Package index • Pmetrics

R6 objects

Pmetrics R6 objects

PM_data stable: Defines the PM_data object
PM_model stable: Defines the PM_model class
PM_cycle stable: Pmetrics Run Cycle Information
PM_cov stable: Contains covariate data
PM_final stable: Final Cycle Population Values
PM_op stable: Observed vs. predicted data
PM_pop stable: Population predictions at short intervals
PM_opt stable: Optimal Sample Times
PM_post stable: Individual Bayesian posterior predictions at short intervals
PM_sim stable: Object to contain results of simulation
PM_load() stable: Load Pmetrics NPAG or IT2B output
PM_result stable: Results of a Pmetrics run
PM_valid stable: Pmetrics validation object

Helpers

Helper functions for R6 object creations

ab() stable: Initial range for primary parameter values
additive() stable: Additive error model
add_renal() stable: Estimate renal function using various equations
cor2cov() stable: Convert correlation matrix to covariance matrix
model_lib(): Model Library
msd() stable: Initial mean/SD for primary parameter values
proportional() stable: Proportional error model
interp() stable: Model covariate declaration
PM_tree() PMtree() stable: Create a new Pmetrics folder tree
makeAUC() stable: Calculation of AUCs
makeErrorPoly() stable: Assay error polynomial coefficients
makeNCA(): Non-compartmental analysis
makePTAtarget() stable: Make a Percent Target Attainment (PTA) Target
make_NCA(): Non-compartmental analysis

Plot

Functions for plotting Pmetrics output

plot(<PM_cov>) stable: Plot Pmetrics Covariate objects
plot(<PM_cycle>) stable: Plot Cycle Information
plot(<PM_cycle_data>) stable: Plot PM_cycle_data objects
plot(<PM_data>) stable: Plot PM_data Time-Output Data
plot(<PM_final>) stable: Plot Pmetrics Final Cycle Parameter Value Distributions
plot(<PM_final_data>) stable: Plot PM_final_data objects
plot(<PM_model>) stable: Plot PM_model objects
plot(<PM_op>) stable: Plot Pmetrics Observed vs. Predicted Objects
plot(<PM_op_data>) stable: Plot PM_op_data objects
plot(<PM_opt>) stable: Plot Pmetrics Multiple-Model Optimal Sampling Objects
plot(<PM_pop>) stable: Plot PM_pop Prediction Data
plot(<PM_post>) stable: Plot PM_post Prediction Data
plot(<PM_pta>) stable: Plot PM_pta Percent Target Attainment objects
plot(<PM_sim>) stable: Plot Pmetrics Simulation Objects
plot(<PM_valid>) stable: Plot Pmetrics Validation Objects
plot(<PMvalid>) superseded: Plot Pmetrics Validation Objects
plotlygg() stable: Convert a plotly object to ggplot
ab_line() stable: Add lines to plotly plot
add_shapes() stable: Add shapes to plotly plot
add_smooth() stable: Add regression to plotly plot
export_plotly() stable: Export plotly plot
sub_plot() stable: Display multiple plotly plots
click_plot() stable: Click on plotly plot to highlight traces
getPalettes() stable: Get color palette
getDefaultColors() stable: Get a list of default colors
rgba_to_rgb() stable: Convert RGBA to RGB
opposite_color() stable: Find opposite color with max contrast

Summary

Functions for summarizing Pmetrics output

summary(<PM_cov>) stable: Summarize Covariates and Bayesian Posterior Parameter Values
summary(<PM_cycle>) stable: Summarize Final Cycle Statistics
summary(<PM_cycle_data>) stable: Summarize PM_cycle_data objects
summary(<PM_data>) stable: Summarize PM_data objects
summary(<PM_final>) stable: Summary Statistics for Final Cycle
summary(<PM_final_data>) stable: Summarize PM_final_data objects
summary(<PM_op>) stable: Summarize Observations and Predictions
summary(<PM_op_data>) stable: Summarize PM_op_data objects
summary(<PM_pop>) stable: Summarize Observations and Predictions
summary(<PM_post>) stable: Summarize Observations and Predictions
summary(<PM_pta>) stable: Summarize Percent Target Attainment
summary(<PM_sim>) stable: Summarize Pmetrics Simulation Objects
PM_report() stable: Generate a report

Print

Functions for printing Pmetrics output

print(<PM_compare>): Print method for PM_compare objects
print(<PMerr>) stable: Print Data Errors
print(<PMnpc>) stable: Print NPC
print(<summary.PM_cycle>) stable: Print Summary of Cycle Statistics
print(<summary.PM_data>) stable: Print Summary of Pmetrics Data
print(<summary.PM_final>) stable: Print Summary of Parameter Values and Credibility Intervals
print(<summary.PM_op>) stable: Print Summary of Observations and Predictions
print(<summary.PM_sim>) stable: Print Summary of Simulations

Auxilliary

Auxilliary functions

all_is_numeric() stable: Check if all values are numeric
build_model(): Launch Model Builder app
build_plot(): Launch Plot Builder app
qgrowth() stable: Extract CDC pediatric growth charts
mtsknn.eq() stable: Compare discrete distributions
zBMI() stable: Extract CDC pediatric BMI z-scores
ss.PK() stable: Sample size calculations for Phase 1 PK study design
PM_compare(): Compare runs
PMgetCRCL() deprecated: Add CRCL
PM_step() superseded: Stepwise covariate-parameter regressions
getCov() stable: Extract covariate information
getDefaultColors() stable: Get a list of default colors
getFixedColNum() stable: Number of fixed columns
getPMoptions() stable: Get Pmetrics User Options
getPalettes() stable: Get color palette

Datasets

Pmetrics datasets

NPex: Example NPAG Output with validation
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
locales: Pmetrics locales
mic1: Example MIC data
modEx: Pmetrics model object
model: Pmetrics model
simEx: Example simulator output

Data processing

Data processing and interconversion

NM2PM() stable: Convert NONMEM to Pmetrics Data Files
PMwrk2csv() stable: Convert Old .wrk Files to .csv Matrix File
PMmatrixRelTime() superseded: Convert Absolute Dates and Times to Relative Hours
PMreadMatrix() superseded: Read a Pmetrics data file
PMwriteMatrix() superseded: Write a Pmetrics .csv Matrix File

Utility

Utility functions

PM_build() stable: Build Pmetrics
PM_help() stable: Get Help and Report Issues
PMcheck() superseded: Check Pmetrics Inputs for Errors
PMpatch(): Download and install Pmetrics patches
PMtest() stable: Test Pmetrics
PM_tutorial() stable: Pmetrics tutorial
setPMoptions() stable: Set Pmetrics User Options

Internal

Internal and low-level functions

compile_model(): Compiles the text representation of a model into a binary file.
dummy_compile(): Dummy function to cache compilation artifacts.
simulate_all(): Simulates all subjects in the data set using the model at the given path.
simulate_one(): Simulates the first subject in the data set using the model at the given path.
fit(): Fits the model at the given path to the data at the given path using the provided parameters.
is_cargo_installed(): Checks if Cargo is installed on the system.
model_parameters(): Retrieves the model parameters from the compiled model at the given path.
temporary_path(): Retrieves the temporary path used for building models.

Reference

Reference functions

PM_manual(): Open user and function manuals.
Pmetrics-package Pmetrics: Parametric and non-parametric modeling and simulation of pharmacokinetic-pharmacodynamic systems.