search for: dist2

Hi all, I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5

Hello, I wonder if it is possible to change pxelinux.0's tftp prefix... I want to setup a repository like that: |-- dist1 | |-- pxelinux.cfg | | `-- default | `-- pxelinux.0 |-- dist2 | |-- pxelinux.cfg | | `-- default | `-- pxelinux.0 |-- pxelinux.cfg | |-- default | `-- menu.c32 `-- pxelinux.0 The file /pxelinux.cfg/default would contain something like that: > LABEL dist1 > MENU LABEL dist1 > KERNEL dist1/pxelinux.0 > LABEL dist2 >...

...ce "delta_yrsed" with what "\Delta \widehat{yrsed}" represents in TeX, but the [xyz]lab parameters of title3d appear to only accept character strings. require("rgl") fn.delta.yrsed <- function(dist, delta.dist, beta.dist=-0.1376463, beta.dist2=0.0088698) { delta.yrsed <- (beta.dist + 2*beta.dist2*dist)*delta.dist + beta.dist2*delta.dist^2 return(delta.yrsed) } plot.deeffect <- function(scolor="blue") { delta.dist <- dist <- seq(0, 16, .5) delta.yrsed <- outer(dist, delta.dist, fn.delta.yrsed) rgl.open...

...abandon+land_use+ca_old, data=ba12, xv="p") Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : Variable lengths differ When computing the matrices directly... ba12.dist1 <- gdist (ba12[,18:29], method="maximum", full=T, sq=F) ba12.dist2 <- vegdist (ba12[,18:29], method="jaccard", diag=T, upper=T) ba12.dist3 <- dist (ba12[,18:29], method="minkowski", p=1, diag=T, upper=T) and looking at them, there appears to be no difference though only ba12.dist1 works with mvpart. With the other two I get the same err...

I have spatial data on a sphere (the Earth) for which I would like to run an gls model assuming that the errors are autcorrelated, i.e. including a corSpatial correlation in the model specification. In this case the distance metric should be calculated on the sphere, therefore metric = "euclidean" in (for example) corSpher would be incorrect. I would be grateful for help on how to

I want to read data from a number of files into R. Reading individual files one by one requires writing enormous amount of code that will look something like the following. **************** maptools:::dbf.read("wb-01vc.dbf")->dist1 maptools:::dbf.read("wb-02vc.dbf")->dist2 maptools:::dbf.read("wb-03vc.dbf")->dist3 maptools:::dbf.read("wb-04vc.dbf")->dist4 maptools:::dbf.read("wb-05vc.dbf")->dist5 maptools:::dbf.read("wb-06vc.dbf")->dist6 maptools:::dbf.read("wb-07vc.dbf")->dist7 maptools:::dbf.read(&quo...

Dear all, I am fitting an nonlinear glm() using optim() by first minimising glm(resp~ var1 + var2, family=binomial, data=data)$deviance where var1= exp(-a1*dist1), and var2= exp(-a2*dist2), where a1 and a2 are parameters and dist1 and dist2 are independent variables. Next, I calculate the value of var1 (and var2) by plugging in the value of al1 (and al2) that minimises deviance, and fit glm(resp~ var1+var2 , family=binomial, data=data) Var1 in this model thus includes two paramet...

...e programmed some simulated studies. I have testes with 72,576 different combinations of the initial values and now I got an error in only 4 situations. The error comes from the function grad() and I don't understand why. This is the output: Error in grad.default(Sstar, x = t, dist1 = T1pdist, dist2 = T2pdist, : function returns NA at 3.90625e-071.01927622979798e-087.7105723770202e-075.27096223871154e-087.28540377612885e-071.25230637383194e-076.56019362616806e-072.21329924168263e-075.59920075831737e-073.324709613353e-074.487790386647e-070.0001000016964206937.79553579306956e-072.72822299391...

...e discovered a bug. It seems that, when I use weights during an initial least-squares regression fit, and later try to add terms using stepAIC(), it uses the weights when looking to remove terms, but not when looking to add them: hills.lm <- lm(time ~ dist + climb, data = hills, weights = 1/dist2) small.hills.lm <- stepAIC(hills.lm) stepAIC(small.hills.lm, time ~ dist + climb) In the first stepAIC(), it says that the AIC for the full "time ~ dist + climb" is 94.41. Yet, during the second stepAIC, it says adding climb would produce an AIC of 212.1 (and an RSS of 12633.3). I...

Hi all, this is OT, but maybe someone can give me a clue. I've got data from eye tracker experiments (750 data points). These figures show how the data lock like |** * ***** |*** ****** | ** **** | * * | | * * | | * |-------------- |--------------- Y axes display velocity, x axes display time, * are the data points.

...1.000000000 1.000000000 1.000000000 1.000000000 NaN 1.000000000 1.000000000 NaN I searched all the details of metaMDS where it is suggested to avail the argument 'zerodist' So I tried both X.dist1 <- metaMDSdist(X, method="bray",zerodist = "ignore") X.dist2 <- metaMDSdist(X, method="bray",zerodist = "add") But for both the cases I still have those NaN values in some distances. I have read, one of the discussion says modify zero dissimilarities as: If there is a good reason, and you want to include all samples, then you'll n...

Hi, At each iteration in my program,I need to generate tree vectors,X1,X2,X3, from exponential distribution with parameters a1,a2,a3. Can you help me please how can I do it such that it take a little time? thank you khazaei

Dear All, I would like to ask how to customize the graph corresponding to a procrustes analysis. I have to distance matrices, that I transform to two set of coordinates by means of muti dimensional scaling: library(mva) c1<-cmdscale(mat.dist1) c2<-cmdscale(mat.dist2) I vant to rotate c2 on c1, and I use the "procrustes" analysis from the {vegan} library. library(vegan) mod.pro<-procrustes(c1,c2) plot(mod.pro) My problem is that I need to change the graphical output of plot(mod.pro). The standard output gives empty circles for the rotated c2...

I wrote a function to calculate cosine distances between rows of a matrix. It uses two loops and is slow. Any suggestions to speed this up? Thanks in advance. theta.dist <- function(x){ res <- matrix(NA, nrow(x), nrow(x)) for (i in 1:nrow(x)){ for(j in 1:nrow(x)){ if (i > j) res[i, j] <- res[j, i] else { v1 <- x[i,] v2 <- x[j,]

Hello, this is probably trivial but I failed to find this particular snippet of code. What I got: my_dataframe (contains say a 40k rows and 4 columns) distances (vector with euclidean distances between a query vector and each of the rows of my_dataframe) What I do: after scaling data my_dataframe I calculate distances. order them then extract top five hits my_dataframe <-

Hi, I am trying to plot two distribution graph on one plot. But I dont know how. I set them to the same x, y limit, even same x, y labels. Code: x1=rnorm(25, mean=0, sd=1) y1=dnorm(x1, mean=0, sd=1) x2=rnorm(25, mean=0, sd=1) y2=dnorm(x2, mean=0, sd=1) plot(x1, y1, type='p', xlim=range(x1,x2), ylim=range(y1, y2), xlab='x', ylab='y') plot(x2, y2, type='p',

Version 1 of the patch, for discussion, but not to be applied. It does work, but needs a lot more testing. This removes all the psychopathic gettextify cruft, and replaces it with a 99 line Makefile.am. A large win, I think. The third patch implements gettext support in the OCaml tools. The fourth patch is just for illustration. It shows the consequent changes to libguestfs.pot and the po

...8 1.5224318 1.4444836 1.3682047 1.0048085 2.8425813 1.8464349 2.7853605 9 4.5321276 4.5859822 3.8178836 5.4277885 5.7703245 3.7731505 5.6657106 10 4.0389095 1.6702235 2.7327563 3.5495557 5.4279792 2.3611163 0.5540045 8 9 2 3 4 5 6 7 8 9 5.1082493 10 2.5924107 6.0248981 > dist2 1 2 3 4 5 6 7 2 0.9364828 3 1.4333876 1.9160376 4 0.2523886 1.1884864 1.3697080 5 2.3753105 2.5185909 3.7830808 2.4140423 6 1.7928748 1.6959363 1.0841587 1.8848077 4.0827074 7 2.5117723 1.6858232 2.7455418 2.7406021 4.0115957 1.81400...