search for: ancestral

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matri...

Hello, I am trying to get Personal Ancestral File (which is free Genealogy software from The Church of Latter Day Saints) to run with wine. I have tried configuring wine in different ways following different suggestions in the HOWTOs and Wine user guides with varying results. I have also tried installing the software using Wine rather tha...

Hi, I have reconstructed ancestral character states on a phylogeny using MuSSE in the diversitree package and plotted the character state probabilities as pie charts on the nodes. I would, however, like to colour the character states of my extant species, i.e. the tip labels, the same colours as my pie charts, such that all species...

...line... in practical terms, I am attributing haplotypes to a pedigree, so I have to give the haplotypes to the parents before I give them to the offspring. The vectors *zippo* and *zappo* are the chances of getting one or the other hap from the sire and dam respectively. *gp* is the vectors of non-ancestral animals. *new* is a two col matrix where the haps are stored. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imper...

I'm running Personal Ancestral File (PAF) 5.2 under Wine 0.9.26, and it defaults to the bizarre "Captain Podd" font as its default screen and print font. It appears there are no knobs or registry entries to override this default font for some things when printing. My Wine is compiled from source to include the patch...

...D=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> ##FILTER=<ID=q10,Description="Quality below 10"> ##FILTER=<ID=s50,Description="Less...

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch

I do the these passages: library(Geneland) set.seed(1) data <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) geno <- data$genotypes coord <- t(data$coord.indiv) path.mcmc <-

I''m about to embark on a project and am seeking advice on my approach. I have an automotive site that needs to have shared categories. I''ve checked out different nested set, ancestral, acts_as_tree, acyclic plugins but feel they don''t exactly fit. So I am about to roll my own simple solution. Any feedback as to whether this looks good is appreciated. Essentially I have: Sections - Automotive, Marine, Air Groups - Cars, Trucks, Bikes Categories - Pickup, SUV, Utili...

Hello RUser! I try to use ace for an ancestral state reconstruction but got back an error message. ace(FacVar,Tree, type="discrete") Warning messages: 1: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) : NA/Inf durch gr??te positive Zahl ersetzt (NA/Inf replaced by positive number) 2: In nlm(funct...

Hi everyone I am trying to reconstruct ancestral character states with R. I used the ace function of the package ape. I have discrete characters and tried to use the ER and ARD model. The problem is, that I get negative lik$anc values. Does anybody by chance have an idea what might be wrong? Thanks in advance [[alternative HTML version delete...

Wayne, I see you committed my man page improvements for --filter (from a long time ago) and --hard-links, except you omitted the mention of --link-dest as a second potential source of unwanted hard links among destination files (the original focus of bug 3693). You don't think this is worthy of mention? Matt

...sly length 0, the mode of the vector is coerced to 'logical'. For example, here's the normal behaviour: test> x1_ 5 test> x1[1]_ NA test> x1 [1] NA test> mode( x1) [1] "numeric" No coercion was required because 'logical' (the default mode of NA) is "ancestral" to 'numeric'. Note also that assigning to a hitherto non-existent element of x1, e.g. x1[2]_ NA, also does not coerce. But: test> x0_ numeric( 0) test> x0[1]_ NA test> mode( x0) [1] "logical" Similar things happen with vectors of mode 'complex' and even &...

...e very dawn of the world. We're hardly more than an eyeblink away from the fall of Troy, and scarcely an interglaciation removed from the Altamira cave painters. We live in extremely interesting ancient times. I like this idea. It encourages us to be earnest and ingenious and brave, as befits ancestral peoples; but keeps us from deciding that because we don't know all the answers, they must be unknowable and thus unprofitable to pursue." -- Teresa Nielsen Hayden, 1995

Windows 2000 R 1.4 I have a split-split plot design that I am analyzing with model <- aov(). I tried using model.tables(model) and it replied "Error: subscript out of bounds." I have monkeyed with it a little, but am wondering if this is indicative of something in particular. Thanks, Hank Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami

Dear R gurus, I need to know the length of a variable (let's call that X) that is mentioned in a formula. So obviously I look for the environment from which the formula is called and then I have two options: - using eval(parse(text='length(X)'), envir=environment(formula) ) - using length(get('X'), envir=environment(formula) ) a bit of

Hi, Was wondering if it is possible to pass function name as a parameter, smth along this line param.to.pass<-c(1,'max','h') dd<-function(dfd, param=param.to.pass,...){ ttime.int <- format(ttime,fmt) data.frame( param[3] = tapply(dfd[,param[1]],ttime.int,param[3]), ...) } I know there is a as.formula expression but not quite sure if there is some

...e Old Republic launcher locks up on icon highlighting 29689 Crash wincfg on graphics tab with LC_ALL=ja_JP 29869 Re-Volt is missing an HUD element 29883 Game created with RPG Tkool VX Ace (Japanese version of RPG Maker VX Ace): can not write save data (Save*.rvdata2) 29949 PAF (Personal Ancestral File) help viewer unhandled page fault 29981 Galactic Civilizations 2 is unplayable due to possible severe memory leak 29992 Rally Trophy: crashes on startup when Logitech G25 plugged in 30038 Detect CPU speed by using sysctl "hw.clockrate" instead of "dev.cpu.0.freq"...

...Endless Space crashes on startup 37684 Free YouTube to MP3 Converter 3.12 installer crashes on unimplemented function msvcr120.dll._wcsset_s 37700 Propellerhead Reason 8 needs COMCTL32.dll.381 LoadIconWithScaleDown() 37701 Propellerhead Reason 8 needs mfplat.dll.MFStartup 37714 Personal Ancestral File 5 crashes when a new line is added in 'Notes' panel 37723 Elevated demo silently exits 37727 Saya no Uta: sound is all over the place after update 37735 Propellerhead Reason 8 installer complains "interface not supported" during install 37752 Airport Tycoon 2 demo...

Dear list users, I need to learn about MCMC methods, and since there are several packages in R that deal with this subject, I want to use them. I want to buy a book (or more than one, if necessary) that satisfies the following requirements: - it teaches well MCMC methods; - it is easy to implement numerically the ideas of the book, and notation and concepts are similar to the corresponding R