This is Fortran format that is trying to keep within the alloted spaced for the number while expressing values less than 1e-100. Users may select the following format to express the exponent over 3 digits instead of the usual 2: FORMAT=s,1PE16.8E3 the FORMAT option may be used on $EST or $TABLE statements (these act only on FILE outputted tables).
Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 286-0769 Email: [email protected] Web: www.icondevsolutions.com ________________________________ From: [email protected] [mailto:[email protected]] On Behalf Of Fidler,Matt,FORT WORTH,R&D Sent: Tuesday, September 14, 2010 9:33 AM To: Justin Wilkins; Chandramouli Radhakrishnan Cc: [email protected] Subject: RE: [NMusers] is there a way to change fit to csv Chandramouli, Justin's solution is elegant and works on most datasets produced. However, occasionally NONMEM outputs "numbers" formatted like the following 1.00-103 which should be 1.00E+103. I have created a small function that reads in NONMEM datasets and fixes this problem: read.nm<-function(file,na.strings=c("NA","."),...){ nmf<-readLines(file,n=-1)[-1] nmf<-gsub("+",",",nmf) nmf<-gsub("^,","",nmf) nmf<-gsub("([0-9])([-+])([0-9])","\\1E\\2\\3",nmf) tf<-tempfile() cat(nmf,file=tf,sep="\n") d<-read.csv(tf,na.strings=na.strings,...) unlink(tf) return(d) } Once this function is sourced, all you need to do is read NONMEM in through the new function: d<- read.nm("table.tbl") Matt. From: [email protected] [mailto:[email protected]] On Behalf Of Justin Wilkins Sent: Tuesday, September 14, 2010 1:24 AM To: Chandramouli Radhakrishnan Cc: [email protected] Subject: Re: [NMusers] is there a way to change fit to csv Dear Chandramouli Typically something like > fit <- read.table("run1.fit", head=T, skip=1) (where run1.fit is a typical NONMEM table file, with headers) should do what you need. If not, have a look at the NONMEM table in a text editor - NONMEM tables are basically space-delimited text files, which R's read.table function ought to be able to handle easily. Best Justin On 14 September 2010 07:42, Chandramouli Radhakrishnan <[email protected]> wrote: Hi I am trying to use R to produce plots from NONMEM fit file. However, I could not get R to read the fit file Can any one help? Kind Regards Chandramouli Radhakrishnan -- Justin Wilkins ----------------------------- Colmarerstrasse 31 4055 Basel Switzerland ----------------------------- Email: [email protected] Skype: kestrel_za2002 Mobile: +41 76 561 0949 ________________________________ This e-mail (including any attachments) is confidential and may be legally privileged. If you are not an intended recipient or an authorized representative of an intended recipient, you are prohibited from using, copying or distributing the information in this e-mail or its attachments. If you have received this e-mail in error, please notify the sender immediately by return e-mail and delete all copies of this message and any attachments. Thank you. ICON plc made the following annotations. ------------------------------------------------------------------------------ This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that ICON plc can arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835
