software
LifeDesks
18-06-2009 10:09
Yesterday I created a new LifeDesk on Neotropical
snails.
The site provides tools for classification, taxon pages, bibliography and image galleries.
Potentially this is a great tool and I hope that, in the end, it may contain all information that gives a relevant and accurate picture of this group. At least, I will start to supply data for the Orthalicidae. With one taxon page and one bibliographic item put up, the start has been made. Until now, I was unable to upload an image that I wanted to complement the taxon page.
The first potential improvement I noticed is a link to other sites, like e.g. MorphBank, that gather partially the same information (images, bibliography). It is a nuisance to do double work and to go through different learning curves; each site has its own way of navigating and managing. Inevitable, but tedious. Integration by linking should be the direction to move forward.
This is part of the ongoing Encyclopedia of Life project, aiming at making taxonomy available to anyone at a click of your keybord. However, to make this authoritative one has to rely on the few experts that are available. But also non-experts may contribute, albeit the tools are not in place yet for making direct contributions.
If you feel you can make a useful contribution to document the biodiversity of Neotropical snails, please become a member of the team. You are more than welcome!
The site provides tools for classification, taxon pages, bibliography and image galleries.
Potentially this is a great tool and I hope that, in the end, it may contain all information that gives a relevant and accurate picture of this group. At least, I will start to supply data for the Orthalicidae. With one taxon page and one bibliographic item put up, the start has been made. Until now, I was unable to upload an image that I wanted to complement the taxon page.
The first potential improvement I noticed is a link to other sites, like e.g. MorphBank, that gather partially the same information (images, bibliography). It is a nuisance to do double work and to go through different learning curves; each site has its own way of navigating and managing. Inevitable, but tedious. Integration by linking should be the direction to move forward.
This is part of the ongoing Encyclopedia of Life project, aiming at making taxonomy available to anyone at a click of your keybord. However, to make this authoritative one has to rely on the few experts that are available. But also non-experts may contribute, albeit the tools are not in place yet for making direct contributions.
If you feel you can make a useful contribution to document the biodiversity of Neotropical snails, please become a member of the team. You are more than welcome!
Maxent and sample size
12-09-2008 19:05
From earlier posts you may know that I’m a fan of
Maxent. Recently a new paper* appeared in which
different software on species modeling were compared.
This time there was special emphasis on the
performance with the use of a small number of
occurrences. This is usually problematic for many
modeling programs. Here is the result: Maxent has
about “the best predictive power across all samples
sizes”.
This is certainly good news, but it doesn’t solve a problem what I have with the modeling of endemic, range-restricted species. These are usually known from very few localities (up to 4). So far, I haven’t seen solutions proposed for working with these small numbers. But if anybody has an idea for an approach that could solve this nifty problem, please keep me posted! You would certainly make my day.
Reference:
Wisz, M. S., Hijmans, R.J., Li, J., Peterson, A.T., Graham, C.H., Guisan, A. & NCEAS Working Group (2008). Effects of sample size on the performance of species distribution models. Diversity and Distributions, 14, 763-773.
This is certainly good news, but it doesn’t solve a problem what I have with the modeling of endemic, range-restricted species. These are usually known from very few localities (up to 4). So far, I haven’t seen solutions proposed for working with these small numbers. But if anybody has an idea for an approach that could solve this nifty problem, please keep me posted! You would certainly make my day.
Reference:
Wisz, M. S., Hijmans, R.J., Li, J., Peterson, A.T., Graham, C.H., Guisan, A. & NCEAS Working Group (2008). Effects of sample size on the performance of species distribution models. Diversity and Distributions, 14, 763-773.
Biomapper
08-05-2008 21:14
Biomapper is another software program for species
distribution modeling. Personally I have run it only
once (on my old Windows machine, but I prefer
cross-platform solutions). Their discussion forum,
however, is very informative, issuing regularly an
update on recent literature dealing with ENFA or
Biomapper. I wished some other groups also delivered
this service... Below are the 6 most recent
publications, all available as PDFs on the
Biomapper
site.
References:
* Calenge, C., Darmon, G., Basille, M., Loison, A. & Jullien, J.M. (2008) The factorial decomposition of the Mahalanobis distances in habitat selection studies. Ecology, 89(2), 555-566.
* Strubbe, D. & Matthysen, E. (2008) Predicting the potential distribution of invasive ring-necked parakeets Psittacula krameri in northern Belgium using an ecological niche modelling approach. Biol Invasions, on-line.
* Allouche, O., Steinitz, O., Rotem, D., Rosenfeld, A. & Kadmon, R. (2008) Incorporating distance constraints into species distribution models. Journal of Applied Ecology, 45(2), 599-609.
* Long, P.R., Zefania, S., Ffrench-Constant, R.H. & Szekely, T. (2008) Estimating the population size of an endangered shorebird, the Madagascar plover, using a habitat suitability model. Animal Conservation, 11(2), 118-127.
* Praca, E. & Gannier, A. (2008) Ecological niches of three teuthophageous odontocetes in the northwestern Mediterranean Sea. Ocean Science, 4(1), 49-59.
* Skov, H., Humphreys, E., Garthe, S., Geitner, K., Gremillet, D., Hamer, K.C., Hennicke, J., Parner, H. & Wanless, S. (2008) Application
of habitat suitability modelling to tracking data of marine animals as a means of analyzing their feeding habitats. Ecological Modelling, 212(3-4), 504-512.
References:
* Calenge, C., Darmon, G., Basille, M., Loison, A. & Jullien, J.M. (2008) The factorial decomposition of the Mahalanobis distances in habitat selection studies. Ecology, 89(2), 555-566.
* Strubbe, D. & Matthysen, E. (2008) Predicting the potential distribution of invasive ring-necked parakeets Psittacula krameri in northern Belgium using an ecological niche modelling approach. Biol Invasions, on-line.
* Allouche, O., Steinitz, O., Rotem, D., Rosenfeld, A. & Kadmon, R. (2008) Incorporating distance constraints into species distribution models. Journal of Applied Ecology, 45(2), 599-609.
* Long, P.R., Zefania, S., Ffrench-Constant, R.H. & Szekely, T. (2008) Estimating the population size of an endangered shorebird, the Madagascar plover, using a habitat suitability model. Animal Conservation, 11(2), 118-127.
* Praca, E. & Gannier, A. (2008) Ecological niches of three teuthophageous odontocetes in the northwestern Mediterranean Sea. Ocean Science, 4(1), 49-59.
* Skov, H., Humphreys, E., Garthe, S., Geitner, K., Gremillet, D., Hamer, K.C., Hennicke, J., Parner, H. & Wanless, S. (2008) Application
of habitat suitability modelling to tracking data of marine animals as a means of analyzing their feeding habitats. Ecological Modelling, 212(3-4), 504-512.
Phylogeographer
20-04-2008 21:08
Another piece of software, that looks potentially
useful.
Phylogeographer
is designed to test phylogeographic hypotheses,
allowing the hypotheses to be converted into distance
matrices. These can be used to calculate correlations
between various hypotheses and genetic distance
matrices. This way dispersal routes can be explored
with a graphical interface.
The (condensed) information on the homepage suggests that this piece of software is relatively easy to operate, once you stick to some basic requirements (formats). One of the big advantages is that it runs under Java, so platform-independent.
Later this year I hope to have enough data for a further exploration. So this topic might return.
The (condensed) information on the homepage suggests that this piece of software is relatively easy to operate, once you stick to some basic requirements (formats). One of the big advantages is that it runs under Java, so platform-independent.
Later this year I hope to have enough data for a further exploration. So this topic might return.
Treebase
20-04-2008 20:10
Google Earth (GE) has been mentioned in this blog
several times or at least I have shown results using
this nifty piece of software.
Today I stumbled upon the site of the CIPRES project, one of its aims is the development of TreeBASE II, re-engineered to allow for the use of GE. They provide a prototype tree viewer which included some sample trees. One of them is based on the article of Gittenberger et al. (2004) with land snails from Europe. I know it is a small diversion from the theme of this blog, but it's nice to see the work of a friend and colleague being used in an innovative way.
The site also allows for uploads of trees, I suppose they will potentially be included as examples in a next version. Nice piece of work...
Reference:
Gittenberger, E, W. H. Piel and D. Groenenberg. 2004. The Pleistocene glaciations and the evolutionary history of the polytypic snail species Arianta arbustorum (Gastropoda, Helicidae). Molecular Phylogenetics and Evolution, 30(1): 64-67
Today I stumbled upon the site of the CIPRES project, one of its aims is the development of TreeBASE II, re-engineered to allow for the use of GE. They provide a prototype tree viewer which included some sample trees. One of them is based on the article of Gittenberger et al. (2004) with land snails from Europe. I know it is a small diversion from the theme of this blog, but it's nice to see the work of a friend and colleague being used in an innovative way.
The site also allows for uploads of trees, I suppose they will potentially be included as examples in a next version. Nice piece of work...
Reference:
Gittenberger, E, W. H. Piel and D. Groenenberg. 2004. The Pleistocene glaciations and the evolutionary history of the polytypic snail species Arianta arbustorum (Gastropoda, Helicidae). Molecular Phylogenetics and Evolution, 30(1): 64-67
Google Earth and map making
25-02-2008 15:22
Since I was struggling with making a map for my
Ecuador paper, I was very happy with some tips from a
colleague. The first one was about online map making.
There are several sites, of which online map creation
(OMC)
has the basic functionality. A handy feature is
that it supports Postscript-output, which makes it
easy for publication although you might need
commercial software to process it further. The
same format is supported by
Planiglobe,
although I don't like like scaling feature as it
gives me not enough flexibility.
A second tip seems even more handy: the use of GPSVisualizer to transfer (distribution) data to KML or KMZ files as an overlay in Google Earth. Unfortunately, in the end this doesn't produce maps that are suitable for publication (unless you are the happy owner of the commercial version of GE), but after much fiddling I was able to obtain a map with localities in Ecuador.
Thanks for the tips, Bas!
A second tip seems even more handy: the use of GPSVisualizer to transfer (distribution) data to KML or KMZ files as an overlay in Google Earth. Unfortunately, in the end this doesn't produce maps that are suitable for publication (unless you are the happy owner of the commercial version of GE), but after much fiddling I was able to obtain a map with localities in Ecuador.
Thanks for the tips, Bas!
With some help and inspiration
13-10-2007 19:55
The Maxent package I
previously wrote about has a - like most freeware
software - a discussion group
which in my case was
helpful to solve some initial problems. One
problem - the grid output file that should be
suitable for input in DIVA-GIS - was a bug in the
beta version that I ran and was fixed very swiftly
by the Steven Phillips, the main author. After
this I could use the software to do useful
analyses on the Ecuadorian data. The result is a
series of distribution maps on (sub)generic level.
Although several studies (e.g. Elith et al., 2006;
Pearson et al., 2007) have shown that Maxent is
robust enough to handle datasets with only a few
occurrences per species, I preferred to do the
analyses on aggregated data to get a more
comprehensive result. Here is one of the maps,
obtained by processing the grid output file of
Maxent in DIVA-GIS.
Ecological niche model for Plekocheilus. The blue dots are localities where the genus is present. Colours represent logistic values of likelihood for occurrence: from 0-0.2 (dark green) to 0.8-1.0 (red).
When I out of curiousity tried to feed Maxent with occurrence data (also Plekocheilus) from the Guayana Shield, the resulting picture of the distribution showed a remarkable disjunct pattern. An inspirational indication that my hypothesis about linkages between the Pantepui region in Venezuela and the Andes in Colombia is worth further investigation!
Ecological niche model for Plekocheilus from Venezuela, Pantepui, as depicted by Maxent.
This even becomes more clear when all the known localities of Plekocheilus from Venezuela are taken into account.
Ecological niche model for all Plekocheilus known from Venezuela, as depicted by Maxent.
See also this blog for comments on Maxent.
References:
Elith, J. e. a. (2006). Novel methods improve prediction of species' distributions from occurrence data. Ecography, 26, 129-151.
Pearson, R. G., C.J. Raxworthy, M. Nakamura & A. Townsend Peterson. (2007). Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos from Madagascar. J. Biogeogr, 34, 102-117.
Ecological niche model for Plekocheilus. The blue dots are localities where the genus is present. Colours represent logistic values of likelihood for occurrence: from 0-0.2 (dark green) to 0.8-1.0 (red).
When I out of curiousity tried to feed Maxent with occurrence data (also Plekocheilus) from the Guayana Shield, the resulting picture of the distribution showed a remarkable disjunct pattern. An inspirational indication that my hypothesis about linkages between the Pantepui region in Venezuela and the Andes in Colombia is worth further investigation!
Ecological niche model for Plekocheilus from Venezuela, Pantepui, as depicted by Maxent.
This even becomes more clear when all the known localities of Plekocheilus from Venezuela are taken into account.
Ecological niche model for all Plekocheilus known from Venezuela, as depicted by Maxent.
See also this blog for comments on Maxent.
References:
Elith, J. e. a. (2006). Novel methods improve prediction of species' distributions from occurrence data. Ecography, 26, 129-151.
Pearson, R. G., C.J. Raxworthy, M. Nakamura & A. Townsend Peterson. (2007). Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos from Madagascar. J. Biogeogr, 34, 102-117.
Mapping on your computer with insight
23-09-2007 13:53
Ecological niche
development has caught my attention before
(application in this presentation),
but when I wanted to do some analyses on the
Ecuadorian data, I did a quick survey for suitable
(and affordable) software to use on my
MacBook. DIVA-GIS is still my favorite, but
unfortunately it only runs on Windows machines. So
here are some findings on what is available for
the Mac community.
A nice starting point is a review found on Cartographica.com, reviewing 4 software packages: MyWorldGis, QuantumGIS, uDig and ESRI Arcexplorer. My conclusion from the verdicts was that none of the programs was actually good for my purposes. MyWorldGIS is aimed at high school level and too simple, Arcexplorer is a viewer rather than a full GIS system, while the other two programs need more development before they can be used for analysis. There was the promise of a second part of the review, dealing with a.o. GRASS GIS, but I haven't spotted it yet.
While I'm mostly interersted in a low-cost solution, a list of open source GIS software came in handy. QuantumGIS and uDig are also listed here, as well as GRASS GIS. I downloaded all three, but was unsatisfied with uDig while the two others proved to raise some stumbling-blocks in my attempts to quickly getting them working.
Digging around, it struck me that the GIS community is very prolific in producing all sorts of data. A nice portal with many links to useful sites is the EDEN project.
Finally I explored a program that is Java-based - hence cross-platform - and looks terrific judging from the sketchy tutorial: the Maxent package. The training data set on the site runs as expected, but when I try one of my own data sets I quickly ran into problems.
All this clearly illustrates that there are no quick-fixes when it comes to scientific analyses....
A nice starting point is a review found on Cartographica.com, reviewing 4 software packages: MyWorldGis, QuantumGIS, uDig and ESRI Arcexplorer. My conclusion from the verdicts was that none of the programs was actually good for my purposes. MyWorldGIS is aimed at high school level and too simple, Arcexplorer is a viewer rather than a full GIS system, while the other two programs need more development before they can be used for analysis. There was the promise of a second part of the review, dealing with a.o. GRASS GIS, but I haven't spotted it yet.
While I'm mostly interersted in a low-cost solution, a list of open source GIS software came in handy. QuantumGIS and uDig are also listed here, as well as GRASS GIS. I downloaded all three, but was unsatisfied with uDig while the two others proved to raise some stumbling-blocks in my attempts to quickly getting them working.
Digging around, it struck me that the GIS community is very prolific in producing all sorts of data. A nice portal with many links to useful sites is the EDEN project.
Finally I explored a program that is Java-based - hence cross-platform - and looks terrific judging from the sketchy tutorial: the Maxent package. The training data set on the site runs as expected, but when I try one of my own data sets I quickly ran into problems.
All this clearly illustrates that there are no quick-fixes when it comes to scientific analyses....
The Beast in snails
01-07-2007 20:07
Some time ago I got
aware of the software published by
Andrew
Rambaut.
It's very nicely done, as it is open source and
cross-platform. There are several packages, each
for a specific step in the workflow; the main step
is called Beast. Most is well documented, but it
is clearly a project in progress.
So far I've used it while I'm trying to fiddle around with some Nexus files that Bernhard Hausdorf sent me. From what I experience I feel that one should be reasonably seasoned in molecular genetics to make the best out of it. While I follow the (rather frequent) stream of Q&A on the Beast Mailing-list, I flatter myself with the knowledge that I'm not the only one who is struggling with all the nitty-gritty details that rule the software. Some day we'll overcome!
So far I've used it while I'm trying to fiddle around with some Nexus files that Bernhard Hausdorf sent me. From what I experience I feel that one should be reasonably seasoned in molecular genetics to make the best out of it. While I follow the (rather frequent) stream of Q&A on the Beast Mailing-list, I flatter myself with the knowledge that I'm not the only one who is struggling with all the nitty-gritty details that rule the software. Some day we'll overcome!