similar to: behavior of L-BFGS-B with trivial function triggers bug in stats4::mle

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! 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),

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)

Hi I have the following formula (I hope it is clear - if no, I can try to do better the next time) h(x, a, b) = integral(0 to pi/2) ( ( integral(D/sin(alpha) to Inf) ( ( f(x, a, b) ) dx ) dalpha ) and I want to do an mle with it. I know how to use mle() and I also know about integrate(). My problem is to give the parameter values a and b to the

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 everyone! I am using the mle {stats4} to estimate the parameters of distributions by MLE method. I have a problem with the examples they provided with the mle{stats4} html files. Please check the example and my question below! *Here is the mle html help file * http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html

Hello to all, I'm a biologist trying to tackle a "fish" (Poisson Regression) which is just too big for my modest understanding of stats!!! Here goes... I want to find good literature or proper mathematical procedure to calculate a confidence interval for an inverse prediction of a Poisson regression using R. I'm currently trying to analyse a "dose-response"

R 2.3.0 Linux, SuSE 10.0 Hi I have two problems with mle - probably I am using it the wrong way so please let me know. I want to fit different distributions to an observed count of seeds and in the next step use AIC or BIC to identify the best distribution. But when I run the script below (which is part of my original script), I get one error message for the first call of mle: Error in

I am using mle as a wrapper from optim( ). How would I extract the convergence code, to know that optim( ) converged properly? Thanks, Stephen Collins, MPP | Analyst Global Strategy | Aon Benfield [[alternative HTML version deleted]]

Dear All, There are two things about mle() that I wasn't so sure. 1) can mle() handle vector based parameter? say ll<-function(theta=rep(1,20)){..............} I tried such function, it worked for "optim" but not for "mle". 2) is there a general suggestion for the maximum number of parameters allowed to use in mle() or optim()? Thank you. Regards, MJO

Hi R fans, As a newbie following the five-hour rule (after hitting my head against the wall for five hours, post to this list), I am appealing for some help understanding geom_rect() in ggplot2. What I want to do is very simple. I want to generate a plot of rectangles. Each one represents a business cycle. The x-values will be pairs representing the start and end of each cycle. The y-values

plot.hclust: Setting up a window for a dendrogram assumes the first link is the shortest and the last is the longest. This is not always the case when the clustering was done with hclust, method="median" or method="centroid", and the dendrogram sometimes doesn't fit within the window. I propose the fix listed below. src/main/ --- plot.c Wed Sep 17 01:03:39 2003 +++

Dear R-ers, I hope there is a really simple solution to my problem. I've written a function that I saved in an .r file. I source this file in my code. For a while it worked fine. But then when I run the line: source("F mylineplot.r") I started getting a warning: In readLines(file) : incomplete final line found on 'F mylineplot.r' I have no idea why - I tried to check and

Hi the list, I am experiencing several issues with profile.mle (and consequently with confint.mle) (stat4 version 2.9.2), and I have to spend a lot of time to find workarounds to what looks like interface bugs. I would be glad to get feedback from experienced users to know if I am really asking too much or if there is room for improvement. * Problem #1 with fixed parameters. I can't

Hello I have created a graph using the following commands: <<< startBReP3O1T <- diffs$BReP3O1T - diffs$diff_BReP3O1T endBReP3O1T <- diffs$BReP3O1T x <- seq(47,89, length = 10) ymin <- min(min(startBReP3O1T), min(endBReP3O1T)) ymax <- max(max(startBReP3O1T), max(endBReP3O1T)) y <- seq(ymin, ymax, length = 10) plot(x,y, type = 'n', xlab = 'Age', ylab =

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: >

Dear R gurus, I want to wrap labels that are too long for a plot. I have looked at strsplit(), substr(), nchar(), and strwrap(). I think it's some combination but I'm having difficulty trying to figure out the right combo. I think I need to create some new matrix containing the labels already split, though I'm not sure if maybe there is a quick and dirty way to address this

I have a xml exported by Manifold GIS but I'm not being able to import it into R using XLM package. The file have this structure: <?xml version="1.0" encoding="UTF-8" ?> - <layout> <name>Layout 2</name> <pagesByX>1</pagesByX> <pagesByY>1</pagesByY> - <elements> <legend

Greetings! I would like to be able to specify a fixed (say) lower limit for plotting, while leaving the upper limit "floating, when plotting. The context is that the maximum in the data to be plotted is unpredictable, being the consequence of a simulation, whereas I know that it cannot be less than (say) 0; and I want to fix the lower limit at 0 in any plot, leaving the upper limit to be