welcome bienvenue bienvenidos - lapk · © laboratory of applied pharmacokinetics and...
TRANSCRIPT
![Page 1: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/1.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
ITAG 4Individualized Therapeutic Approach Group
Welcome Bienvenue
Bienvenidos
![Page 2: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/2.jpg)
Review of Pre-Workshop Exercise
![Page 3: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/3.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Key concepts
• library() loads installed R packages into memory so that the commands are available for use in the current session, e.g. library(Pmetrics)
• setwd() changes the working directory, so that R knows where your files are, e.g. setwd(“C:/Pmetrics”). Note that forward slashes “/“ separate folders, even in Windows.
![Page 4: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/4.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Default Rstudio WD
Windows: Tools -> Options Mac: Rstudio -> Preferences
![Page 5: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/5.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Key concepts
• getwd() returns the current working directory, e.g.
getwd() [1] "/Users/Neely/Pmetrics"
![Page 6: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/6.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
PMtree
• PMtree() sets up a new Pmetrics project in the current working directory
• The name of the project will be the same as the argument to PMtree(), e.g. PMtree(“Cefepime”)
![Page 7: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/7.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
PMtree
• PMtree() creates 4 sub-folders
• /Rscript contains a skeleton script
• /Runs is the folder for all Pmetrics runs
• /Sim is a folder for simulations
• /src is a folder to contain source data documents
![Page 8: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/8.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
ITAG project
![Page 9: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/9.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Copy files to /Runs
![Page 10: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/10.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Open ITAG4.R
or use File -> New in Rstudio to make a new script.
![Page 11: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/11.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
R Script
![Page 12: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/12.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
The Rstudio IDE
![Page 13: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/13.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
The Rstudio IDE
Scripting
Console
Files Plots
Packages Help
Environment History
![Page 14: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/14.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Updated Script
![Page 15: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/15.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Executing scripts
Keyboard shortcuts equivalent to clicking “Run” Windows: CTRL-Return Mac: Command-Return
Also see http://www.lapk.org/Video_tutorials/R_console_script.php.
![Page 16: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/16.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
NPrun
• NPrun() executes a Non-Parametric (NPAG) run
• At minimum, you must supply the model and data file names
• There are other arguments which modify the run behavior; use ?NPrun in R to get help
![Page 17: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/17.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Pre-flight check
Model file and data file are copied to /Runs folder
Working directory in R is set to /Runs folder with setwd()
NPrun() command properly entered
![Page 18: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/18.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Lift off!
![Page 19: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/19.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Mac
![Page 20: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/20.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Windows
![Page 21: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/21.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
After a run
![Page 22: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/22.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Obs-Pred
![Page 23: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/23.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Convergence
![Page 24: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/24.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Marginals
![Page 25: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/25.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Parameter values
![Page 26: Welcome Bienvenue Bienvenidos - LAPK · © Laboratory of Applied Pharmacokinetics and Bioinformatics ITAG 4 Individualized Therapeutic Approach Group Welcome Bienvenue Bienvenidos](https://reader033.vdocuments.net/reader033/viewer/2022042921/5f69ceb43b094854e7641605/html5/thumbnails/26.jpg)
© Laboratory of Applied Pharmacokinetics and Bioinformatics
Run summary
Hint: The red asterisk tells you the run did not converge.