search for: dnase1

Displaying 17 results from an estimated 17 matches for "dnase1".

Did you mean: dnase
2018 May 05
0
Bug in profile.nls with algorithm = "plinear"
...ar sirs It seems like there is a bug in `profile.nls` with `algorithm = "plinear"` when a matrix is supplied on the right hand side. Here is the bug and a potential fix ##### # example where profile.nls does not work with `plinear` but does with # `default` require(graphics) set.seed(1) DNase1 <- subset(DNase, Run == 1) x <- rnorm(nrow(DNase1)) f1 <- nls(density ~ b1/(1 + exp((xmid - log(conc))/scal)) + b2 / x, data = DNase1, start = list(xmid = 0, scal = 1, b1 = 1, b2 = 1)) coef (f1) #R> xmid scal b1 b2 #R> 1.5055308 1.0455951 2.370796...
2017 Apr 01
6
Intervalos de confianza de la varianza de los residuos en un modelo no lineal.-
Hola amigos, Supongamos que se quiere ejecutar un modelo no lineal con nls. Pensemos en el ejemplo de la ayuda: DNase1 <- subset(DNase, Run == 1) fm1DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1) summary(fm1DNase1) Aquí se está modelando la densidad óptica de un ensayo relacionada de forma no lineal (logística) con (el logaritmo) de la concentración de una proteína. ¿Sabe alguien si e...
2012 Jan 20
1
nobs() and logLik()
...weights into account while nobs.nls() does not. Admittedly, the help page of nobs() states that: For 'lm' and 'glm' fits, observations with zero weight are not included. i.e. does not comment on what nls does. But I wonder whether the following behaviour is desirable: R> DNase1 <- subset(DNase, Run == 1) R> fm3DNase2 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)), + data = DNase1, weights=c(0,rep(1,14),0), + start = list(Asym = 3, xmid = 0, scal = 1)) R> nobs(fm3DNase2) [1] 16 > logLik(fm3DNase2) 'log Lik.' 42.62777 (df=4...
2004 Jul 16
1
Does AIC() applied to a nls() object use the correct number of estimated parameters?
I'm wondering whether AIC scores extracted from nls() objects using AIC() are based on the correct number of estimated parameters. Using the example under nls() documentation: > data( DNase ) > DNase1 <- DNase[ DNase$Run == 1, ] > ## using a selfStart model > fm1DNase1 <- nls( density ~ SSlogis( log(conc), Asym, xmid, scal ), DNase1 ) Using AIC() function: > AIC(fm1DNase1) [1] -78.41642 Using number of estimable coefficients (including residual error): > -2*logLik(fm1DNase1...
2007 May 31
1
predict.nls - gives error but only on some nls objects
Dear list, I have encountered a problem with predict.nls (Windows XP, R.2.5.0), but I am not sure if it is a bug... On the nls man page, an example is: DNase1 <- subset(DNase, Run == 1) fm2DNase1 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)), data = DNase1, start = list(xmid = 0, scal = 1)) alg = "plinear", trace = TRUE) Now consider prediction: > predict(fm2DNase1) [1] 0.0...
2008 Sep 10
3
writing simple function through script
Hi all, I try to write a simple function in a script. The script is as follows yo<-function(Xdata) { n<-length(Xdata[,1]) Lgm<-nls(formula=LgmFormula, data=Xdata, start=list(a=1500,b=0.1),weights=Xdata$Qe) return(Lgm) } After the execution of the script, when I call the function yo on data called NC60.DATA I get an error. #yo(NC60.DATA) Erreur dans eval(expr, envir, enclos)
2009 Nov 09
1
Parameter info from nls object
...y of a model for a large number of experimental data I thought it to be interesting to check the information provided by the summary method programmatically. Still I could not find out which method to use to get to those data. Example (not my real world data, but to show the point): [BEGIN] > DNase1 <- subset(DNase, Run == 1) > fm1DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1) > summary(fm1DNase1) Formula: density ~ SSlogis(log(conc), Asym, xmid, scal) Parameters: Estimate Std. Error t value Pr(>|t|) Asym 2.34518 0.07815 30.01 2.17e-13 ***...
2012 Sep 19
0
Discrepancies in weighted nonlinear least squares
Dear all, I encounter some discrepancies when comparing the deviance of a weighted and unweigthed model with the AIC values. A general example (from 'nls'): DNase1 <- subset(DNase, Run == 1) fm1DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1) This is the unweighted fit, in the code of 'nls' one can see that 'nls' generates a vector wts <- rep(1, n). Now for a weighted fit: fm2DNase1 <- nls(density...
2013 Feb 12
0
Deviance and AIC in weighted NLS
Dear All, I encounter some discrepancies when comparing the deviance of a weighted and unweigthed model with the AIC values. A general example (from 'nls'): DNase1 <- subset(DNase, Run == 1) fm1DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1) Now for a weighted fit: fm2DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1, weights = rep(1:8, each = 2)) in which I assign increasing weights for e...
2006 Apr 18
1
Nonlinear Regression model: Diagnostics
Hi, I am trying to run the following nonlinear regression model. > nreg <- nls(y ~ exp(-b*x), data = mydf, start = list(b = 0), alg = "default", trace = TRUE) OUTPUT: 24619327 : 0 24593178 : 0.0001166910 24555219 : 0.0005019005 24521810 : 0.001341571 24500774 : 0.002705402 24490713 : 0.004401078 24486658 : 0.00607728 24485115 : 0.007484372
2006 Sep 11
4
syntax of nlme
...and random effects without a startup object ? I thought it would be a mixture of nls and lme. after trying very hard, I ask for help on using nlme. Can someone hint me to some examples? I constructed a try using the example from nls: #variables are density, conc and Run #all works fine with nls DNase1 <- subset(DNase, Run == 1 ) fm2DNase1 <- nls( density ~ 1/(1 + exp((xmid - log(conc))/scal)), data = DNase1, start = list(xmid = 0, scal = 1), trace = TRUE) #Now I want to do a mixed model with covariate Run #how is the syntax? DNase12...
2004 Jul 16
0
Does AIC() applied to a nls() object use the correctnumber of estimated parameters?
...aley at csiro.au wrote: > > I'm wondering whether AIC scores extracted from nls() objects using > > AIC() are based on the correct number of estimated parameters. > > > > Using the example under nls() documentation: > > > > > data( DNase ) > > > DNase1 <- DNase[ DNase$Run == 1, ] > > > ## using a selfStart model > > > fm1DNase1 <- nls( density ~ SSlogis( log(conc), Asym, > xmid, scal ), > > DNase1 ) > > > > Using AIC() function: > > > > > AIC(fm1DNase1) > > [1] -78.41642 > &g...
2010 Jun 10
1
nls model fitting errors
What am I failing to understand here? The script below works fine if the dataset being used is DNase1 <- DNase[ DNase$Run == 1, ] per the example given in help(nlrob). Obviously, I am trying to understand how to use nls and nlrob to fit curves to data using R. #package=DAAG attach(codling) plot(pobs~dose) #next command returns 'step factor reduced below min factor error' m.nl...
2007 Jun 07
2
Nonlinear Regression
Hello I followed the example in page 59, chapter 11 of the 'Introduction to R' manual. I entered my own x,y data. I used the least squares. My function has 5 parameters: p[1], p[2], p[3], p[4], p[5]. I plotted the x-y data. Then I used lines(spline(xfit,yfit)) to overlay best curves on the data while changing the parameters. My question is how do I calculate the residual sum of squares.
2006 Jul 18
4
How can I extract information from list which class is nls
Hello! I work with : R : Copyright 2006, The R Foundation for Statistical Computing Version 2.3.1 (2006-06-01) On Windows XP Professional (Version 2002) SP2. At this moment I use the function "nls" combined with a selfStar model (SSmicmen, related to Michaelis-Menten equation, and provided by the "stats" package). When I realise the following operation (cf. p 59 of the
2000 Feb 14
2
Error in the inverse of a diagonal matrix?
I?m new to R so maybe this issue has been asked before and I still could not read the complete set of past messages sent to the list. I found a weird behabiour that I will explain with a simple example. Lets consider the following block of commands: > x <- diag(c(1,4,10)) > x [,1] [,2] [,3] [1,] 1 0 0 [2,] 0 4 0 [3,] 0 0 10 > invx <- x^-1 > invx
2008 Jul 08
2
nls and "plinear" algorithm
hello all i havnt had a chance to read through the references provided for the "nls" function (since the libraries are closed now). can anyone shed some light on how the "plinear" algorithm works? also, how are the fitted values obtained? also, WHAT DOES THE ".lin" below REPRESENT? thanking you in advance ###################################### i have a quick