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R6 objects

Create Pmetrics R6 objects

PM_batch()
Execute a Batch of PM_fit objects
PM_cov
Contains covariate data
PM_cycle
Pmetrics Run Cycle Information
PM_data
Defines the PM_data object
PM_final
Final Cycle Population Values
PM_fit
Object to define and run a model and data in Pmetrics
PM_load()
Load Pmetrics NPAG or IT2B output
PM_model
Defines the PM_model class
PM_op
Observed vs. predicted data
PM_pop
Population predictions at short intervals
PM_post
Individual Bayesian posterior predictions at short intervals
PM_pta
Define object for PTA
PM_result
Results of a Pmetrics run
`$`
Object to contain results of simulation
PM_simlist
Object to contain list of results of simulation
PM_tutorial()
Introductory tutorial to Pmetrics
PM_valid
Pmetrics validation object

Make functions

Functions for making Pmetrics objects

PMtree()
Create a new Pmetrics folder tree
PMcheckMatrix()
Deprecated functions.
makeAUC()
Calculation of AUCs
makeCov()
Extract covariate data
makeCycle()
Summarize Pmetrics Run Cycle Information
makeErrorPoly()
Assay error polynomial coefficients
makeFinal()
Summarize NPAG or IT2B Final Cycle Population Values
makeNCA()
Non-compartmental analysis
makeOP()
Generated observed vs. predicted data
makePTA()
Calculation of PTAs
makePTAtarget()
Make PTA target object
makePop()
Individual Bayesian population prior predictions at short intervals
makePost()
Individual Bayesian posterior predictions at short intervals
makeValid()
Create a Pmetrics validation object
make_NCA()
Non-compartmental analysis
make_valid()
Create a Pmetrics validation object

Optimal sampling

Functions to calculate optimal sample times

Dopt()
Compute D-optimal Sample Times
MM_opt()
Compute MM-optimal Sample Times

Plot

Functions for plotting Pmetrics output

plot(<MMopt>)
Plot Pmetrics Multiple-Model Optimal Sampling Objects
plot(<PM_data>)
Plot PM_data Time-Output Data
plot(<PM_final>)
Plot Pmetrics Final Cycle Parameter Value Distributions
plot(<PM_op>)
Plot PM_op objects
plot(<PM_pta>)
Plot PM_pta Percent Target Attainment objects
plot(<PM_sim>)
Plot Pmetrics Simulation Objects
plot(<PM_simlist>)
Plot list of Pmetrics Simulation Objects
plot(<PM_valid>)
Plot PM_valid objects
plot(<PMcov>)
Plot Pmetrics Covariate objects
plot(<PMcycle>)
Plot NPAG Cycle Information
plot(<PMdopt>)
Plot Pmetrics D-optimal Times
plot(<PMfinal>)
Plot Pmetrics Final Cycle Parameter Value Distributions
plot(<PMmatrix>)
Plot PMmatrix Time-Output Data
plot(<PMop>)
Plot PMop objects
plot(<PMpta>)
Plot PMpta Percent Target Attainment objects
plot(<PMsim>)
Plot Pmetrics Simulation Objects
plot(<PMvalid>)
Plot Pmetrics Validation Objects
plot(<tidy_cov>)
Wrapper function for plot.PMcov
plot(<tidy_op>)
Wrapper function for plot.PM_op
ab_line()
Add lines to plotly plot
add_shapes()
Add shapes to plotly plot

Summary

Functions for summarizing Pmetrics output

summary(<PM_cov>)
Wrapper function for summmary.PMcov
summary(<PM_data>)
Summarize a Pmetrics PM_data object
summary(<PM_final>)
Wrapper function for summmary.PMfinal
summary(<PM_op>)
Wrapper function for summmary.PMop
summary(<PM_pta>)
Wrapper function for summmary.PMpta
summary(<PMcov>)
Summarize Covariates and Bayesian Posterior Parameter Values
summary(<PMdopt>)
Summarize PMdopt objects
summary(<PMfinal>)
Summary Statistics for PMfinal Objects
summary(<PMmatrix>)
Summarize PMmatrix objects
summary(<PMop>)
Summarize Observations and Predictions
summary(<PMpta>)
Summarize Percent Target Attainment

Print

Functions for printing Pmetrics output

print(<MMopt>)
Print Pmetrics Multiple-Model Optimal Sampling Objects
print(<PMdopt>)
Print PMdopt
print(<PMerr>)
Print Data Errors
print(<PMnpc>)
Print NPC
print(<summary.PMfinal>)
Print Summary of Parameter Values and Credibility Intervals
print(<summary.PMmatrix>)
Summarize Covariates and Bayesian Posterior Parameter Values
print(<summary.PMop>)
Print Summary of Observations and Predictions

Run

Run functions for modeling or simulating data

ERRrun()
Execute an Assay Error Estimation run.
ITrun()
Execute an IT2B run.
NPrun()
Execute an NPAG run.
SIMrun()
Run the Pmetrics Simulator

Parse/load

Parse functions for loading modeled or simulated data

ITparse()
Parse Pmetrics IT2B Output
NPparse()
Parse Pmetrics NPAG Output
SIMparse()
Parse Pmetrics Simulator Output
PMload()
Load Pmetrics NPAG or IT2B output (Legacy)

Auxilliary

Auxilliary functions

qgrowth()
Extract CDC pediatric growth charts
zBMI()
Extract CDC pediatric BMI z-scores
ss.PK()
Sample size calculations for Phase 1 PK study design
mtsknn.eq()
Multivariate two-sample test based on k-nearest neighbors
PMcompare()
Compare NPAG or IT2B runs
PMgetCRCL()
Add Jelliffe Creatinine Clearance
PMstep()
Stepwise covariate-parameter regressions

Datasets

Pmetrics datasets

ITex
Example IT2B Output
NPex
Example NPAG Output
badData
Pmetrics data file with errors
cdc_bmi
CDC Pediatric and Adolescent BMI Table
dataEx
Pmetrics data file
ger_bmi
CDC Pediatric and Adolescent BMI Table
growth
CDC Pediatric and Adolescent Growth Data Table
mic1
Example MIC data
modEx
Pmetrics model object
simEx
Example simulator output

Data processing

Data processing and interconversion

NM2PM()
Convert NONMEM to Pmetrics Data Files
PMwrk2csv()
Convert Old .wrk Files to .csv Matrix File
PMmb2csv()
Convert Old .mb or USC*PACK Files to .csv Matrix File
PMmatrixRelTime()
Convert Absolute Dates and Times to Relative Hours
PMreadMatrix()
Read a Pmetrics .csv Matrix Input File
PMwriteMatrix()
Write a Pmetrics .csv Matrix File

Utility

Utility functions

PMFortranConfig()
Read or define the Fortran compiler and command line template
PMbuild()
Build Pmetrics
PMcheck()
Check Pmetrics Inputs for Errors
PMcode()
Pmetrics GUI Tutor
PMlogin()
Login a user in the remote server
PMlogout()
Login a user in the remote server
PMpatch()
Download and install Pmetrics patches
PMregister()
Register a new user in the remote server
PMreport()
Summarize NPAG or IT2B Run
ERRreport()
Summarize ERR Run
PMsave()
Save Pmetrics objects
PMtest()
Test Pmetrics
PMupdate()
Download and install Pmetrics updates
getPMoptions()
Get Pmetrics User Options
setPMoptions()
Set Pmetrics User Options
update_gfortran()
Download and install Gfortran updates

Reference

Reference functions

PMFortranConfig()
Read or define the Fortran compiler and command line template
PMmanual()
Open user and function manuals.
PMnews()
Pmetrics changelog
Pmetrics-package Pmetrics
Parametric and non-parametric modeling and simulation of pharmacokinetic-pharmacodynamic systems.