similar to: Error in library (nls)

Hi everybody, i'm trying to draw rarefaction curves to estimate a population size from genotyped faeces. I used the Gimlet software which gave me a script and a "rarefaction.txt" file. I've copied both files in the work directory of R. I changed library(nls) by library(stats) in the script. But now, i'm still unable to run it. If i ask to show error messages, the software

Here's a question for ecologists on the r-help list-- I'm addressing this to ecologists in particular because they're most likely to be familiar with the equation in question but I'll be happy to discuss the problem with anyone who's willing to take a whack at it. I'm trying to write a function to calculate the large sample variance of species richness estimates by

Hello! I am eager to learn if I only have a data about the relationship between otu and sample, could I use the function capscale, and final make a point plot that x-axis is CAP1 and y-axis is CAP2? Besides, what function could I use to make the different rarefaction curve with different color in the a plot in R? Appreciate very much.

Hi, I've noticed I get different results fitting a function to some data on my laptop to when I do it on my computer at work. Here's a code snippet of what I do: ##------------------------------------------------------------------ require(circular) ## for Bessel function I.0 ## Data: dd <- c(0.9975948929787, 0.9093316197395, 0.7838819026947, 0.9096108675003, 0.8901804089546,

I've been struggling to get a loop to work. I want to create a new variable in each loop with data from some function. for example: # part of the names for the variables to be created Frags <- c("F04", "F05", "F07", "F09", "F11", "F13", "F14", "F17", "F18", "F19", "P20",

Dear all community, My issue is related to the R package (made4) that permits me to calculate the RV coefficient of co-inertia. However, it is a theoretical question. And if I am not mistaken, the list Usenet groups sci.stat.consult is not currently active. Let me explain briefly: Through different microbiota datasets, I have plotted PCoA, db-RDA and sPLS-DA using 3 different types of

Hi List, I’m using the vegan function specaccum to produce a rarefaction curve. In the function’s help it says: “Function ‘specaccum’ finds species accumulation curves or the number of species for a certain number of sampled sites or individuals”. Well, I would like to finds this curve for individuals, but when I compute it the function (using the ‘rarefaction’ method) gives me Sites, Richness

Dear all Nobody responded to my previous post so far so I try with more offending subject. I just encountered a strange problem with nls formula. I tried to use nls in cycle but I was not successful. I traced the problem to some parse command. Here is an example DF<-data.frame(x=1:10, y=3*(1:10)^.5+rnorm(10)) coef(lm(log(DF[,2])~log(DF[,1]))) (Intercept) log(DF[, 1]) 0.7437320

I'm drawing a fitted normal distribution over a histogram. The use case is trivial (fitting normal distributions on densities) but I want to extend it to other fitting scenarios. What has stumped me so far is how to take the list that is returned by nls() and use it for curve(). I realize that I can easily do all of this with a few intermediate steps for any specific case. But I had expected

I haven't followed your example closely, but can't you use the predict() method for this? To draw a curve, the function that will be used in curve() sets up a newdata dataframe and passes it to predict(fit, newdata= ...) to get predictions at those locations. Duncan Murdoch On 17/10/2020 5:27 a.m., Boris Steipe wrote: > I'm drawing a fitted normal distribution over a

Dear Friends. I tried to use nls.control() to change the 'minFactor' in nls( ), but it does not seem to work. I used nls( ) function and encountered error message "step factor 0.000488281 reduced below 'minFactor' of 0.000976563". I then tried the following: 1) Put "nls.control(minFactor = 1/(4096*128))" inside the brackets of nls, but the same error message

Hi all, I used R (vegan package) to make rarefaction curves and I calculated the Chao index for each curve. However, the plateau is far from reached. What I want to do now is the following: Based on the Chao index, I want to extrapolate the curve so I get an x-value which gives me an estimation of the total number of clones I'd have to pick up and sequence in order to have a full coverage of

Dear R helpers, For an allometric analysis (allometric equation y = a*x^b) I would like to apply a non-linear regression instead of using log-log transformations of the measured parameters x and y and a Model II linear regression. Since both of the variables x and y are random, I would like to apply a Model II non-linear analog of either Reduced Major Axis or Major Axis Regression. The

Dear List-Members, since 3 weeks I have been heavily working on reproducing the results of an economic paper. The method there uses the numerical solution of an integral within nonlinear least squares. Within the integrand there is also some parameter to estimate. Is that in the end possible to implement in R [Originally it was done in GAUSS]? I'm nearly into giving up. I constucted an

Dear friends. I use nls() and encounter the following puzzling problem: I have a function f(a,b,c,x), I have a data vector of x and a vectory y of realized value of f. Case1 I tried to estimate c with (a=0.3, b=0.5) fixed: nls(y~f(a,b,c,x), control=list(maxiter = 100000, minFactor=0.5 ^2048),start=list(c=0.5)). The error message is: "number of iterations exceeded maximum of

Hello, I am running a simple nls model (which a friend ran OK) but I get the following error: Error in nls(y ~ R * (1 - (x/K)^2), data = nls.dat, start = list(R = 0.3, : object 'R_nls_iter' not found Does anyone know what the 'R_nls_iter' error is? The data are: x=1:8 ; y=c(14,19,25,34,43,56,69,76) # starting values: R=.3, K=94 Thanks in advance. Jeff

Dear list, I have encountered a problem with predict.nls (Windows XP, R.2.5.0), but I am not sure if it is a bug... On the nls man page, an example is: DNase1 <- subset(DNase, Run == 1) fm2DNase1 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)), data = DNase1, start = list(xmid = 0, scal = 1)) alg = "plinear", trace =

Hi all, I need to use the parameter estimates of nls() for further analysis. I know how to do in S+, e.g. nls(...)$parameters. In R, the attributes(nls(...)) does not have parameters, how would one get the parameter values out of nls()? Thanks in advance. Nancy

I want to fit the model y=a*x^b using nls; where "a" should be different for each level of a factor. What is the easiest way to fit it? Can i do it with nls? I've looked the help pages and the MASS example in page 249 but the formula is different and I don't know how to specify it for my model. Thanks, Manuel [[alternative HTML version deleted]]

Hello, I am trying to bootstrap a function that extracts the log-likelihood value and the nls coefficients from an nls object. I want to sample my dataset (pdd) with replacement and for each sampled dataset, I want to run nls and output the nls coefficients and the log-likelihood value. Code: x<-c(1,2,3,4,5,6,7,8,9,10) y<-c(10,11,12,15,19,23,26,28,28,30) pdd<-data.frame(x,y)