Function reference • Pmetrics

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.