the next one should be in Spanish, who knows. Read more

A protocol towards a general theory of community ecology

3 minute read

Published:

Definitive answers are scarce in biology 1 2 but if we want the advance of ecological knowledge we should reach a point where we have a theory we can trust, and can be used for prediction.

  1. Hubbell SP (2005) Neutral theory in community ecology and the hypothesis of functional equivalence. Funct Ecol 19: 166–172. doi:10.1111/j.0269-8463.2005.00965.x. 
  2. http://oikosjournal.wordpress.com/2013/11/22/the-typical-ecological-answer-it-depends/ 
Read more

confussion

The neutral bomb

2 minute read

Published:

This is not a sex bomb, but who knows. A couple of weeks ago I was giving a talk at the Escuela Argentina de Matemática y Biología about neutral and non-neutral models in ecology. I was pointed to the paper of  Clark 2012 The coherence problem with the Unified Neutral Theory of Biodiversity with the commentary: the neutral theory is uninformative. And the paper  basically says that neutral models or neutral theory is based on ignorance and that they are incoherent.
I think this is very interesting, but I disagree, here I review the last four points of the article:

(i) Incoherence: Neutral models assume all individuals are equal then go on and predict things like SADs and SARs, what is this telling us about the niche? The individuals are all equal, the species can have different effective probabilities to reach a place, different densities, but there is no niche. In this sense it can be thought as a null model for niches, other kinds of null models for niche can be constructed and maybe they are better, but I don't see incoherence.  Competition and niche are not the only things relevant to coexistence of species.

(ii) Ignorance: I am sure we are ignorant about nature, but assuming that all individuals are equal is not equal probability and equal probability is not a null model for sameness. Anyway the equivalence of individuals is certainly not ignorance is an assumption.


(iii)Victory: There are no victories here, but models or theories to explain nature patterns and we need to confront them with data in several ways, and much better in several ways at the same time.

(iv)Applying neutral models in conservation: you have to be careful to apply a model to conservation practices, neutral or not neutral does not matter at all. Models are not reality, always have simplifications, aproximations, or assumptions and we can select which is better for our problem (see Model selection in ecology and evolution).


The real issue I think is a matter of scale: which are the microscale processes that determine macroscale patterns. If niche models predicts the same patterns that neutral models and both are consistent with real data (see Niche and neutral models predict asymptotically equivalent...) a parsimonious interpretation is that we don't need niche. But if real data does not match the model we do need to add more complexities.

I think that neutral models are usefull both intellectually and practically, more about this in Neutrality without incoherence: a response to Clark
Read more

Why don’t you take a bath?

less than 1 minute read

Published:

I had a hard day, lots of data, many papers, many ideas crossing my mind, all ended in confusion, nothing was clear

I went home and my wife said why do not you take a bath?
 

Under the shower, soaping me, suddenly, everything was fixed in my head.
 

But this always happens to me, the best ideas come while I am taking a shower.
 

It looks like someone did the experiment and found the same:


Why greater ideas come when you are not trying?

(Went to bath)
...
(came back from bath)

The problem is that sometimes an hour passes and I am still under the shower, and I realize that because my fingers get wrinkled.

PS: next post will be about ecology: stochastic aggregation. 
Read more

ecological theory

Metacommunities or self organization principles

3 minute read

Published:

I am thinking of writing in Spanish, because Spanish is my mother language, but there seem to be not much people writing about ecological science in Spanish. At the end I started to think in English and then write in English, so the next one should be in Spanish, who knows. Read more

A protocol towards a general theory of community ecology

3 minute read

Published:

Definitive answers are scarce in biology 1 2 but if we want the advance of ecological knowledge we should reach a point where we have a theory we can trust, and can be used for prediction.

  1. Hubbell SP (2005) Neutral theory in community ecology and the hypothesis of functional equivalence. Funct Ecol 19: 166–172. doi:10.1111/j.0269-8463.2005.00965.x. 
  2. http://oikosjournal.wordpress.com/2013/11/22/the-typical-ecological-answer-it-depends/ 
Read more

ecology

Metacommunities or self organization principles

3 minute read

Published:

I am thinking of writing in Spanish, because Spanish is my mother language, but there seem to be not much people writing about ecological science in Spanish. At the end I started to think in English and then write in English, so the next one should be in Spanish, who knows. Read more

A protocol towards a general theory of community ecology

3 minute read

Published:

Definitive answers are scarce in biology 1 2 but if we want the advance of ecological knowledge we should reach a point where we have a theory we can trust, and can be used for prediction.

  1. Hubbell SP (2005) Neutral theory in community ecology and the hypothesis of functional equivalence. Funct Ecol 19: 166–172. doi:10.1111/j.0269-8463.2005.00965.x. 
  2. http://oikosjournal.wordpress.com/2013/11/22/the-typical-ecological-answer-it-depends/ 
Read more

eureka

Why don’t you take a bath?

less than 1 minute read

Published:

I had a hard day, lots of data, many papers, many ideas crossing my mind, all ended in confusion, nothing was clear

I went home and my wife said why do not you take a bath?
 

Under the shower, soaping me, suddenly, everything was fixed in my head.
 

But this always happens to me, the best ideas come while I am taking a shower.
 

It looks like someone did the experiment and found the same:


Why greater ideas come when you are not trying?

(Went to bath)
...
(came back from bath)

The problem is that sometimes an hour passes and I am still under the shower, and I realize that because my fingers get wrinkled.

PS: next post will be about ecology: stochastic aggregation. 
Read more

generalized dimensions

hierarchical competition models

Come together

1 minute read

Published:


Aggregation of objects is widespread phenomena in several sciences and of course in biology and ecology. Two cases I found and seem interesting to me are: the aggregation  in niche space: The clumping transition in niche competition, and the aggregation in neutral models: Clustering in neutral ecology.

This seems to depend only on the discreteness and finiteness of the objects and space. And in both cases the clumps have sizes distributed as power laws.
Furthermore when you have aggregation is possible that you will find multifractals, so is very possible that multifractals are widespread on ecological and biological phenomena.

All this introduction is because my article in Oikos is available as early view:

Multifractal growth in periphyton communities
Read more

ideas

landscape ecology

markdown

How to make slides without powerpoint (or LibreOffice Impress)

1 minute read

Published:



I started to use R Markdown with RStudio, but what is Markdown? :

"Markdown is a simple markup language designed to make authoring web content easy for everyone"

So it's easy to do a report of the millions of figures and analysis  while experimenting with a dataset or developing a manuscript.

A good stating point is the post of Jeromy Anglim's Blog about that.

Then I found that you could produce slides for presentations with only an additional step pandoc. The Markdown generated by RStudio can be converted to html slides and there are different "kinds" of slides you can convert to, and they look nice.
I have to prepare two talks for the RAE2012, so why not?

I was happy because I thought I would end with the curse of Powerpoint/Impress

But it was not so easy, things were not always as they should be. I was pressed to finish and tables don't get formated, figures don't get in the places I wanted, and the videos don't work at all. 

After endless try and error cycles  I finished, I have to learn a little of html and the posts of Markus Gesmann and Christopher Gandrud  were invaluable. I decided to use slidy and as there was no internet connection at the conference room everything must be included in the html file so I used the following pandoc command:

pandoc --self-contained -s -S -i -t slidy -V slidy-url=slidy  RAE2012_Charla.md -o RAE2012_Charla_slidy.html

for use this you have to download the Slidy code in a local folder called "slidy" 


 The source of one of talks is here and the slides are
 here




One drawback is that if I upload talk to figshare the html code is displayed and not like when uploading a pdf, it shows the formated talk ...

I think it's a matter of experience, things get easier after some work,  but I'm not sure if I get rid of powerpoint/impress... next time we'll see.





Read more

multifractals

Come together

1 minute read

Published:


Aggregation of objects is widespread phenomena in several sciences and of course in biology and ecology. Two cases I found and seem interesting to me are: the aggregation  in niche space: The clumping transition in niche competition, and the aggregation in neutral models: Clustering in neutral ecology.

This seems to depend only on the discreteness and finiteness of the objects and space. And in both cases the clumps have sizes distributed as power laws.
Furthermore when you have aggregation is possible that you will find multifractals, so is very possible that multifractals are widespread on ecological and biological phenomena.

All this introduction is because my article in Oikos is available as early view:

Multifractal growth in periphyton communities
Read more

neutral models

The neutral bomb

2 minute read

Published:

This is not a sex bomb, but who knows. A couple of weeks ago I was giving a talk at the Escuela Argentina de Matemática y Biología about neutral and non-neutral models in ecology. I was pointed to the paper of  Clark 2012 The coherence problem with the Unified Neutral Theory of Biodiversity with the commentary: the neutral theory is uninformative. And the paper  basically says that neutral models or neutral theory is based on ignorance and that they are incoherent.
I think this is very interesting, but I disagree, here I review the last four points of the article:

(i) Incoherence: Neutral models assume all individuals are equal then go on and predict things like SADs and SARs, what is this telling us about the niche? The individuals are all equal, the species can have different effective probabilities to reach a place, different densities, but there is no niche. In this sense it can be thought as a null model for niches, other kinds of null models for niche can be constructed and maybe they are better, but I don't see incoherence.  Competition and niche are not the only things relevant to coexistence of species.

(ii) Ignorance: I am sure we are ignorant about nature, but assuming that all individuals are equal is not equal probability and equal probability is not a null model for sameness. Anyway the equivalence of individuals is certainly not ignorance is an assumption.


(iii)Victory: There are no victories here, but models or theories to explain nature patterns and we need to confront them with data in several ways, and much better in several ways at the same time.

(iv)Applying neutral models in conservation: you have to be careful to apply a model to conservation practices, neutral or not neutral does not matter at all. Models are not reality, always have simplifications, aproximations, or assumptions and we can select which is better for our problem (see Model selection in ecology and evolution).


The real issue I think is a matter of scale: which are the microscale processes that determine macroscale patterns. If niche models predicts the same patterns that neutral models and both are consistent with real data (see Niche and neutral models predict asymptotically equivalent...) a parsimonious interpretation is that we don't need niche. But if real data does not match the model we do need to add more complexities.

I think that neutral models are usefull both intellectually and practically, more about this in Neutrality without incoherence: a response to Clark
Read more

Come together

1 minute read

Published:


Aggregation of objects is widespread phenomena in several sciences and of course in biology and ecology. Two cases I found and seem interesting to me are: the aggregation  in niche space: The clumping transition in niche competition, and the aggregation in neutral models: Clustering in neutral ecology.

This seems to depend only on the discreteness and finiteness of the objects and space. And in both cases the clumps have sizes distributed as power laws.
Furthermore when you have aggregation is possible that you will find multifractals, so is very possible that multifractals are widespread on ecological and biological phenomena.

All this introduction is because my article in Oikos is available as early view:

Multifractal growth in periphyton communities
Read more

pandoc

How to make slides without powerpoint (or LibreOffice Impress)

1 minute read

Published:



I started to use R Markdown with RStudio, but what is Markdown? :

"Markdown is a simple markup language designed to make authoring web content easy for everyone"

So it's easy to do a report of the millions of figures and analysis  while experimenting with a dataset or developing a manuscript.

A good stating point is the post of Jeromy Anglim's Blog about that.

Then I found that you could produce slides for presentations with only an additional step pandoc. The Markdown generated by RStudio can be converted to html slides and there are different "kinds" of slides you can convert to, and they look nice.
I have to prepare two talks for the RAE2012, so why not?

I was happy because I thought I would end with the curse of Powerpoint/Impress

But it was not so easy, things were not always as they should be. I was pressed to finish and tables don't get formated, figures don't get in the places I wanted, and the videos don't work at all. 

After endless try and error cycles  I finished, I have to learn a little of html and the posts of Markus Gesmann and Christopher Gandrud  were invaluable. I decided to use slidy and as there was no internet connection at the conference room everything must be included in the html file so I used the following pandoc command:

pandoc --self-contained -s -S -i -t slidy -V slidy-url=slidy  RAE2012_Charla.md -o RAE2012_Charla_slidy.html

for use this you have to download the Slidy code in a local folder called "slidy" 


 The source of one of talks is here and the slides are
 here




One drawback is that if I upload talk to figshare the html code is displayed and not like when uploading a pdf, it shows the formated talk ...

I think it's a matter of experience, things get easier after some work,  but I'm not sure if I get rid of powerpoint/impress... next time we'll see.





Read more

periphyton

power laws

A protocol towards a general theory of community ecology

3 minute read

Published:

Definitive answers are scarce in biology 1 2 but if we want the advance of ecological knowledge we should reach a point where we have a theory we can trust, and can be used for prediction.

  1. Hubbell SP (2005) Neutral theory in community ecology and the hypothesis of functional equivalence. Funct Ecol 19: 166–172. doi:10.1111/j.0269-8463.2005.00965.x. 
  2. http://oikosjournal.wordpress.com/2013/11/22/the-typical-ecological-answer-it-depends/ 
Read more

psicology

Why don’t you take a bath?

less than 1 minute read

Published:

I had a hard day, lots of data, many papers, many ideas crossing my mind, all ended in confusion, nothing was clear

I went home and my wife said why do not you take a bath?
 

Under the shower, soaping me, suddenly, everything was fixed in my head.
 

But this always happens to me, the best ideas come while I am taking a shower.
 

It looks like someone did the experiment and found the same:


Why greater ideas come when you are not trying?

(Went to bath)
...
(came back from bath)

The problem is that sometimes an hour passes and I am still under the shower, and I realize that because my fingers get wrinkled.

PS: next post will be about ecology: stochastic aggregation. 
Read more

slides

How to make slides without powerpoint (or LibreOffice Impress)

1 minute read

Published:



I started to use R Markdown with RStudio, but what is Markdown? :

"Markdown is a simple markup language designed to make authoring web content easy for everyone"

So it's easy to do a report of the millions of figures and analysis  while experimenting with a dataset or developing a manuscript.

A good stating point is the post of Jeromy Anglim's Blog about that.

Then I found that you could produce slides for presentations with only an additional step pandoc. The Markdown generated by RStudio can be converted to html slides and there are different "kinds" of slides you can convert to, and they look nice.
I have to prepare two talks for the RAE2012, so why not?

I was happy because I thought I would end with the curse of Powerpoint/Impress

But it was not so easy, things were not always as they should be. I was pressed to finish and tables don't get formated, figures don't get in the places I wanted, and the videos don't work at all. 

After endless try and error cycles  I finished, I have to learn a little of html and the posts of Markus Gesmann and Christopher Gandrud  were invaluable. I decided to use slidy and as there was no internet connection at the conference room everything must be included in the html file so I used the following pandoc command:

pandoc --self-contained -s -S -i -t slidy -V slidy-url=slidy  RAE2012_Charla.md -o RAE2012_Charla_slidy.html

for use this you have to download the Slidy code in a local folder called "slidy" 


 The source of one of talks is here and the slides are
 here




One drawback is that if I upload talk to figshare the html code is displayed and not like when uploading a pdf, it shows the formated talk ...

I think it's a matter of experience, things get easier after some work,  but I'm not sure if I get rid of powerpoint/impress... next time we'll see.





Read more

slidy

How to make slides without powerpoint (or LibreOffice Impress)

1 minute read

Published:



I started to use R Markdown with RStudio, but what is Markdown? :

"Markdown is a simple markup language designed to make authoring web content easy for everyone"

So it's easy to do a report of the millions of figures and analysis  while experimenting with a dataset or developing a manuscript.

A good stating point is the post of Jeromy Anglim's Blog about that.

Then I found that you could produce slides for presentations with only an additional step pandoc. The Markdown generated by RStudio can be converted to html slides and there are different "kinds" of slides you can convert to, and they look nice.
I have to prepare two talks for the RAE2012, so why not?

I was happy because I thought I would end with the curse of Powerpoint/Impress

But it was not so easy, things were not always as they should be. I was pressed to finish and tables don't get formated, figures don't get in the places I wanted, and the videos don't work at all. 

After endless try and error cycles  I finished, I have to learn a little of html and the posts of Markus Gesmann and Christopher Gandrud  were invaluable. I decided to use slidy and as there was no internet connection at the conference room everything must be included in the html file so I used the following pandoc command:

pandoc --self-contained -s -S -i -t slidy -V slidy-url=slidy  RAE2012_Charla.md -o RAE2012_Charla_slidy.html

for use this you have to download the Slidy code in a local folder called "slidy" 


 The source of one of talks is here and the slides are
 here




One drawback is that if I upload talk to figshare the html code is displayed and not like when uploading a pdf, it shows the formated talk ...

I think it's a matter of experience, things get easier after some work,  but I'm not sure if I get rid of powerpoint/impress... next time we'll see.





Read more

spatially explicit models

Come together

1 minute read

Published:


Aggregation of objects is widespread phenomena in several sciences and of course in biology and ecology. Two cases I found and seem interesting to me are: the aggregation  in niche space: The clumping transition in niche competition, and the aggregation in neutral models: Clustering in neutral ecology.

This seems to depend only on the discreteness and finiteness of the objects and space. And in both cases the clumps have sizes distributed as power laws.
Furthermore when you have aggregation is possible that you will find multifractals, so is very possible that multifractals are widespread on ecological and biological phenomena.

All this introduction is because my article in Oikos is available as early view:

Multifractal growth in periphyton communities
Read more