Displaying 20 results from an estimated 300 matches similar to: "What is the degrees of freedom in an nlme model"
2011 May 27
1
Put names in the elements of lapply result
Dear list,
I am running some linear regressions through lapply,
>lapply(c('EMAX','EC50','KOUT','GAMMA'),function(x)confint(lm(get(x)~RR0,dataset2)))
I got results like
[[1]]
2.5 % 97.5 %
(Intercept) 0.6595789212 0.8821691261
RR0 -0.0001801771 0.0001489083
[[2]]
2.5 % 97.5 %
(Intercept) -63.83694930
2008 Nov 26
1
Request for Assistance in R with NonMem
Hi
I am having some problems running a covariate analysis with my
colleage using R with the NonMem program we are using for a graduate
school project. R and NonMem run fine without adding in the
covariates, but the program is giving us a problem when the covariate
analysis is added. We think the problem is with the R code to run the
covariate data analysis. We have the control stream, R code
2005 Jul 13
1
Fieller's Conf Limits and EC50's
Folks
I have modified an existing function to calculate 'ec/ld/lc' 50 values
and their associated Fieller's confidence limits. It is based on
EC50.calc (writtien by John Bailer) - but also borrows from the dose.p
(MASS) function. My goal was to make the original EC50.calc function
flexible with respect to 1) probability at which to calculate the
expected dose, and 2) the link
2005 Aug 25
4
covariance matrix under null
Hello
I am fitting a Cox PH model using the function coxph(). Does anyone know how
to obtain the estimate of the covariance matrix under the null hypothesis.
The function coxph.detail() does not seem to be useful for this purpose.
Thanks,
KD.
[[alternative HTML version deleted]]
2009 Aug 19
3
Fitting a logistic regression
Hello,
I have this data:
Time AMP
0 0.2000000
10 0.1958350
20 0.2914560
40 0.6763628
60 0.8494534
90 0.9874526
120 1.0477692
where AMP is the concentration of this metabolite with time. If you plot
the data, you can see that it could be fitted using a logistic
regression. For this purpose, I used this code:
AMP.nls <- nls(AMP~SSlogis(Time,Asym, xmid, scal), data
2009 May 20
2
drc results differ for different versions
Hello,
We use drc to fit dose-response curves, recently we discovered that
there are quite different standard error values returned for the same
dataset depending on the drc-version / R-version that was used (not
clear which factor is important)
On R 2.9.0 using drc_1.6-3 we get an IC50 of 1.27447 and a standard
error on the IC50 of 0.43540
Whereas on R 2.7.0 using drc_1.4-2 the IC50 is
2002 Aug 27
5
probit etc. for dose-response modeling
Hello all
I have done some fitting of pnorm functions to dose-response data, so I could
calculate EC50 values (dose where the response is 0.5). I used the nlm function
for this, so I did not get any information about the confidence intervals of
the fitted parameters.
What would be a good way to do such a probit fit, or is there a package which I
could use?
Best regards
Johannes Ranke
2011 Oct 12
2
Nonlinear regression aborting due to error
Colleagues,
I am fitting an Emax model using nls. The code is:
START <- list(EMAX=INITEMAX, EFFECT=INITEFFECT, C50=INITC50)
CONTROL <- list(maxiter=1000, warnOnly=T)
#FORMULA <- as.formula(YVAR ~ EMAX - EFFECT * XVAR^GAMMA / (XVAR^GAMMA + C50^GAMMA)) ## alternate version of formula
FORMULA <- as.formula(YVAR ~ EMAX - EFFECT / (1 + (C50/XVAR)^GAMMA))
FIT <-
2010 Nov 22
2
Probit Analysis: Confidence Interval for the LD50 using Fieller's and Heterogeneity (UNCLASSIFIED)
Classification: UNCLASSIFIED
Caveats: NONE
A similar question has been posted in the past but never answered. My
question is this: for probit analysis, how do you program a 95%
confidence interval for the LD50 (or LC50, ec50, etc.), including a
heterogeneity factor as written about in "Probit Analysis" by
Finney(1971)? The heterogeneity factor comes into play through the
chi-squared
2008 Jul 22
1
Lattice: How to draw curves from given formulae
Dear R Users:
I have a list function as:
Flat: y = 0
Linear: y = -(1.65/8)d
Logistic: y = 0.015 - 1.73/{1+exp[1.2(4-d)]}
Umbrella: y= -(1.65/3)d + (1.65/36)d^2
Emax: y = -1.81d/(0.79+d)
Sigmoid Emax: y = -1.70d^5/(4^5+d^5)
And want draw the figure as attached (those material are extracted from a
paper). Could anyone give me a sample code to do this?
Thanks
2014 Feb 18
1
Problems with admin interface / beta4
Hi folks,
I've been running icecast-2.3.99.3 in production since it was released.
It solved a problem of the icecast process terminating from time to time
and appears quite stable.
In the process of moving to new servers I noticed beta 4 and compiled it
for FreeBSD 10 on a dell poweredge.
I have been unable to get the administrative interface working properly.
You can view
2011 Sep 13
0
nls, the four parameter logistic equation, and prediction band
The error msg is telling you that R cannot evaluate the loss function, so you should not
expect answers.
You might try examining the data -- Are there NA or Inf entries?
Or prepare a dataframe with just X and Y, sort by X and graph.
Then check the nls computations by sampling, say, every 100 X's to give you a dataset with
about 160 observations. If that doesn't work, it is at least
2011 Sep 13
0
nls, the four parameter logisitc equation, and prediction band
I have uploaded a datafile that contains the following two variables: time
(X value) and response (Y value). This is a fairly extensive file (with >
16000 entries). I have two questions:
1. I want to use the following equation to regress Y on X: Y-hat = min +
(max-min)/(1 + (X/EC50)^Hillslope).
Here is my R command:
nlsout <- nls(Y ~ (0 - (100-0)/(1 + (X/EC50)^hill)), start=c(EC50=125,
2009 Dec 07
0
Help required with NLME syntax
Hi there,
I am attempting to analyse data from a crossover study using a mixed
effect Emax model in R using nlme. I am having problems ascertaining how
to fit the model.
Subjects are randomly assigned to 1 of 4 treatments in a complete block
design. The response variable of interest is recorded once within each
period. So, subjects have a response for each period.
Specifically, I want to fit
2014 Jun 13
2
no x label using axis.Date
I have tried multiple different methods to figure out how to get a date axis
of my preference (start date of each month). Any assistance would be
appreciated.
The below section is not producing a date axis:
plot(totaldays$totaldays,totaldays$y,type="n",ylim=c(0,Emax),xaxt="n")
*xlabels<-(strptime(totaldays$totaldays,"%Y-%m-%d",tz=""))
2009 Aug 19
1
Best performance measure?
Hello,
I working on a model to predict probabilities.
I don't really care about binary prediction accuracy.
I do really care about the accuracy of my probability predictions.
Frank was nice enough to point me to the val.prob function from the
Design library. It looks very promising for my needs.
I've put together some tests and run the val.prob analysis. It produces
some very
2011 Oct 22
5
interpreting bootstrap corrected slope [rms package]
Dear List:
Below is the validation output of a fitted ordinal logistic model
using the bootstrap in the rms package. My interpretation is that
most of the corrected indices indicate little overfitting, however the
slope seems to indicate that the model is too optimistic. Given that
most of the corrected indices seem reasonable, would it be appropriate
to use this model on future data if the
2005 May 26
0
Confidence intervals for prediction based on the logistic equation
Greetings,
We are performing a meta-analysis of mink pup survival data versus
chemical concentration. We have modeled percent survival successfully
using nls as shown below and the plot. What we need to do is construct a
confidence interval on the concentration at which we get 50% survival
(aka the EC50, although we may want other percent survivals in the
future). My first question is, what seems
2011 May 15
5
Question on approximations of full logistic regression model
Hi,
I am trying to construct a logistic regression model from my data (104
patients and 25 events). I build a full model consisting of five
predictors with the use of penalization by rms package (lrm, pentrace
etc) because of events per variable issue. Then, I tried to approximate
the full model by step-down technique predicting L from all of the
componet variables using ordinary least squares
2006 Oct 12
0
4PL algorithm
WinXP, Splus7 and R2.3.1.
All,
I have been using the SSfpl and SSlogis self-starting functions
in the nlme library to fit 4PL and restricted 4PL models. I need
to adapt these routines to fit the alternative model
f(x) = A + (B-A)/(1 + abs(x/EC50)^C)
My Question: How do I obtain good starting values for this alternative
model?
(The pseudo-code found on pages 517 - 520 of "Mixed