tag:blogger.com,1999:blog-4890093519663715581.post7665565780113733377..comments2023-10-22T08:30:53.073-07:00Comments on Species In Space: New test version of ENMTools with model selectionDan Warrenhttp://www.blogger.com/profile/07528161395964087899noreply@blogger.comBlogger59125tag:blogger.com,1999:blog-4890093519663715581.post-20488386541969011352020-05-21T01:52:12.319-07:002020-05-21T01:52:12.319-07:00This comment has been removed by the author.Debanjan Sarkarhttps://www.blogger.com/profile/14713542058346398112noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-31639323177193709662020-02-19T18:47:49.649-08:002020-02-19T18:47:49.649-08:00AIC is able to compare models with different numbe...AIC is able to compare models with different numbers of variables and parameters. As for there being limitations: the application of AIC to Maxent models is still a bit of a hack despite being quite widely used. Maxent's use of lasso regularlization means that there's a disconnect between the number of parameters and the effective degrees of freedom, and we don't really understand fully how that affects model selection for species distribution modeling. The simulations that have been done largely support the utility of AIC, but we still know that it might be "wrong" to some unknown level - over-penalizing model complexity to some extent. I'm pretty comfortable with that based on my general preference for very simple models, but there are definitely some very smart people who have a different perspective on it.Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-45331701252908232402020-02-19T07:15:18.003-08:002020-02-19T07:15:18.003-08:00I have a question about the application of ENMTool...I have a question about the application of ENMTool model selection. Does it make sence to compare the models with the different number of variables, or is it just to compare the model with different parameters? Are there limitations for model comparisons with this tool at all? Anna Namyatovahttps://www.blogger.com/profile/03122231790027903971noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-60922762274596045832018-03-28T04:57:43.630-07:002018-03-28T04:57:43.630-07:00Certainly it would suggest that modeling approach ...Certainly it would suggest that modeling approach A was doing a better job than B. <br /><br />I'm not sure what you mean when you say "in this manner", but in general AICc is the way to go. It corrects for small sample size when your sample sizes are small, but if sample size is large it converges on regular AIC anyway.Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-24705572809424111522018-03-27T08:30:49.044-07:002018-03-27T08:30:49.044-07:00Okay, great thanks! That makes sense and confirms ...Okay, great thanks! That makes sense and confirms some suspicions I had about AIC. I suppose if all replicates from model A have lower AIC than all replicates model B I could conclude that A has better performance than B as measured by AIC. I need to research this more but since I'm here, would calculating in this manner be AICc or normal AIC? I_study_pygmieshttps://www.blogger.com/profile/15136086465185966521noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-6411775187560488672018-03-26T00:54:31.625-07:002018-03-26T00:54:31.625-07:00Each replicate would have to be on a separate line...Each replicate would have to be on a separate line and treated as a separate model. The next question is of course how you use AIC values from all of those replicates to get some sort of overall AIC value for your model, and the answer is that there's not really an accepted way to do that. One of several reasons that AIC is a bit of an odd approach for Maxent models as typically constructed.Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-26612723558675642642018-03-23T09:28:18.903-07:002018-03-23T09:28:18.903-07:00Hi Dr. Warren,
I would also like to compare Mode...Hi Dr. Warren, <br /><br />I would also like to compare Models A, B, and C each of which have five replicates. To clarify, I should put the three arguments (or line with the csv, asc, and lambda file) for each replicate in say Model A, in one row of the excel (csv) input file. Then all of the arguments for all replicates in Model B on the second row and all for Model C in the third row, correct? Rows being the actual numbered rows as in excel, not just lines of addresses entered on top of each other for ease of visualizing.<br /><br />Does it matter how the model replicates themselves are spaced? The person above seemed to keep each replicate on a separate "line" does this mean a distinct row in the excel (csv) file or was each replicate in the same row technically? <br /><br />Thanks so much and thanks for the tools...and the tunes!<br />Ian I_study_pygmieshttps://www.blogger.com/profile/15136086465185966521noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-77729987245077663662018-01-07T21:41:37.396-08:002018-01-07T21:41:37.396-08:00I had similar error. In my case I had wrongly spec...I had similar error. In my case I had wrongly specified the folder with the climatic layers.Obrero Futuristahttps://www.blogger.com/profile/16842510514609609076noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-72727724443629342862016-11-18T08:56:44.576-08:002016-11-18T08:56:44.576-08:00This comment has been removed by the author.nishmahttps://www.blogger.com/profile/10131647021511442210noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-73588573908658390802016-07-19T15:07:30.441-07:002016-07-19T15:07:30.441-07:00Probably, but it depends on your computer. It may...Probably, but it depends on your computer. It may take a while! <br /><br />If it doesn't run in ENMTools, there are functions in dismo for doing this as well.Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-55837338974660051522016-07-19T07:13:36.493-07:002016-07-19T07:13:36.493-07:00Yes i am looking for statistic significance of my ...Yes i am looking for statistic significance of my models predictions,so i just put 25 000?will ENMTools work with that much data?Anonymoushttps://www.blogger.com/profile/06893137331419834833noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-72872145388194706642016-07-18T14:19:20.941-07:002016-07-18T14:19:20.941-07:00Hard to diagnose just from this, but my guess is t...Hard to diagnose just from this, but my guess is that Maxent isn't actually being run. Do you see the GUI pop up?Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-36799722102699446402016-07-18T14:18:53.144-07:002016-07-18T14:18:53.144-07:00Do you mean you're looking for statistical sig...Do you mean you're looking for statistical significance of the model predictions, as in Raes and ter Steege 2007?<br /><br />If so you should put in the number of points that you have in your empirical data set.Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-34702191132499820092016-07-18T08:18:07.421-07:002016-07-18T08:18:07.421-07:00Hi Dan
For some reason I don't know yet, I can...Hi Dan<br />For some reason I don't know yet, I can't get a niche identity test using enmtools v1.3 on windows. I could do it last year, but now when I add two files for 25 replicates, I get the message "Niche identity test are finished" very quickly but I don't get any result. Can you please help me and let me know what I might have done wrong? Thanks!CAPhttps://www.blogger.com/profile/14691674315626298209noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-16848859831700658442016-07-18T03:04:42.155-07:002016-07-18T03:04:42.155-07:00i am using wolf movement data(telemetry data),and ...i am using wolf movement data(telemetry data),and plan to develop habitat suitability model( later use that to draw corridors in Gis) using maxent,after i run it, I would like to check my results in ENMTools by developing a null modelAnonymoushttps://www.blogger.com/profile/06893137331419834833noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-25741256005389930852016-07-16T14:49:18.960-07:002016-07-16T14:49:18.960-07:00What are you building the null model for?What are you building the null model for?Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-34442034564047048062016-07-16T14:00:01.912-07:002016-07-16T14:00:01.912-07:00Hi,i know it is a simple question but i just start...Hi,i know it is a simple question but i just started to use ENMTools, when i try to build a null model using resample from raster,what should i put in the number of points per replicate? I have one species(different wolfs) and 25 000 data (gps coordinates)?Anonymoushttps://www.blogger.com/profile/06893137331419834833noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-78068934394031712402016-02-28T21:38:15.844-08:002016-02-28T21:38:15.844-08:00Nope, haven't seen them. Did you send them to...Nope, haven't seen them. Did you send them to dan.l.warren@gmail.com?Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-70508225556800885582016-02-26T16:09:54.908-08:002016-02-26T16:09:54.908-08:00I sent the files, but not sure if they made it to ...I sent the files, but not sure if they made it to you...Anonymoushttps://www.blogger.com/profile/15926051022899319604noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-11992288994221073452016-02-24T17:52:33.139-08:002016-02-24T17:52:33.139-08:00Could you email me your .csv file?Could you email me your .csv file?Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-49254922109524454572016-02-24T16:59:37.812-08:002016-02-24T16:59:37.812-08:00Hello,
I am trying to use the background test in ...Hello,<br /><br />I am trying to use the background test in ENMTools, but keep getting the same error (below). It appears that the program is creating a number of empty files in my output folder and then not being able to reopen them. My input files are .csv files with two columns with the headers "LAT" and "LONG" Any idea what the problem might be? Thanks in advance for any help that you can give!<br /><br /><br />Can't open C:/Users/rtelemeco/Documents/Alligator Lizards/Niche Modelling/ENMTools_ElgariaOutput/34.23442.asc!!<br /><br />Can't open C:/Users/rtelemeco/Documents/Alligator Lizards/Niche Modelling/ENMTools_ElgariaOutput/34.23442.asc!!<br /><br /><br /> while executing<br />"::perl::CODE(0x36b5578)"<br /> invoked from within<br />".b5 invoke "<br /> invoked from within<br />".b5 instate !disabled { .b5 invoke } "<br /> invoked from within<br />".b5 instate pressed { .b5 state !pressed; .b5 instate !disabled { .b5 invoke } } "<br /> (command bound to event)Anonymoushttps://www.blogger.com/profile/15926051022899319604noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-54769478732187286782016-01-28T12:06:37.123-08:002016-01-28T12:06:37.123-08:00Got it. Thanks so much!Got it. Thanks so much!Unknownhttps://www.blogger.com/profile/05226488006663339198noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-12209491723160712192016-01-28T11:52:38.684-08:002016-01-28T11:52:38.684-08:00Yes indeed!Yes indeed!Dan Warrenhttps://www.blogger.com/profile/07528161395964087899noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-86381886661521047062016-01-28T11:27:38.767-08:002016-01-28T11:27:38.767-08:00Hello,
I've done some searching and haven'...Hello,<br /><br />I've done some searching and haven't found a specific answer to this question. I know I need a line in the model selection script for each csv/asc/lambda. So if I'm running multiple replicates (say 10) for one model, will my input model look like c:\data\points.csv\,c:\data\species_0.asc,c:\data\species_0.lambda<br />c:\data\points.csv\,c:\data\species_1.asc,c:\data\species_1.lambda<br />c:\data\points.csv\,c:\data\species_2.asc,c:\data\species_2.lambda<br />etc for each replicate on this model?<br />Will I then include similar lines for a separate model that also has 10 replicates?<br /><br />Thanks!Unknownhttps://www.blogger.com/profile/05226488006663339198noreply@blogger.comtag:blogger.com,1999:blog-4890093519663715581.post-29080482959563667912014-09-29T01:34:06.183-07:002014-09-29T01:34:06.183-07:00Hi Elizabeth,
I hope I'm not too late. I rec...Hi Elizabeth, <br /><br />I hope I'm not too late. I recently faced a similar issue, and I solved it by adding an extra column to the front of my csv file with occurrence data. My extra column was filled with "junk" data (the header was "Status" and values were all "Africa"). It seems to be a bug; without this extra column, the mac version of ENMtools doesn't recognize some points in the csv file given, and so the sample size of points used to calculate AICc/AIC/BIC is smaller than that given in the input csv file. Hope this helps. <br /><br />-Bi WeiBi Weihttps://www.blogger.com/profile/01911472392198772112noreply@blogger.com