Recent Changes

Breakout — by Melanie Murphy — last modified 2010-05-24 11:48

•Lisette - On-line components: Meet Expert/Discussion Board  - More visible/ promote, timing/time zones, make more useful – other formats • Sam & Niko - Formats for repeating course: bring people together, distributed, fully on-line, real-time lectures, timing •Melanie & Stephanie  - Curriculum – selection of topics, integration, order, prereqs, background lectures, readings, references lists/background readings, advance information •Steve - Assignments – discussion questions, readings, lab, student activities, availability of key, etc •Rodney - Role of local teaching – discussion, going through slides, how to do this, good ideas – what worked well and what needed.  Local vs. distributed teaching.  Being able to ask questions in class. •Helene  -Projects – What would future projects look like?  Other types of projects?  What made it a good (or not so good) experience?  How to make more efficient/effective.  Distributed vs. local.  Own data?

improvement and comments — by Sylvain MAILLARD — last modified 2010-05-24 11:37

Please go to: https://groups.nceas.ucsb.edu/landscape-genetics be aware that you wont be able to log in, but all thhe content are publicly available!   following the discussion of this morning, here is a list of improvment to do: annd explanations of the different concept: not only a glossary of terms, but more a wikipedia-like place add technical / methodological Howto add scipts or other tools, either on the software page or in the technical howto add links to usefull datasets: landscape, genetics, climatic, seescape, ... add more paper from the existing database do 2 groups of paper: one with the "basic" paper that explain the concept, the other be just a review of paper add links to books, liket rodney pdf book have a bbetter directory of people, with there research fielsds, area of interrest, and perhaps links to some papers improve the meeting / job board add rss feed, and perhaps an rss aggregator ...   Please tell s what do you think of the current website, and what kind of improvment do you want to see ont the website!

Re: Software packages for Mantel's tests and significance testing — by Niko Balkenhol — last modified 2010-04-07 02:59

The problem is that most programs do not explicitly state how they do the randomization.  Also, there are actually several ways for permuting "residuals" for the partial Mantel test and I think the permutation of residuals of a null model (Anderson & Legendre 1999) is appropriate, while the permutation of one residualized matrix (Smouse et al 1986) is not.  Another (safe and in my view most intuitive) option is to simply permute the "dependent" matrix...and it's what's implemented in R package ecodist.  There is still a lot of debate with respect to the most appropriate permutation method for the partial Mantel test... If the software you want to use does not explicitly state which method is used, you might want to check with the author of the program. Hope this helps and doesn't add to the confusion :O)   Niko

Mantel correlograms — by Daria Koscinski — last modified 2010-04-05 08:56

Hello everyone, In the week 10 lecture Sam presented some Mantel correlograms in the CDPop validation/evaluation of the black bear study. I was wondering why in the plot of Mantel r vs. time the Mantel value goes much higher than in the Mantel correlogram. E.g. slide 66: the Mantel r reaches nearly 0.7 after 200 years but the r value in the corresponding correlogram never exceeds 0.2 at the smallest distance class. Why? Thanks! Daria  

Software packages for Mantel's tests and significance testing — by Daria Koscinski — last modified 2010-04-05 08:35

Hi everyone, Our group has been discussing Mantel's tests and the appropriate permutation tests to assess significance. We would like to find out if there is a consensus on which software packages are best - i.e. do the correct permutation tests (permute residuals). Any suggestions would be greatly appreciated. Thanks. Daria Some packages we know of that perform Mantel's tests: R package Vegan for R FSTAT Arlequin

Re: additional citations — by Stephanie Manel — last modified 2010-03-28 07:55

Thank you Niko. Stéphanie Hi Stephanie,   Your lecture looks great!  I only have a couple of minor suggestions:   You might want to point out some more that edge detection and clustering methods have similar goals in genetics, even though they are analytically different.  Perhaps we should think about combining these complementary analyses more often.  (Maybe cite Jacquez, G.M., Kaufmann, A., Goovaerts, P (2008) Boundaries, links and clusters: a new paradigm in spatial analysis? Environmental and Ecological Statistics 15(4): 403-419.) I think it’s important that students in the course realize that they should always use more than one program, for example one spatial and one non-spatial clustering method.  It’s also crucial that we start to report exactly how we interpreted outputs of these programs and what decisions we made to derive final conclusions.   For the sampling effects on Structure results, you might also want to cite: Schwartz MK, McKelvey KS (2009) Why sampling scheme matters: the effect of sampling scheme on landscape gnetic results. Conserv Genet. doi:10.1007/s10592-008-9622-1   Finally, on slide 47, where you suggest that assignment probability can be linked to the landscape, you might wan to cite: Murphy, M.A., Evans, J.S., Cushman, S.A., Storfer, A. (2009) Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies.  Ecography 31: 685-697.    

Re: Mapping WOMSOFT results in GIS — by Stephanie Manel — last modified 2010-03-22 06:10

Ok. Is it done? What are the result? Stéphanie

Re: Mapping WOMSOFT results in GIS — by Stephanie Manel — last modified 2010-03-16 04:27

No there is no literature at my knowlege. But what do you want to do exactly? Since files are .txt file and geo-referecenced, they can easely be imported in Arcview, I assume. Stéphanie

Re: Mapping WOMSOFT results in GIS — by Kennith Peters — last modified 2010-03-10 11:46

From a glance at the WOMSOFT output it appears you will need to reformat the output to get it in without writing your own import script. I'll try my hand at seeing how easy it is to get it in to ArcGIS.

Mapping WOMSOFT results in GIS — by Dawn Davis — last modified 2010-03-05 09:47

Is there any literature you can direct us to that would provide details on how we can convert our results from WOMSOFT into a GIS coverage?

Landscape data posted — by Melanie Murphy — last modified 2010-03-04 20:40

Hi All - Landscape data are posted for the spotted frog study area.

Re: Toad paper and data — by Melanie Murphy — last modified 2010-02-22 20:37

Spotted frog data up. 

Re: Toad paper and data — by Melanie Murphy — last modified 2010-02-22 14:38

Spotted frog paper now up as well.  Will post the data soon.  It would be very helpful to know from the group 1) what questions you are interested in and 2) what type of data you need to answer the questions.  This will help me figure out the best way to make data available to you (and what to include). 

Recording up — by Melanie Murphy — last modified 2010-02-22 13:53

Hi All - The recording of the lecture is up.  Marratech was not cooperating, so used some alternative methods.  The powerpoint show option is likely best if you have access to the software.  Otherwise, play either the avi or mp4 file.  The sound volume on these recordings is VERY low, I will keep trying for a fix to this issue. 

Toad paper and data — by Melanie Murphy — last modified 2010-02-19 11:10

Paper and data are up.

Rosenburg 2005 missing... :) — by Tabitha Graves — last modified 2010-02-17 07:52

Lecture Up! — by Rodney Dyer — last modified 2010-02-10 13:45

Hey, I was incapable of making marratech behave so I just uploaded a straight mp4 of this lecture. If you have any problems let me know. Rodney

Re: Excelent class, thanks — by Lisette Waits — last modified 2010-02-08 08:09

Previously Milton Ribeiro wrote: Glad to hear it was helpful and clear! Lisette Hi Profa. Lisette, As a computer scientist interested on integrate computer-based simulations and landscape genetics I wish to thanks for the cool class! It is really a very good introductory material. The readings and assignments were also interesting. cheers miltinho

Re: landscape genetic in R — by Milton Ribeiro — last modified 2010-02-06 07:08

Mutchissimas gracias :-) milton Previously Yessica Rico wrote: This is the link; is a list of publications, the third one is the manual "Biological analysis using R" http://dyerlab.bio.vcu.edu/publications/

Re: landscape genetic in R — by Yessica Rico — last modified 2010-02-06 06:10

This is the link; is a list of publications, the third one is the manual "Biological analysis using R" http://dyerlab.bio.vcu.edu/publications/

Excelent class, thanks — by Milton Ribeiro — last modified 2010-02-05 19:36

Hi Profa. Lisette, As a computer scientist interested on integrate computer-based simulations and landscape genetics I wish to thanks for the cool class! It is really a very good introductory material. The readings and assignments were also interesting. cheers miltinho

Animal movement & starting the project — by Milton Ribeiro — last modified 2010-02-05 19:05

Dear all, I just wrote to the professors, but may be interesting we stimulate our start of discussion here in this forun. May be interesting to know how is involved on this potential study. best regards milton ribeiro === De: Miltinho [mailto:miltinho_astronauta@yahoo.com.br] Enviada em: February-05-10 3:47 PM Para: 'sfspear@uidaho.edu'; 'nbalkenhol@vandals.uidaho.edu'; 'astorfer@wsu.edu'; 'lwaits@uidaho.edu' Assunto: Landscape genetic and animal movement   Dear professors,   I choose animal movement for the landscape genetic seminar project, and yesterday I know that my name is in the list. I write you to say that I am ready to start discuss the project. I would like to be happy if you could suggest some reading as well as to introduce all other students involved on the same project.   Cheers   milton ribeiro

project — by Christopher Blair — last modified 2010-02-05 13:52

Hi all, Just wanted to introduce myself ad maybe try to discuss some of the possible scenarios we would like to investigate for the project. Chris

landscape genetic in R — by Milton Ribeiro — last modified 2010-02-04 20:55

Hi all, Helene Wagner suggested us to read a material ( a kind of book) that deal with landscape genetics analysis in R. Could someone share the link? By the way, Biondutor project also include some R solution for landscape genetics analysis? Thanks a lot milton

Individual Based Model and Landscape genetic — by Milton Ribeiro — last modified 2010-02-04 20:50

Dear all, I would be happy if someone could suggest some reading dealing with landscape genetic and individual based model (IBM) simulations. Chees milton

Re: Meet the expert — by Lisette Waits — last modified 2010-02-02 13:38

WHich students from Idaho joined?  They must have joined as individuals.  Our class plants to join this Thurs but I am out of town so Steve Spear is handling this. Lisette Previously Helene Wagner wrote: Only two students from Idaho joined the first meet-the-expert session, and we had problems with the sound - they could (eventually) hear me, but I could not hear them. We had a nice chat, nevertheless, using the instant messaging function of Marratech. When participating, please remember to press the microphone button whenever you want to speak. Also, best use a camera (and press the camera button upon joining), seeing each other makes it much more interactive. To join, paste the following into the top line in Marratech, then go to Auditorium: http://meet.nceas.ucsb.edu

More Fragstats material — by Melanie Murphy — last modified 2010-02-02 13:24

If you are interested in using Fragstats with your own work or learning more, there is a link on the Fragstats website for workshop materials: http://www.umass.edu/landeco/research/fragstats/workshops/fragstats_workshops.html These materials are very, very nice. 

Re: source of data for lab exercise — by Helene Wagner — last modified 2010-02-02 04:04

Images, raster files, grids etc. typically have a format where each pixel/cell has a single value and only these values are stored in the file. <br /><br />In ASCII format, all values for one row of the image/grid are written into one line of the file. In our case, the values are numerical codes for the land-use/land-cover class. <br /><br />While Fragstats asks us to enter the number of rows and columns and some other information about the file in the parameter dialog box, other software such as ArcGIS expects that information to be included in the file as a header (first few lines of the file). The header for the madison files looks like this (xllcorner and yllcorner could be used to provide coordinates for the lower left corner of the image/grid):<br /><br />ncols 800 <br />nrows 575 <br />xllcorner 0 <br />yllcorner 0 <br />cellsize 30 <br />nodata_value 999<br /><br /><br />

source of data for lab exercise — by Christopher Blair — last modified 2010-01-31 12:47

I worked through the assignment so I could learn a bit about the program and had a question. How are the input data gathered for analyses such as these? I examined the data in wordpad and I am assuming that the different numbers correspond to different habitat-types throughout a landscape. Does anyone recommend any paper(s) that we should check-out? Thanks in advance! Chris

Re: Meet the expert — by Helene Wagner — last modified 2010-01-31 06:10

Only two students from Idaho joined the first meet-the-expert session, and we had problems with the sound - they could (eventually) hear me, but I could not hear them. We had a nice chat, nevertheless, using the instant messaging function of Marratech. When participating, please remember to press the microphone button whenever you want to speak. Also, best use a camera (and press the camera button upon joining), seeing each other makes it much more interactive. To join, paste the following into the top line in Marratech, then go to Auditorium: http://meet.nceas.ucsb.edu

Re: Lab Exercise — by Helene Wagner — last modified 2010-01-31 06:05

This must have to do with the fact that (in ArcGIS) I split one large grid into four grids, and there was an uneven number of rows to start with. One way to deal with the zero's would be to change the "no data" code to 0 (in the madison.fsc file and in the parameters dialog), as there are no other no-data values, I think. Sorry about the inconvenience!

Re: Lecture Notes — by Helene Wagner — last modified 2010-01-31 06:02

Thanks for the "flowers"! Helene Wagner

Meet the expert — by Melanie Murphy — last modified 2010-01-29 18:31

Anyone attend the "meet the expert" session?  I am wondering how these are working.  Class is going great!

Lab Exercise — by Melanie Murphy — last modified 2010-01-29 18:30

In Landscapes 3 and 4, one of the students noticed that the Madison files have a "0" field.  I believe she was working off of the fixed data.  Is this no data?  An error? 

Re: Lecture Notes — by Milton Ribeiro — last modified 2010-01-28 19:07

I totally agree with Sarah about the lecture notes. On my point of view the first lecture was great, as was equally great the interaction between our "heterogeneous" classmates herein Toronto + those from University of Western Ontario that joined us. Another point is that the technology (Marratech, Skype etc) is doing a good job. I wish all other groups spread around the world are equally happy with this great seminar. milton ribeiro

Lecture Notes — by Sarah Bisbing — last modified 2010-01-28 14:17

Thank you for the fabulous lecture notes. I'm a visual learner and greatly appreciate all of the graphs, schematics, flow charts, and screen shots. These notes could easily be transformed into a book chapter.

Problem with madison data files — by Helene Wagner — last modified 2010-01-27 06:41

Please note that I have updated the data files by removing the ascii header. Make sure you download the folder with the revised files, posted Wed Jan 27. Sorry for the inconvenience. Helene

Underlying Mechanics — by Rodney Dyer — last modified 2010-01-27 06:39

Hey, For those interested in this student project, I wanted to clarify that you do not have to know how to program HTML or create database backends and run servers. I will take care of that. Participants in this project will build content and provide design, I will take care of the underlying mechanics of how it goes on the web. Rodney -- Rodney J. Dyer, PhD http://dyerlab.bio.vcu.edu

Dates on uploaded/updated material filenames — by Milton Ribeiro — last modified 2010-01-23 13:18

Dear all, I suggest everytime one upload a file, or update a old one, include the date on the end of the file, so it would be easy us to follow, and to know if we need or not to update the files we download previously. Addictionally I suggest we adopt the same way of include dates, like 2010_01_d20 (d for day). So when we download a new version, all files will be sorted correctely on our file system. If we use jan-fev-mar to identify the months, it will not be sorted on cronological sequence, and if we use only number like 2010_01_04, one will not know if it is January 4th or April 1st. Cheers milton

Sincronization between week topics and feedbacks — by Milton Ribeiro — last modified 2010-01-23 12:09

Dear all, I suggest we sincronize the Weeks IDs between the topics it self, and the feedback on draft lecture slides and materials. For example, next week (2) we will have an introduction on "Alternative views of Landscape Ecology". But on the "feedback on draft lecture slides and materials" section the Week2 is dedicated to discuss "week-2-what-is-genetic-diversity-and-how-do-we-measure-it". Almost on the beginning will be easy to follow all the material related to each Week/topic. :-) Best regards, milton

Fragstats and ArcGrid format — by Milton Ribeiro — last modified 2010-01-23 11:43

Dear all On the lecture notes of this topic (Lecture-Notes-Week2.pdf), pg. 16, on the item Calculating landscape metrics from raster maps there are a note about problems with ArcGrid format on Fragstats. One suggestion to bypass/activate it is to add the directory "c:\programfile\ArcGis\bin" (check where the bin directory under your AGis installlation) on the PATH of the windows environment. Almost to me it works fine for XP and Vista OS. Salut milton

Re: Formats — by Sylvain MAILLARD — last modified 2010-01-20 09:41

you can also use openoffice &gt;= 3.0, it can read the docx format

Re: Years vs. Generations — by Erin Landguth — last modified 2009-03-23 09:19

Good point!

Re: Programs — by Rodney Dyer — last modified 2009-03-20 07:27

The server popgraph is a go, I think. R

Re: Programs — by Melanie Murphy — last modified 2009-03-19 20:40

Very good point.  Will do.  Is popgraph up and working yet?

Re: Overlap? — by Niko Balkenhol — last modified 2009-03-19 14:10

Yes, we need to check on that.  I compare it to the Schwartz &amp; McKelvey paper to make the point that simulation results depend on their underlying assumptions.  If you explain the Latch et al paper, it would actually save me time.  But I could also find another example..

Programs — by Rodney Dyer — last modified 2009-03-19 07:01

You may want to link to the web pages of any software that you are going to use so that updates are reflected (also because there are binaries for other platforms besides windows as well). 

Re: move up? — by Rodney Dyer — last modified 2009-03-17 11:15

If we want to include the assignment test for an animal example, we may want to also throw in a "mixed-stock analysis" as well.  I don't think that has been covered anywere else yet.

Re: move up? — by Rodney Dyer — last modified 2009-03-17 11:13

I can see it going there and there is a bit of "pre-distance" jargon that they get here as that is how I teach 2Gener &amp; relatedness measures to prepare for wherever 8 ends up.<br />

Re: False discovery rate — by Niko Balkenhol — last modified 2009-03-17 08:12

2nd try: http://www.math.tau.ac.il/~ybenja/MyPapers/benjamini_hochberg1995.pdf http://www.math.tau.ac.il/~ybenja/MyPapers/benjamini_yekutieli_ANNSTAT2001.pdf