similar to: Help on adding a negative binomial density plot

> On Oct 2, 2017, at 2:05 AM, David <dasolexa at hotmail.com> wrote: > > Dear list, > > > I am just starting on analysis of count data in R 3.4.0. My dataset was obtained from counting particles on a surface before andd after a cleaning process. The sampling positions on the surface are pre-defined and are the same before and after cleaning. I have ~20% of 0's. I

Dear David, thanks ever so much for your answer. Do you mean predicting the original values based on the fitted model and then comparing observed vs. predicted by, for example, a scatterplot? Thanks, David ________________________________ De: David Winsemius <dwinsemius at comcast.net> Enviado: lunes, 2 de octubre de 2017 18:18:36 Para: David Cc: R-help Asunto: Re: [R] Help on

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 15-03-23 12:55 PM, Thierry Onkelinx wrote: > Dear Ben, > > Last week I was struggling with incorporating lme4 into a package. > I traced the problem and made a reproducible example ( > https://github.com/ThierryO/testlme4). It looks very simular to > the problem you describe. > > The 'tests' directory contains

I'm sorry I haven't boiled this down to a more-minimal example yet, but ... I'm working on an S3 method (tidy.merMod, in the 'broom' package). It normally handles 'merMod' objects from the lme4 package, but I'm trying to make it handle 'merModLmerTest' objects from the lmerTest package too. The merModLmerTest class inherits (as an S4) class from the

Hi, The R CMD check is successful in R 3.0.1 but fails to install package lmerTest under R-devel r63910, Here is what I get: ** preparing package for lazy loading Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : no definition was found for superclass "merMod" in the specification of class "merModLmerTest" In DESCRIPTION file I have:

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 WARNING: this is long. Sorry I couldn't find a way to compress it. Is there a reasonable way to design an update method so that it's robust to a variety of reasonable use cases of generating calls or data inside or outside a function? Is it even possible? Should I just tell users "don't do that"? * `update.default()` uses

Hi, The code below is giving me this error message: Error in while (err > eps) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In dnbinom(x, size, prob, log) : NaNs produced 2: In dnbinom(x, size, prob, log) : NaNs produced I know from the help files that for dnbinom "Invalid size or prob will result in return value NaN, with a warning", but I am not able

Hepp! I am sitting in a remote country trying to reboot my server at home. Services are running, but the filesystem seems to be unreachable. I can ssh into the system, but when entering interactive mode, nothing happens and the session is terminated. Then I thought - what if sshd had builtins like bash, so that i could send a "reboot" command to the ssh daemon instead "ssh system

Full_Name: Andrey Pavlov Version: 2.7.1 (2008-06-23) OS: Windows Vista Submission from: (NULL) (67.193.233.43) Dear developers, I discovered an issue with the dnbinom function while fitting a negative binomial model to my data. I was using the size and mu parameterization. When the size gets large enough, the function begins to return 1, while it should instead return the respective Poisson

This came up on r-help but indicates a bug. dnbinom(x,n,p) calls dbinom_raw(n-1,...) which returns 0 for n<1. -thomas ---------- Forwarded message ---------- Date: Thu, 08 Feb 2001 17:10:23 +0000 From: Yudi Pawitan <yudi@stat.ucc.ie> To: Mark Myatt <mark@myatt.demon.co.uk> Cc: R-Help <r-help@stat.math.ethz.ch> Subject: Re: [R] Goodness of fit to Poisson / NegBinomial

Dear R-help gurus (and T.Yee, the VGAM maintainer) - I've been banging my head against the keyboard for too long now, hopefully someone can pick up on the errors of my ways... I am trying to use optim to fit a zero-inflated negative binomial distribution. No matter what I try I can't get optim to recognize my initial parameters. I think the problem is that dnbinom allows either

Dear R community, I would like to compare the degree of aggregation (or dispersion) of bacteria isolated from plant material. My data are discrete counts from leaf washes. While I do have xy coordinates for each plant, it is aggregation in the sense of the concentration of bacteria in high density patches that I am interested in. My attempt to analyze this was to fit negative binomial

Dear All, I hope I am not asking a FAQ. I am dealing with a problem of graph theory [connected components in a non-directed graph] and I do not want to rediscover the wheel. I saw a large number of R packages dealing for instance with the k-means method or hierarchical clustering for spatially distributed data and I am basically facing a similar problem. I am given a set of data which are the

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 ~ turns out I don't need to look at the C code. ~ if one uses the mu/size parameterization of the negative binomial, R computes size/(size+mu) to switch parameterizations. If size>>mu this gets rounded to 1 ... should be easy enough to test and return NA under these circumstances? function (x, size, prob, mu, log = FALSE) { ~ if

Hello veryone, I am interested in the diffusion of particles inside a sphere, and its release through a small pore on the sphere surface. Unfortunately, I have not found the way to do this in R. Could you help me? Thank very much in advance for your help

Hello, After putting together interaction code that worked for a single pair of interactions, when I try to evaluate two pairs of interactions( flowers*gopher, flowers*rockiness) my computer runs out of memory, and the larger desktop I use just doesn't go anywhere after about 20 minutes. Is it really that big a calculation? to start: mle2(minuslogl = Lily_sum$seedlings ~ dnbinom(mu = a,

Dear Ben, you answerd to Nancy Shackelford about Clarks 2Dt function. Since the thread ended just after your reply, I would like to ask, if you have an idea how to use this function in R I defined it the following way: function(x , p, u) { (p/(pi*u))*(1+(x^2/u))^(p+1) } and would like to fit this one to my obeservational data (count) [,1] [,2] [1,] 15 12 [2,] 45 13 [3,]

All, I have some data on parasites on apple leaves and want to do a goodness of fit test to a Poisson distribution. This seems to do it: mites <- c(rep(0,70), rep(1,38), rep(2,17), rep(3,10), rep(4,9), rep(5,3), rep(6,2), rep(7,1)) tab <- table(mites) NSU <- length(mites) N <-

I am using the package Multicore/Parallel to do importance sampling. I have 5 cores on my computer. And I have let's say 10 000 particles to generate. What I did was to send 5 particles in each time, calling the package parallel. Which means in all I am calling the parallel command 2000 times. What happens is in the end somewhere along the way I end up with the error message error in fork

Hi, Maybe this is more a programming questions than a specific R-project question, but maybe there is someone who can point me in the right direction. I have a picture of cirkels which I took with a digital camera. Now I want to use the diameter of the cirkels on the picture for analysis in R. I can use pixmap to import the picture, but how do I find the outside cirkels and calculate the