similar to: Q. regarding optim()

Dear mailing group, This is my first time here. Glad to have this resource! I am currently trying to load an Excel file into R (limma package loaded) using the source(*name of directory*) command, but it cannot open the file. I renamed the file as .R and .RData, to no avail. The Excel data contains one gene name per row and about 100 data points per gene (columns). I am only used to

the following code apprantely, for some grand old reason, induces a syntax error: if (seq[i] = "A") m <- trans[1,] where seq is a vector and trans is a matrix. I cannot for the life of me see why this is wrong. Syntax error is: Error: syntax error in "if (seq[i] =" Sincerely, Norman Goodacre ---------------------------------

Dear group, I am nearly beside myself. After an entire night spent on a niggling little detail, I am no closer to to the truth. I loaded an Excel file in .csv form into R. It apparentely loads as a list, but not the kind of list you can use. Oh no, it converts into a list that cannot be converted into an integer, numeric, or vector, only a matrix, whihc is useless without integers.

Dear help group, Just fyi a markov chain is a sequence of transitions between states (say A,T,G,C - on a gene) with a given probability for each transition. In this case there'd be 16 different kinds, each with a different weight. Given a transition matrix (4x4) filled with all transition probabilities of course, how can I generate a random sequence of a given length, say 200?

Dear R-helpers, The function optim implements algorithms that I would like to use. I have function implemented in R, which given the parameters of which minimization is to take place returns a scalar as well as the gradient. Unfortunately optim requires two function _fn_ and _gr_ where fn returns the function value and gr the gradient. Splitting my function in two functions would be easy,

Dear R mailing group, I am having extreme - and mysterious - trouble installing R. I tried simply dl ing R-2.3.1.tar.gz, and unzipping it, but after doing so, nowhere could I find a file called R-2.3.1.exe. I did however find an R-2.3.1.exe.manifest. I therefore tried the command line installation command - given in R-admin.pdf. This command is: tar zxvf R-2.3.1.tgz This is strange

Hello everybody, i already searched the archieves, but i still don't know what is wrong in my implementation, mybe anybody coud give me some advice ll1<-function(rho,theta,beta1,beta2,beta3,beta4,t,Szenariosw5,Testfaellew5,X1,X2) { n<-length(t) t<-cumsum(t) tn<-t[length(t)] Szenn<-Szenariosw5[length(Szenariosw5)]

Dear mailing group, I have loaded an Excel file into R by calling it ".csv" and using the "read.csv" function in R. However then I want to use the (limma package specific, I believe) function "hclust", which clusters data in a tree dendrogram, by similarity. However, I receive the errors msg.s: 1) "missing observations in cov/cor" 2) "In

Hola! santes<-c(210,169,187,160,167,176,185,206,173,146,174,201,198,148,154) sdespues<-c(201,165,166,157,147,145,168,180,147,136,151,168,179,129,131) dantes<-c(130,122,124,104,112,101,121,124,115,102,98,119,106,107,100) ddespues<-c(125,121,121,106,101,85,98,105,103,98,90,98,110,103,82) presion<-data.frame( santes, sdespues, dantes, ddespues) logvero <-

Hi, R guys: I'm using L-BFGS-B method of optim for minimization problem. My function called besselI function which need non-negative parameter and the besselI will overflow if the parameter is too large. So I set the constraint box which is reasonable for my problem. But the point outside the box was test, and I got error. My program and the error follows. This program depends on CircStats

Hi everyone. I have a problem that I have been unable to determine either the best way to proceed and why the methods I'm trying to use sometimes fail. I'm using the pf() function in an optimization function to find a noncentrality parameter that leads to a specific value at a specified quantile. My goal is to have a general function that returns the noncentrality parameter that

Hi all, I am using optim() to get estimate for parameter 'a' which will minimize the output of lprob.catch(a) and I got an error message: > optim(2,lprob.catch(x, freq,1, 0.5,0.5, a,- 0.7, 1, -0.7,0.1, 1,0.2,2,1,data.sf.mont)) Error in catch2.fun(k, f1, f2, a, b, A, B, R, n0, av, index.n) : Object "a" not found Why wasn't the initial value of a=2 passed to

Hi All! I'm a new subscriber to this mailing list. I'm writing an R extension with C linked code having a minimization function letting me pass it an objective function with a GENERIC number of arguments and letting me to optimize over a specific one among them if there are many. ################################################# ############### IPOTETICAL MAIN ###############

Hi, I think that there something wrong with the 'constrOptim' max/minimization function because she doesn?t send extra arguments to 'optim' call. Fact: When I use optim in a f(x,theta)-like function, everything goes ok. But using constrOptim with the same function leads to error... Proof: Make a small change in the 'Rosenbrock Banana function' (taken from the Examples

Dear all, I have used optim a lot in contexts where it would useful to be able to iterate function myfun that, in addition to the primary objective to be minimized ('minimize.me'), could return other values such as alternative metrics of the minimization, informative intermediate values from the calculations, etc. myfun <- function() { ... return(list(minimize.me = minimize.me, R2 =

Dear R-users, I have just joint the list and much appreciate any thoughts on 2 issues. Firstly, I want to reproduce some minimization results conducted in MATLAB. I have suceeded with nlm and optim-method CG. I have been told that I should get also with other optim methods. Actually, I found the same results when testing a very straightforward equation. However with a more complicated model it

[sorry, forgot some details...] I'm using optim(param, fun, method='L-BFGS-B', lower=lo, upper=up) to minimize a certain function. Often the minimization ends with the message: ERROR: ABNORMAL_TERMINATION_IN_LNSRCH What is optim() trying to say? What have I to change in my function to make the minimization succeed? Do you think using BBoptim() instead of optim() changes anything?

The setup is a samba server with mixed clients (samba clients and windows clients). The problem, I want the linux client to mount there home to their home share on the server. The problem is, I have followed the guide mentioned below and everything works except that the linux usernames have the format domeinnaam+username as a result of which pam_mount wants to mount

Dear All, I need to calculate the optimal number of clusters for a classification based on a large number of observations (tens of thousands). Thibshirani et al. proposed the gap statistic for this purpose. Is any R code or fucntion available for this? Any help would be appreciated, including suggestions about other alternatives for the selection of an optimal number of cluster from large

Dear kind R-experts. Does anybody have an experience to use optim function? If yes, what is the main difference between two method "BFGS" vs "L-BFGS-B"? I used "BFGS" method and got what I wanted. But when I used "L-BFGS-B" the error message said that "L-BFGS-B needs finite values of fn". So that means "BFGS" method can handle even if fn