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ITAG 4Individualized Therapeutic Approach Group

Welcome Bienvenue

Bienvenidos

Review of Pre-Workshop Exercise

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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.

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Default Rstudio WD

Windows: Tools -> Options Mac: Rstudio -> Preferences

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Key concepts

• getwd() returns the current working directory, e.g.

getwd() [1] "/Users/Neely/Pmetrics"

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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”)

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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

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ITAG project

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Copy files to /Runs

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Open ITAG4.R

or use File -> New in Rstudio to make a new script.

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R Script

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The Rstudio IDE

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The Rstudio IDE

Scripting

Console

Files Plots

Packages Help

Environment History

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Updated Script

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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.

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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

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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

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Lift off!

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Mac

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Windows

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After a run

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Obs-Pred

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Convergence

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Marginals

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Parameter values

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Run summary

Hint: The red asterisk tells you the run did not converge.