Re: [NMusers] How to format output table as purely comma-separated file

data.table::fread should automatically detect the character separators and parse it (lightning fast and parallelized i might add), so if using R, that is a great swiss army knife that can read multihundred megabyte files virtually instantly. If that isn't working there is PKPDmisc::read_nonmem - I

Re: [NMusers] Context-free lexer for NM-TRAN

Hi all, A couple thoughts on this. First, I would suggest constructing a parse tree over an abstract syntax tree, as it will likely be important to retain additional metadata such as comments, as I presume such a tool would provide a foundation for automatic things such as refactoring, reformattin

[NMusers] make your work shiny after PAGE

Ready to wow your colleagues with informative dashboards, or give the potential to run complex analyses directly to decision makers or non technical users? Jump start your journey learning directly from myself (Devin), an Rstudio expert consultant, to compress months of self-experimentation into tw

[NMusers] Correct Shiny Course Link

Apologies for the followup - here is the correct public link: https://www.eventbrite.com/e/shiny-for-pharmacometrics-tickets-42986594060 Please do not hesitant to reach out with questions, requests, or thoughts about the course and material covered. Devin

[NMusers] Shiny at PAGE is live - and an extra announcement!

Dear all, Thank you so much for the enthusiastic response regarding the previous email about a R Shiny workshop prior to PAGE. Based on feedback, it will be a two day course (monday/tuesday the 28th/29th). Check out the syllabus and sign up details on eventbrite here: https://www.eventbrite.c

[NMusers] Shiny for Pharmacometrics Workshop PAGE 2018

We are excited to announce a new public course debuting at PAGE 2018. Shiny for Pharmacometrics is an accelerated course that build on the modern R course to leverage shiny to develop tools and applications to support pharmacometric activities. This course has been taught privately with great succe

Re: [NMusers] Failure to execute NONMEM from R

I believe the problem is actually that is cross referenced http://discuss.go-isop.org/t/psn-execute-failed-to-start-when-called-from-rstudio/1119 It is not a path issue Mike and I have had a small amount of offline exploration and can confirm it a pervasive issue with NM74 being called from Rstudi

Re: [NMusers] Use of ACCEPT in $DATA

Similar to Bill, I also have an inelegant, but workable, solution, which is to brute force the ignore times by templating them in R. For example, you can use a simple glue template to churn out ignore statements. For simplicity this could then be then just copied into control streams. library(whi

[NMusers] tidyverse for pharmacometrics June 5-6 at PAGE

st, only a couple spots remain! Look forward to seeing everyone at PAGE, Devin Pastoor and Vijay Ivaturi

[NMusers] tidyverse for pharmacometrics - PAGE 2017

-33043259278 *Register for early bird pricing by april 14th and get 20% off with the code EARLYBIRD* Curious whether this course is right for you? Please reach out to me at devin.past...@gmail.com and we can discuss any questions. Look forward to seeing everyone at PAGE, Devin Pastoor and Vijay

Re: [NMusers] RE: question about random seed for simulation

Hi Penny, I would highly encourage you to check out mrgsolve. It will be the fastest (and IMO easiest) to do flexible designs. That said, given that you seem to just be changing the sampling, per your email, why don't you just simulate the richest design you need, then in post processing filter o

Re: [NMusers] Generating random numbers within a range

Hi Paul, You could probably just resent your FF at each dosing event (amt gt 0) based on the ADHERENCE = 0.4 IF (AMT.GT.0) THEN CALL RANDOM(2, R) # second random number so can access uniform distribution IF (R.LT.ADHERENCE) THEN FF = 0 ELSE FF = 1 ENDIF ENDIF ... $S

Re: [NMusers] covariate on transit compartment model parameters

rate of dissolution then you could tie back the contributions in shape to both ntr and mtt. Devin Pastoor Center For Translational Medicine, University of Maryland Baltimore On Sun, Sep 25, 2016 at 9:01 AM Jing Niu wrote: > Dear NMusers, > I am modeling long-acting injectable formulation

Re: [NMusers] Usage of parallel nonmem in tendem with SGE

Paul, I would think you can just use the parallel environments flag to reserve (by_node) the required slots and execute once they are available. Either way though, can be pretty inefficient, as you're going to be 'wasting' compute resources waiting for the additional nodes to become available. It

Re: [NMusers] Error in table step

Mark, Does it work when you omit that individual? If so, I would go through that ID's data records with a fine-toothed comb to make sure their wasn't a 0 floating around somewhere that it shouldn't be thats causing a divide by 0 error or some other data error. The other thing that I might look t

Re: [NMusers] pcVPC or NPDE

would likely work well. Devin Pastoor Clinical Research Scientist, PhD student Center for Translational Medicine University of Maryland, School of Pharmacy On Fri, Sep 11, 2015 at 10:38 AM ZhaoChenyan wrote: > Dear all: > > I'm now having a set of TDM data, only troughs （C0 ） availa

Re: [NMusers] Humongous log file with parallel NONMEM

Alas it was a long shot - good to know it won't work. Thanks Ron/Erik. I also wouldn't think I/O would outstrip CPU with how computationally intensive nonmem runs are. On Mon, Jun 22, 2015 at 3:30 PM Ron Keizer wrote: > >> The problem with those solutions is they don't actually address the I/O >

Re: [NMusers] Humongous log file with parallel NONMEM

Ron and Erik, The problem with those solutions is they don't actually address the I/O concern. While you will save some disk space at any given time (which I assume shouldn't be an issue for Bill on AWS) , you are actually *increasing *the I/O burden (eg now you have to deal with creation and dele

Re: [NMusers] Fwd: Should we generate VPCs with or without uncertainty?

l describes the data - include a visualization of uncertainty at your own peril :-) So, for better or worse, I would say - it depends, though I would be highly concerned if major decisions rode on inclusion/exclusion of parameter uncertainty, in most cases. Devin Pastoor Center for Transla

Re: [NMusers] 3Rs: Reproducibility, Replicability and Repeatability

Dear Gavin, My two cents are, in the simplest sense: Reproducibility focuses on the ability to arrive to the same final conclusions, even in the presence of some change, as the 'spirit' of the definition should be about arriving to the same conclusions. (eg use of monolix vs phoenix vs nonmem, or

[NMusers] Modern R at PAGE

functions that you and your team can share across projects? Come learn how you can write fast flexible functions that more than double your productivity! Want to know more? Dr. Vijay Ivaturi and Devin Pastoor from The Center for Translational Medicine will be teaching Modern R at the Creta Maris

Re: [NMusers] An LSODA CODE -3 error during simulation

or to be a little larger 0.01 might have some issues with floating point calculations but I could be incorrect here. Something like 0.0001 should still give you negligible error for all intents and purposes. Best of luck! Devin Pastoor Center for Translational Medicine University of Maryland,

Re: [NMusers] SCM error: Multiple instances of label in problem to update

ose should resolve the issue. Devin Pastoor Center for Translational Medicine University of Maryland, Baltimore On Fri, May 1, 2015 at 12:00 PM Amir Youssef wrote: > Dear all, > > I am running the SCM tool in PsN but I am getting the following error: > "Multiple instances

[NMusers] Modern R workshop series starts at PAGE

ilt a functional and flexible clinical trial simulator in R. * For further inquires please contact Devin Pastoor at devin.past...@umaryland.edu Thank you and look forward to seeing you!