similar to: How to use mle or similar with integrate?

So, I've embarked on my threatened modifications to the mle subset of the stats4 package. Most of what I've done so far has *not* been adding the slick formula interface, but rather making it work properly and reasonably robustly with real mle problems -- especially ones involving reasonably complex fixed and default parameter sets. Some of what I've done breaks backward

Hi! This is a repost of an earlier message (with a clearer example demonstrating the problem I ran into). If you run the mle example in stats4 library(stats4) x <- 0:10 y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) ll <- function(ymax=15, xhalf=6) -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) (fit <- mle(ll)) plot(profile(fit),

With the exception of "L-BFGS-B", all of the other optim() methods return the value of the function when they are given a trivial function (i.e., one with no variable arguments) to optimize. I don't think this is a "bug" in L-BFGS-B (more like a response to an undefined condition), but it leads to a bug in stats4::mle -- a spurious error saying that a better fit has been

The mle2 function (bbmle library) gives an example something like the following in its help page. How do I access the coefficients, standard errors, etc in the summary of "a"? > x <- 0:10 > y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) > LL <- function(ymax=15, xhalf=6) + -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) > a <- mle2(LL,

Hi the list, I would need some advice on something that looks like a FAQ: the possibility of providing vectors to optim() function. Here is a stupid and short example summarizing the problem: -------------------------------- example 1 ------------ 8< ---------------------- library(stats4) data <- rnorm(100,0,1) lik1 <- function(m, v, data) { N <- length(data) lik.mean <-

Hi R people, I have a very basic question to ask - I'm sorry if it's been asked before, but I searched the archives and could not find an answer. All the examples I found were much more complicated/nuanced versions of the problem - my question is much more simple. I have data with multiple, nested fixed effects (as I understand it, fixed effects are specified by the experimental design

I sent this in first on 30 July. Now that UseR! is over I'm trying again (slightly extended version from last time). With R 2.5.1 or R 2.6.0 (2007-08-04 r42421) "L-BFGS-B" behaves differently from all of the other optim() methods, which return the value of the function when they are given a trivial function (i.e., one with no variable arguments) to optimize. This is not a bug in

Hi, Does anyone know of a function in R that can handle a fractional variable as the dependent variable? The catch is that the function has to be inclusive of 0 and 1, which betareg() does not. It seems like GLM might be able to handle the fractional logit model, but I can't figure it out. How do you format GLM to do so? Best, Rachael [[alternative HTML version deleted]]

Hello: I wish to again express my appreciation to all who have contributed to making R what it is today. At this moment, I'm particularly grateful for whoever modified the 'mle' code so data no longer need be passed via global variables. I remember struggling with this a couple of years ago, and I only today discovered that it is no longer the case. I'd

Hi, How can we set the environment for the minuslog function in mle()? The call in this code fails because the "ll" function cannot find the object 'y'. Modifying from the example in ?mle: library(stats4) ll <- function(ymax=15, xhalf=6) { -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) } fit.mle <- function(FUN, x, y) { loglik.fun <- match.fun(FUN)

Dear R developers, I noticed a bug in the stats4 package, specifically in the confint method applied to ?mle? objects. In particular, when some ?fixed? parameters define the log likelihood, these parameters are stored within the mle object but they are not used by the ?confint" method, which retrieves their value from the global environment (whenever they still exist). Sample code: >

Hello guys, I'm using llvm 3.3 on windows with mingw (triple: "i386-unknown-mingw32") to compile IR code that my program generates. I do it in two phases: first I emit assembly code and then assemble it. TargetMachine targetMachine = target.createTargetMachine(triple); targetMachine.setAsmVerbosityDefault(true); targetMachine.setFunctionSections(true);

Full_Name: Elizabeth Purdom Version: 1.9.1 OS: Windows XP Submission from: (NULL) (171.64.102.199) It would be nice if names(obj) would give slot names as well. Since for many people slots are new, the first thing that happens is you try to access what's in them and can't find how to do it. If you don't know that slotNames() exists, it can be very frustrating. Moreover, if you

I need to repeat a function many times, with differing parameters held constant across iterations. To accomplish this, I would like to create a list (or vector) of parameters, and then insert that list into the function. For example: q<-("l,a,b,s") genericfunction<-function(q){ } ###### The equivalent code would of course be genericfunction<-function(l,a,b,s){ } Any help

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Hello everybody, I am beginning with loops and functions and would be glad to have help in the following question: If i have a dataframe like this Site Prof H 1 1 24 1 1 16 1 1 67 1 2 23 1 2 56 1 2 45 2 1 67 2 1 46 And I would like to create a new column that subtracts the minimum of H from H, but for S1 and P1 only

Currently it's possible to corrupt FLAC file with flac and metaflac tools. If image filesize is just slightly less than 2^24 bytes then the size of PICTURE metadata block will be more that this limit. The first patch (fix1.patch) adds additional check in /share/grabbag/picture.c/read_file() and removes rather useless check from FLAC__metadata_object_picture_set_data(). It's enough to fix

Hello, I'm trying to estimate a cox model with a frailty variable and time-dependent covariate (below there is the statement I use and the error message). It's seems to be impossible, because every time I add the time-dependent covariate the model doesn't converge. Instead, if I estimate the same model without the time-dependent covariate it's converge. I'd like knowing if

Hi! I am using xen-tools version: 3.9-4 to create domUs: 1. time xen-create-image --verbose --dist=lenny --install-source=/mnt/xen-file-images/lenny-64-template-debootstrap-30Jun09-fix2.tar --hostname dummy --ip xxx.xxx.xxx.xxx --force 2. xm create dummy.cfg Then I get the message Device /dev/vg0/dummy-disk is mounted in the privileged domain, and so cannot be mounted by a guest. 3. When I

Hi, R developers. when running mle inside a loop I found a nasty behavior. From time to time, my model had a degenerate minimum and the loop just crashed. I tracked it down to "vcov <- if (length(coef)) solve(oout$hessian)" line, being the hessian singular. Note that the minimum reached was good, it just did not make sense to calculate the covariance matrix as the inverse of a