similar to: Integration problem: error in invoking an outside function

I am having a problem with optim() using the "L-BFGS-B" method. When I set the lower limit for the third parameter equal to zero I get an error message: > low.lim.3 <- 0 > phi_opt <- optim(phi_, model_lik, NULL, method = "L-BFGS-B", lower=c(0.2, -100, low.lim.3, 0), upper= c(10, 100, 10, 10), control = list(maxit = 1000, parscale = c(0.2, u1, 0.002, 0.002), trace =

Dear All, I would like to use the simprof function (clustsig package) but the available distances do not include Jaccard distance, which is the most appropriate for pres/abs community data. Here is the core of the function: > simprof function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average", method.distance = "euclidean", method.transform =

All, We are researching approaches to parallel R with the end goal of running R in a distributed manner on a Linux cluster. We expect of course to do some work decomposing our problems to be task-parallel or data-parallel, but wouldn't mind getting an initial boost working with "embarrassingly parallel" code sections and one of the approaches below. Incidentally our environment

Dear R Users, I have the following glm, which I am running several times in a loop (I am not including the full code): reduced_model <- NULL; full_model <- NULL; reduced_model <- try(glm.fit(X4,n,family=poisson(link="log"))) full_model <- try(glm.fit(X5,n,family=poisson(link="log"))); On some occasions, an error is produced, which is why I have attempted to work

Dear R-experts, this is not a direct R-problem but I hope you can help me anyway. I would like to minimize || PG-I || over P, where P is a p x p permutation matrix (obtained by permuting the rows and/or columns of the identity matrix), G is a given p x p matrix with full rank and I the identity matrix. ||.|| is the frobenius norm. Does anyone know an algorithm to solve such a problem? And if

Hi, I use nnet for my classification problem and have a problem concerning the calculation of the final value for my validation data.(nnet only calculates the final value for the training data). I made my own final value formula (for the training data I get the same value as nnet): # prob-matrix pmatrix <- cat*fittedValues tmp <- rowSums(pmatrix) # -log likelihood

Dear R Programmers, I am trying to run a Poisson regression on all pairs of variables in a data set and obtain the permutation distribution. The number of pairs is around 100000. It seems my code will take weeks to run, unless I try something else. Could you give me any suggestions on how to improve the speed of the code below, or any general suggestions on how I may accomplish this task. Thanks

Dear all, In my dataset I have 12 columns and 5824 rows. The second column contains information about the height of a claim: it might be zero or positive. I would like to do an analysis on the positive part of this matrix, but I do need the other colums with this. So if there are like 1000 rows where the second column is positive, I would like to extract this 1000x13 matrix into another matrix.

Estimada comunidad, tengo el siguiente problema: Un data.frame con muchas filas de las que debo eliminar aquellas que cumplen varios criterios al mismo tiempo. Por ejemplo este data.frame: sol con dia NCar NIns isom area rep tipo 1 con 0.001 1 160s 0 s 6.083543e-01 1 2 con 0.001 1 161c 1 c 1.391274e-03 1 <NA> 3 con 0.001 1 161c 1 c

Hi there, sorry for troubling everybody once again, I've got a problem rewriting Sarkar's function for rewriting the tick locations in a logaritmic way (s. http://lmdvr.r-forge.r-project.org/code/Chapter08.R): His example works for log 2 but I need log e (natural logarithm). My problem is that if I replace 2 with "e" (using paste()), I get the error message that the location

I have a lattice plot that has 4 pages with 4 columns and 8 rows per page. I wish to have the rows use a separate x-axis since their ranges are quite different, but I wish to have those same limits used on each page. By setting an element of the scales list to something like x = list(limits = lim.list$CFU, lim.list$CFU, lim.list$CFU, lim.list$CFU,

Hola de nuevo. Leí mal. Si vas a eliminar esas filas, entonces usa: sqldf("select * from graph where sol!='lim' and dia!=2") En el correo anterior seleccioné precisamente a esas descartando a las demás. Culpa de mis anteojos... jeje. On Fri, Jul 12, 2013 at 5:20 PM, Freddy Omar López Quintero < freddy.vate01@gmail.com> wrote: > ​Hola.​ > > >> Tengo que

I recently called plot(x,y) where x was an array of POSIXct timestamps, and was pleasantly surprised that it produced a nice plot right out of the box: z <- as.POSIXct(c("2006-10-26 08:00:00 EDT","2007-10-25 12:00:00 EDT")) x <- seq(z[1],z[2],len=100) y <- 1:100 plot(x,y,type="l") The X axis had nice labels, one tick mark every other month. (Plotting on

Dear R devs, For some days now (~ February, 4th), I am not able to build the recent tarballs of R-devel on a FreeBSD test box anymore. The breakage seems to be related to the newest overhaul of src/unix/system.c: [..snip..] gcc49 -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp

Hello list, I wrote a simple program to plot data on polar axes, taking advantage of the plotrix package and its function radial.plot. The basic plot works fine, but I am having difficulties with the formatting. There are three problems, but I thought I would attack them one at a time. Here is the first: If my data set contains values with all vector lengths between 0 and 100 (and various

Bueno, una pequeña vuelta de tuerca más usando ggplot.. Aunque no quedó tan limpio como el de Carlos (gran resolucion) tambien te sirve. Un saludo library(ggplot2) dec.df <- mat[mat$sol=="dec",] lim.df <- mat[mat$sol=="lim",] dol.df <- mat[mat$sol=="dol",] dec.dr<-qplot(dia,V5,sol,data=dec.df,color=con2,geom=c("line"),facets=.~sol) lim.dr

ALL: <<diffserv-gred_10-06>> I have attached the current script that I am using. $TC qdisc add dev $EDEV parent 2:20 gred setup DPs 3 default 2 grio $TC qdisc change dev $EDEV parent 2:20 gred DP 1 limit $lim min $minTh max $maxTh avpkt $avgPL burst $bursty bandwidth $netBand probability 0.02 prio 2 $TC qdisc change dev $EDEV parent 2:20 gred DP 2 limit $lim min $minTh max

Hello I'm a population ecologist and use R for all my stats and modelling. Recently I have been using R to numerically solve integral projection models. This involves constructing several large matrices. The current code by Easterling (Size-specific sensitivity: Applying a new structured population model. Ecology, 2000, 81, 694-708) uses nested loops to construct the matrices. To speed up the

Hi! I'm trying to use readline() to ask for xlim() and ylim() values for a subsequent plot. I'm doing: lim <- readline("Enter xlim and ylim values: ") then would like to use the values in lim for a plot: plot(etc, xlim=lim[1:2],ylim=lim[3:4]) The problem is that lim is a character,i.e., "10,20,-10,50" or "c(10,20,-10,50)" depending on the input to

Good evening, I would like to put the histograms of several matrices on the same graph, together on a unified histogram (instead of having one bar per value on the x-axis, have multiple bars: one representing each matrix, with different colored bars for example to distinguish between the matrices). I couldn't find a function doing that involving "hist", "plot" nor other