Sv: [R] lme problem ?
partha_bagchi@hgsi.com
partha_bagchi at hgsi.com
Thu Jun 3 14:35:53 CEST 1999
I just downloaded and installed R 0.64.1 and all the packages from the NT
distribution. Here is what I get:
R : Copyright 1999, The R Development Core Team
Version 0.64.1 (May 8, 1999)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type "?license" or "?licence" for distribution details.
R is a collaborative project with many contributors.
Type "?contributors" for a list.
Type "demo()" for some demos, "help()" for on-line help, or
"help.start()" for a HTML browser interface to help.
Type "q()" to quit R.
[Previously saved workspace restored]
> library(lme)
> data(Orthodont)
> fm1 <- lme(distance ~ age, data = Orthodont)
> fm1
Linear mixed-effects model fit by REML
Data: Orthodont
Log-restricted-likelihood: -221.3184
Fixed: distance ~ age
(Intercept) age
16.7611111 0.6601852
Random effects:
Formula: ~age | Subject
Structure: General positive-definite
StdDev Corr
(Intercept) 2.3226364 (Intr)
age 0.2259862 -0.607
Residual 1.3100079
> version
_
platform Windows
arch x86
os Win32
system x86, Win32
status
status.rev 0
major 0
minor 64.1
year 1999
month May
day 8
language R
>
My lme package is dated May 30, 1999.
"Troels Ring"
<tring at mail1.stofane To: "Douglas Bates" <bates at stat.wisc.edu>, "R-help"
t.dk> <r-help at stat.math.ethz.ch>
Sent by: cc:
owner-r-help at stat.ma Subject: Sv: [R] lme problem ?
th.ethz.ch
06/02/99 05:14 PM
Dear Douglas Bates. I just downloaded the compiled version (I'm a poor
Windows devil, not yet having found the time to move to a more advanced
platform...) from NT- the files are dated 30.5-1999 so they are not old -
and the problem persisted....wonder what I did wrong ?
R : Copyright 1999, The R Development Core Team
Version 0.64.0 Patched (May 3, 1999)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type "?license" or "?licence" for distribution details.
R is a collaborative project with many contributors.
Type "?contributors" for a list.
Type "demo()" for some demos, "help()" for on-line help, or
"help.start()" for a HTML browser interface to help.
Type "q()" to quit R.
> library(lme)
> data(Orthodont)
> fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
Error: Singular precision matrix in level 1, block 1>
> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
warning: NA/Inf replaced by maximum positive value
Error: Singularity in backsolve at level 2, block 1>
Troels Ring, MD
Department of Nephrology
Aalborg Hospital
Aalborg Denmark
-----Oprindelig meddelelse-----
Fra: Douglas Bates <bates at stat.wisc.edu>
Til: Troels Ring <tring at mail1.stofanet.dk>
Cc: Jose Pinheiro <jcp at research.bell-labs.com>; Saikat DebRoy
<saikat at stat.wisc.edu>
Dato: 2. juni 1999 22:38
Emne: Re: [R] lme problem ?
>"Troels Ring" <tring at mail1.stofanet.dk> writes:
>
>> Dear friends. I tried the session below with 10 MB in both vsize and
>> nsize but didn't get the example work. Is this a problem in LME or
>> in me or both or somewhere else or undefined ?
>
>> > library(lme)
>> > data(Orthodont)
>> > fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
>> Error: Singularity in backsolve at level 2, block 1>
>> > fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
>> Error: singular matrix in chol
>
>That looks to me like a relatively old version of lme. I would
>suggest installing a new version. Your example works fine with the
>"lme du jour" which is version 3.0b8-1, available at the CRAN sites in
>the src/contrib directory.
>
> R> fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
> R> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
> R> gc() # check amounts of storage in use
> free total
> Ncells 575483 800000
> Vcells 2015987 2097152
>
>I'm currently working on the 3.0b8a version that corrects some minor
>gliches in 3.0b8 and enhances the nls capabilities. I hope to upload
>that tomorrow.
>
>This is as good a time as any to announce that we uploaded an nls
>(nonlinear least squares) package for R last weekend. For historical
>reasons the nls package requires that you have the lme package
>installed. Many of the enhancements to nls for S were written as part
>of the NLME library and the R version of NLME is the lme package.
>(Now that I write this all out it doesn't make as much sense as it
>seemed to earlier but ...)
>
>There is also a package for R called NISTnls. This package includes
>the data and models for the nonlinear least squares examples at the
>U.S. National Institute for Standards and Technology (NIST). By
>running the examples in that package you can check the nls function
>itself.
>
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