tag:blogger.com,1999:blog-8499895524521663926.post5132014230889817961..comments2020-05-29T01:01:08.855-04:00Comments on Phylogenetic Tools for Comparative Biology: New, totally rewritten version of make.simmap; new phytools buildLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger19125tag:blogger.com,1999:blog-8499895524521663926.post-48507974033539153702019-08-12T13:11:27.252-04:002019-08-12T13:11:27.252-04:00Hello,
I have the same error as many of you alrea...Hello,<br /><br />I have the same error as many of you already had with make.simmap:<br /><br />Error in xx[tree$tip.label, ] : subscript out of bounds<br /><br /> But I can't figure it out, even with all previous posts.<br /><br /> My tree is of class "phylo" and my character has fivedifferent state ("G","g","f","d","s") and is stored in different object (I tried vector, data frame and matric), but not in my phylo object as in anoletree. My rownames of my object containing my character states correspond to those of my tip labels.<br /><br />Does someone could help me ? I might missing a step here.<br /><br /><br />PS: I noticed that anoletree is both phylo and simmap class. Is it normal?<br />Anonymoushttps://www.blogger.com/profile/07619356389329621802noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-28651822399540406482019-07-16T16:03:55.675-04:002019-07-16T16:03:55.675-04:00Hello, I had the same error as well, so I figured ...Hello, I had the same error as well, so I figured out the following commands to solve this.<br /><br />read.table("Pb.txt",row.names=1,h=T)->Pb #This is my matrix<br />setNames(Pb$states,rownames(Pb))->Pbn #Here I converted it to a simple vector.<br /><br />Then, you can run the following commands.<br /> Andrea C-Románhttps://www.blogger.com/profile/07060294720186958848noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-49867445301227420132019-07-10T15:56:01.153-04:002019-07-10T15:56:01.153-04:00Hi, how would I go about returning the node (or ev...Hi, how would I go about returning the node (or even better, the distance from the root) at which a trait is acquired? I.e. the first occurrence.Jamie Thompsonhttps://www.blogger.com/profile/02619523518595779673noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-10058893594429379822019-05-10T14:21:32.031-04:002019-05-10T14:21:32.031-04:00Hello, I am having the same error, but I am pretty...Hello, I am having the same error, but I am pretty sure it is not due to incorrect matching of tip labels and species labels in my data, because i have removed all species in the data that do not match the tree$tip.labels. the error I receive is <br />"Error in xx[tree$tip.label, ] : subscript out of bounds"<br /><br />I am happy to provide more information if needed. Anonymoushttps://www.blogger.com/profile/17227353618822959424noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-34567478772362690312018-11-26T09:31:40.825-05:002018-11-26T09:31:40.825-05:00Thank Luis, yes, it is usually some fine detail in...Thank Luis, yes, it is usually some fine detail in the " or some inadverted typo.Andréshttps://www.blogger.com/profile/04763931890352626135noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-59791176104584397692018-09-14T15:08:12.344-04:002018-09-14T15:08:12.344-04:00Hi Andrés,I geted the same error with other data, ...Hi Andrés,I geted the same error with other data, in my case that error was a difference on the names of the terminals coming from the tree and those from the data. I am not an exprt on R but to compare the names I extracted to a variable (M) the names of the tree with the tip.tree (M<-mcctree[["tip.label"]])function and then made a matrix with (M<-data.matrix(M)). Then I compared the data of M (the names) with those that comes from the data on a spreadsheet. I hope this helps. Best regards. LuisAnonymoushttps://www.blogger.com/profile/02933480402055636158noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-33460512529517329082018-09-05T17:28:46.627-04:002018-09-05T17:28:46.627-04:00Hi, it was resolved? I'm having the same error...Hi, it was resolved? I'm having the same error but with other functions. <br />ThanksAnonymoushttps://www.blogger.com/profile/16672290510073967392noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-50859608548474015802017-11-28T09:49:12.097-05:002017-11-28T09:49:12.097-05:00Hi flashton. If you email me your R workspace and ...Hi flashton. If you email me your R workspace and the specific command generating the error, I would be happy to try to get to the bottom of it. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-49362762318041938992017-11-28T09:45:09.347-05:002017-11-28T09:45:09.347-05:00Sorry I couldn't make it work with that toy ex...Sorry I couldn't make it work with that toy example and summarized the info in another way since I was in a rush for preparing that material. Andréshttps://www.blogger.com/profile/04763931890352626135noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-40285966034752938982017-11-27T05:34:49.107-05:002017-11-27T05:34:49.107-05:00Hi Andrés, did you solve this problem? I'm hav...Hi Andrés, did you solve this problem? I'm having the same one.flashtonhttps://www.blogger.com/profile/13091856773895064896noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-43582896914112269652017-03-24T13:48:53.604-04:002017-03-24T13:48:53.604-04:00Hi Liam,
I am working on an example to give to a...<br />Hi Liam, <br /><br />I am working on an example to give to a class, I am using this format for trait data (as I previously used)<br /><br />Species 1<br />Species 2<br /><br />and reading it through <br /><br />> dietario <- read.table("fruti.txt", row.names = 1)<br /><br />Then I converted this with the following<br /><br />> XXX <- dietario[,1]<br />> names(XXX) <- row.names(dietario)<br />> XXX -> dietas<br /><br />Then I got this error<br /><br />> make.simmap(arbol, dietas)<br />Error in xx[tree$tip.label, ] : subscript out of bounds<br /><br />The "arbol" and data had the same taxa<br /><br />Thanks for your help!<br />Andréshttps://www.blogger.com/profile/04763931890352626135noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-21888529829239400012017-02-06T16:09:56.760-05:002017-02-06T16:09:56.760-05:00Hi Liam,
I have the same question as Elisa, but I...Hi Liam,<br /><br />I have the same question as Elisa, but I'm not quite clear on your answer. Can you explain what you mean by "the names attribute?" I provided a simple vector like the example Elisa has above and I'm receiving the same error message. Thanks!Anonymoushttps://www.blogger.com/profile/07577018660141610909noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-25668927468818644372016-07-10T11:52:53.318-04:002016-07-10T11:52:53.318-04:00Hi Liam,
Thanks for the detailed explanation. In ...Hi Liam,<br /><br />Thanks for the detailed explanation. In terms of counting how many times a given transformation (e.g. 0->1) has occured, I was wondering if there is a way to generate a histogram if probability distributions for the number of changes based on the joint reconstruction.<br /><br />I have used countSimmap, which returns an integer value for the number of changes, but I'm not sure how this number is calculated from the probability distributions for each node. You mention the possibility of generating histograms in your "Lecture_5.1" on ancestral state reconstructions, but I can't figure out a way of generating such an output.<br /><br />Thanks a lot in advance!Bernardo Santoshttps://www.blogger.com/profile/03700418803879142861noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-14090363673719754192016-07-10T11:51:27.935-04:002016-07-10T11:51:27.935-04:00This comment has been removed by the author.Bernardo Santoshttps://www.blogger.com/profile/03700418803879142861noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-69859143644207845342016-02-02T16:39:21.369-05:002016-02-02T16:39:21.369-05:00Is there a way to fix specific transition rates in...Is there a way to fix specific transition rates in Q while allowing all others to be estimated at their most likely values?Anonymoushttps://www.blogger.com/profile/06848445703593289579noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-13376442809601165672014-03-21T09:04:24.896-04:002014-03-21T09:04:24.896-04:00Hello, hope this question goes in the right place ...Hello, hope this question goes in the right place ;) Am I right that from describe.simmap I can get the transition rates simply by dividing the numbers of different transitions by the total number of all transitions? Sorry if this is silly but I'm still relatively new to comparative stuff and wan't just find similarities between phytools output and BayesTraits which I used so far.Anonymoushttps://www.blogger.com/profile/03164888822727133031noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-68821504235561154062013-09-14T15:07:45.006-04:002013-09-14T15:07:45.006-04:00Hi Elisa.
Yes, just a vector - but the names attr...Hi Elisa.<br /><br />Yes, just a vector - but the names attribute must be the species names in the tree (in any order).<br /><br />If you have uncertain, you can use a prior probability distribution on the tip states. This is described <a href="http://blog.phytools.org/2013/03/estimating-ancestral-states-when-tips.html" rel="nofollow">here</a>. Basically, x becomes a matrix with n rows and m columns for n taxa and m values for the trait. Each element in the prior probability, Pr(i,j), of the ith taxon being in the jth state. In this case, row names should be tip labels and column names should be state names.<br /><br />Let me know if this is what you needed to know. LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-8179863720085693812013-09-13T12:38:57.009-04:002013-09-13T12:38:57.009-04:00Hy Liam,
thank you for making stochastic mapping ...Hy Liam,<br /><br />thank you for making stochastic mapping available for R users.<br />Buy unfortunatelly I'm not getting it. I'll obtain the Q matrix as the output of make.simmap (and to use it in sim.history I have to transpose of the printed matrix Q of make.simmap), right? But when I try to run make.simmap I get the following message: "subscript out of bounds". I don't know what I'm doing wrong. The tree is in phylo format and I'm using SYM model. Can you please give me and example of the vector X ("a vector containing the tip states for a discretely valued character") so I can compare with mine? It is a simple vector like x=c("1","1","0","1")? One more question, how can I indicate missing information on the tip states?Elisahttps://www.blogger.com/profile/10826355411884130352noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-26676870231543167202013-03-17T17:58:53.872-04:002013-03-17T17:58:53.872-04:00If anyone is interested in comparing make.simmap t...If anyone is interested in comparing make.simmap to <a href="http://www.simmap.org" rel="nofollow">SIMMAP</a>, they should check out the phytools function export.as.xml which will create a SIMMAP input file.<br /><br />In my very non-scientific comparison yesterday I found that SIMMAP, under the default conditions for morphology, sampled the same posterior probabilities at nodes as make.simmap - but that the number of changes in SIMMAP were too large (i.e., the 95% distribution did not include the generating number of changes). This might be just a matter of tuning the priors, or it might reflect something deeper. At this point, I just don't know.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.com