Dear Shirley,
If you dont have access to expensive software like Phoenix you can use this
R-script that reads your .lst file and extracts the EPSILON and ETAs. Note:
this script gives you the CORR matrix, if you want the COV matrix just
change it in the 2nd and 3rd row of the script.
#------ Extract EPSILON & ETAS from .lst ---
lst <- readLines(paste("YOUR_LIST_FILE.lst",sep="")) # Read in .lst file
row_startOMEGA <- grep("OMEGA - CORR MATRIX FOR RANDOM EFFECTS - ETAS
*******", lst, fixed=T) # Find the start of CORR MATRIX - ETAS
row_startSIGMA <- grep("SIGMA - CORR MATRIX FOR RANDOM EFFECTS - EPSILONS
***", lst, fixed=T) # Find the start of CORR MATRIX - EPSILON
n_ETAS <- (row_startSIGMA-row_startOMEGA-7)/3 # Find number of ETAs, 7
"emtpy" rows, 3 rows per ETA
CORRMATRIX_ETAS <- lst[row_startOMEGA:row_startSIGMA] # Extract the corr
matrix - ETA
CORRMATRIX_ETAS <- CORRMATRIX_ETAS[seq(7,(n_ETAS-1)*3+7,3)] # Extract the
numbers in the matrix
ETAS <- signif(as.numeric(gsub("\\D", "", CORRMATRIX_ETAS)),3)/1000 # Remove
correlations, signif to get 3 significant digits, /1000 to get %
ETA_character_vector <- paste(rep("ETA",n_ETAS),seq(1,n_ETAS,1),sep="") #
Create a character vector containing ETAn
ETAS <- data.frame(ETAS,ETA_character_vector) # Create data frame
CORRMATRIX_SIGMA <- lst[row_startSIGMA+6] # Extract the corr matrix -
EPSILON
EPS <- signif(as.numeric(gsub("\\D", "", CORRMATRIX_SIGMA)),3)/10000 #
/10000 to get %
#------ End of script ------------
Best regards,
Oskar Alskär
_____________________________________________
Description: uu logo red 60
Oskar Alskär, MSc Pharm
PhD Student
Pharmacometrics group
Department of Pharmaceutical Biosciences
Uppsala University
Box 591
75124 Uppsala
Sweden
[email protected]
From: [email protected] [mailto:[email protected]] On
Behalf Of Simon Davis
Sent: den 3 september 2012 11:36
To: Hou, Xiaoli Shirley; NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear Shirley, If you have access in your group* to the Connect module of
Phoenix you will find that NONMEM jobs executed via this interface will
automatically extract certain information including these as tables for use
in other downstream objects in your workflow which could include R. It
also supports PsN, Xpose, SAS, SigmaPlot and S-plus.
There are some webinars (e.g.
http://www.pharsight.com/events/eventsonline_archive.php#replay_049) that
can expand on my comments if you are interested and an example project in
the User Forum.
Best regards,
Simon.
*I know your organisation already has some float licenses for this.
Alterantively we could set you up with an evaluation license.
___________________________________
[email protected]
Senior Scientific Consultant
Pharsight- A Certara Company
Get tips and discuss Pharsight products with other users;
www.pharsight.com/extranet
___________________________________
http://www.pharsight.com/training/training_upcoming.php
Satellite workshops at PAGE, 5 June 2012, Venice, Italy.
08:30 12:30 Phoenix Connect: Linking Modeling and Simulation Tools,
including NONMEM, R, Xpose & PsN, in Phoenix Workflows register
<https://pharsight.securesites.com/training/course_display_new.php?details_i
d=98> .
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<https://pharsight.securesites.com/training/course_display_new.php?details_i
d=99> .
Introduction to Phoenix WinNonlin 25-27 Sep. 2012 Amsterdam, The
Netherlands
Population Modeling Methodology using Phoenix NLME 2-4 Oct. 2012 Paris,
France
Introduction to Phoenix WinNonlin 4-6 Dec. 2012 London, UK
From: [email protected] [mailto:[email protected]] On
Behalf Of Hou, Xiaoli Shirley
Sent: Sunday, September 02, 2012 10:50 PM
To: NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear NM-Users,
I am doing a simulation using R, in which the within and between subject
variations, "EPSILON" and "OMEGA", are needed. They are automatically listed
in the ***.lst file of the NONMEM outputs. Is there a way I can read them
from my NONMEM output into R?
Thanks,
Shirley
Dr. Xiaoli Shirley Hou
Senior Biometrician, ECDS
351 N. Sumneytown Pike, UG1C36
North Wales, PA. 19454.
Phone (540) 381-9599
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