Displaying 20 results from an estimated 11000 matches similar to: "coding nesting in data for nlme example of Wafer data set."
2004 Sep 05
1
Question to NLME, ML vs. REML
Dear all,
I am planning to use nlme library for analysis of experiments in semiconductor
industry. Currently I am using "lm" but plan to move to "lme" to handle
within wafer / wafer-to-wafer and lot-to-lot variation correctly.
So far everything is working well, but I have a fundamentel question:
NLME offers "maximum likelihood" and "restricted maximum
2005 Sep 29
1
lmer random effect model matrix question
I have one fixed effect, sor, with two levels. I have eight lots and
three wafers from each lot. I have included the data below.
I would like to fit a mixed model that estimates a covariance parameter
for wafer, which is nested in lot, and two covariance parameters for
lot, one for each level of sor. The following command fits the model
that I want, except for it estimates the correlation
2005 Oct 27
1
syntax of nlme with nesting
This may appear too elementary to some on this list, but not to me. My
apologies if this is the case. I have mastered the lme function but the
nlme function has me stumped.
I am attempting to fit a nonlinear mixed model with 4 levels of nesting.
I am getting a cryptic error message and do not know what is wrong with
the syntax of the call. This is the call:
>
2006 Nov 10
1
help with nlme function
Hello. I am trying to fit a nonlinear mixed model involving 3 parameters.
I have successfully made a self-starting function. getInitial() correctly
outputs the initial estimates. I can also use the nlsList with this
function to get the separate nonlinear fits by group. However, I get an
error message when using the nlme function. Here is the relevent code:
2006 Mar 29
1
lmer multilevel
My question relates to problems that I'm having matching lme and lmer
examples in P&B.
using Matix 0.995
In the Oxide example in p167-170 I can't get the level 2 coefficient
estimates to match
the fm1Oxide model in lme is
data(Oxide,package="nlme")
lme(Thickness~1,Oxide)
which I translate in Lmer syntax to
fm3Oxide<-lmer(Thickness~
2006 Feb 08
2
lme syntax for P&B examples
Hi helpeRs,
I've been working through some examples in Pinhiero & Bates( 2000)
trying to understand how to translate to the new Lme4 syntax but without
much luck.
Below is what I think I should do, but either the answers don't come out
the same or I get errors.
In the Oxide problems I'm particularly interested in obtaining the
levels coeficients but this options no longer seems
2005 Nov 09
1
strategies to obtain convergence using nlme
Hello. I am working on an analysis involving the nonlinear mixed model
function (nlme) in R. The data consist of measures of carbon fixation
by leaves as a function of light intensity and the parametric function
(standard in this area because it has a biological interpretation) is a
non-rectangular hyperbola. I cannot get the nonlinear mixed model
(nlme) function to converge cleanly. I am
2007 Jan 12
1
wafer map drawing
Hello R-Users!
Does anyone know of a package to draw/analyze silicon wafer maps?
Here are some examples
http://www.java2s.com/Code/Java/Chart/JFreeChartWaferMapChartDemo.htm
http://dp.pdf.com/site/products/wafermap/binmap.html
I've google'd and searched CRAN with no luck.
It seems possible for R, given the hexbin and hist2d graphs I saw at the
Graph gallery.
2006 Jun 01
1
help with syntax of nlme function
I am having difficulty understanding the syntax of the nlme() function for
nonlinear mixed models. The data frame is called Marouane.chlorophyll. The
model involves a dependent variable (Absorb) and an independent variable
(Ch.surf), which are both numeric variables in the data frame. The data are
hierarchically grouped as Espece, Plante nested within Espece, and Feuille
nested within Plante
2006 Jan 09
2
warning message from nlme
Hi all,
I tried to do a variance components using nlme, but I got the following
warning mesage
#####################################################
not meaningful for factors in: Ops.factor(y[revOrder], Fitted)
######################################################
Can someone point out what is the meaning of this warning message? I
tried to look at Ops.factor, but I don't
2004 Apr 29
1
Plot.lme error
Dear All;
Attempting to reproduce Figure 4.15 of MEMSS (p. 171) in R using
plot(Wafer, outer = ~ Wafer)
yields an error:
> plot(Wafer, outer = ~ Wafer)
Error in order(na.last, decreasing, ...) :
Argument lengths differ
The plot() produces the figure without problems for all versions of
Splus (4.5 to 6.2) on Windows. Noticing that the plot() differs slightly
between
2005 Oct 26
1
help with a self-starting function in nonlinear least squares regression.
Hello. I am having a problem setting up a self-starting function for
use in nonlinear regression (and eventually in the mixed model version).
The function is a non-rectangular hyperbola - called "NRhyperbola" -
which is used for fitting leaf photosynthetic rate to light intensity.
It has one independent variable (Irr) and four parameters (theta, Am,
alpha and Rd). I have created this
2010 Mar 18
2
Please Post Planned Contrasts Example in lme {nlme}
Hi I am running some linear and non-linear mixed effect models and would like to do some planned contrasts (a priori contrasts)
I have looked in the help and in many forums and it seems possible to do so but don't understand how to write the function and I couldn't find an example in Pinheiro and Bates.
lme {nlme} has a contrasts argument but I can't understand how to code it.
2006 Nov 13
0
help with syntax of nlme call.
I am getting an error message in a call to nlme and cannot understand what
is happening. I explain the steps below in the hope that someone can
explain the error and how to correct it.
STEP 1: Data set: name: marouane.data. This is a data frame whose first few
lines are as follows:
> marouane.data[1:13,]
species plant leaf irradiance photosynthesis chlorophyll
1
2009 Aug 21
1
trouble with Vista & reading files
All,
I am having trouble with a "read.table()" function that is inside of
another function. But if I call the function by itself, it works fine.
Moreover, if I run the script on a Mac OS X (with the default Mac OS X
version of R installed, rev 2.8), it works fine. But it does not work if I
run it on windows vista (also default Windows version of R, rev. 2.8).
Again, both
2005 Jul 07
2
Problems with nlme: Quinidine example
This concerns the "Clinical Study of Quinidine" example on page 380
of the book "Mixed-Effects Models in S and S-PLUS" by Pinheiro and Bates (2000).
I have tried to reproduce the example, but get an error:
> library(nlme)
> fm1Quin.nlme <- nlme(conc ~ quinModel(Subject, time, conc, dose, interval, lV,
lKa, lCl),
+ data=Quinidine,
+
2006 Mar 29
1
Lmer BLUPS: was(lmer multilevel)
Paul:
I may have found the issue (which is similar to your conclusion). I
checked using egsingle in the mlmRev package as these individuals are
strictly nested in this case:
library(mlmRev)
library(nlme)
fm1 <- lme(math ~ year, random=~1|schoolid/childid, egsingle)
fm2 <- lmer(math ~ year +(1|schoolid:childid) + (1|schoolid), egsingle)
Checking the summary of both models, the output is
2003 Nov 04
3
help with lme()
Hello. I am trying to determine whether I should be using ML or REML
methods to estimate a linear mixed model. In the book by Pinheiro &
Bates (Mixed-effects models in S and S-PLUS, page 76) they state that
one difference between REML and ML is that « LME models with different
fixed-effects structures fit using REML cannot be compared on the basis
of their restricted likelihoods. In
2006 Oct 30
1
nlme Error: Subscript out of bounds
Hello, I am new to non-linear growth modelling in R and I am trying to
reproduce an analysis that was done (successfully) in S-Plus.
I have a simple non-linear growth model, with no nesting. I have attempted
to simplify the call as much as possible (by creating another grouped
object, instead of using subset= and compacting the fixed and random
expressions.)
This is a what the grouped
2005 Sep 01
1
making self-starting function for nls
Hello. Following pages 342-347 of Pinheiro & Bates, I am trying to
write a self-starting nonlinear function (a non-rectagular hyperbola) to
be used in nonlinear least squares regression (and eventually for a
mixed model). When I use the getInitial function for my self-starting
function I get the following error message:
> getInitial(photo~NRhyperbola(Irr,theta,Am,alpha,Rd),dat)
Error