metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

Pharmacometric tools for common data preparation tasks, stratified bootstrap resampling of data sets, NONMEM control stream creation/editing, NONMEM model execution, creation of standard and user-defined diagnostic plots, execution and summary of bootstrap and predictive check results, implementation of simulations from posterior parameter distributions, reporting of output tables and creation of detailed analysis logs.

AuthorTim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Date of publication2015-10-08 17:48:58
MaintainerBill Knebel <>

View on R-Forge

Man pages

accept: Document Acceptance of an R Installation

acceptance: List the History of Acceptance.

addl: Calculate a NONMEM ADDL data item from explicit records.

align.decimal: Format Numeric Vectors Specially Coerce data unambiguously to numeric or character

as.comment: Create and Manipulate Comment Objects Convert a Block of Lines to Data Frame

as.define: Work with Data Definitions

as.init: Work with Initial Estimates as Objects

as.keyed: Create and Manipulate Keyed Data Frames

as.nm: Create and Manipulate nm Objects

as.nmctl: Create, Manipulate, Read, and Write NONMEM Control Streams

as.pxml: Convert a Param File to XML

as.second: Interconvert Nominal Time Units

as.spec: Create and Manipulate spec Objects Create a Run Log for NONMEM7 using NONMEM6 Format

as.xml: Represent an Object as XML

attribute: Encode an Attribute for an XML Open Tag

AUC: Calculate AUC Using the Trapezoidal Method

aug: Augment a List-like Object

backtrans: Back-transform Columns in a Data Frame

bin: Calculate Bin Sizes and Limits for a Vector

bounds: Calculate Normal Quantiles at Boundaries of Probability...

bracket: Create an XML Tag

breaks: Identify Boundaries Between Sets of Elements

bundleRead: Read Data Files from a Directory into a List

cast-methods: Methods for Function 'cast' in Package 'reshape'

check.subjects: Summarize Columns of Subject Data

CLNR: Delete Files and Directories

closers: Calculate Closing Text for Nested Script Levels

codes: Recover Metadata from spec Objects and their Components

colname: Change Selected Names

combinations: Display Combinations of Column Values

command: Format a Latex Command

compileflag: Develop a Value for a Compiler Resource on the Grid

compiler: Extract the Compiler Name from an NMQual Configuration File

compute.cwres: Compute the Conditional Weighted Residuals

config: Identify the Configuration File in an NMQual-mediated NONMEM...

constant: Test for Nested Factors

contains: Test a Character Vector for Occurences of a Pattern

convertLines: Convert Line Endings

css: Calculate One-Compartment Model Properties

c.temporal: Support for timepoint Classes

cv: Compute Coefficient of Variation for Normal and Log-Normal...

dataFormat: Integrate NONMEM Data for Plotting

dataSynthesis: Build a Standard Plotting Data Set for a Given NONR Run

diagnosticPlots: Create Diagnostic Plots

digest: Diagnose Static Data Relationships

electronicAppendix: Make an FDA-style Electronic Appendix from a Subversioned...

encode: Encode Factor-like Levels and Labels as a Simple String

episcript: Run an Epilog Script in a Pre-populated Environment

extensions: Instantiate Records Implied By Range Data

extract: Extract a Parenthetically-grouped Substring of a Regular...

filename: Construct a Canonical File Name

findNonmemCommand: Find Paths to Available Nonmem Commands

first: Identify Elements Within Cells Meeting Some Instance of a...

fixedwidth: Apply Fixed-width Formatting to a Data Frame

fixProblem: Clean Up a Control Stream

flag: Create and Manipulate Flags

ftable2data.frame: Convert ftable to data.frame

getCovs: Return Non-commented Non-duplicated Rows of a NONMEM Data Set

getCwres: Return the Conditional Weighted Residuals Pertinent to a...

getdname: Extract the Path and File from the DATA Block in the Control...

getPars: Return the Non-duplicated (ID) Rows Corresponding to the...

getTabs: Return the Observation Rows (EVID==0) Corresponding to the...

glue: Paste Items with No Space

groupnames: Construct a Single Vector of Group Names from Possibly...

half.matrix: Interconvert Between a Symmetric Matrix and a Triangular...

hash: Supply Comment Characters with Output

helpAdminister: metrumrg: Administrative

helpBrowse: metrumrg: Extended Examples

helpClasses: metrumrg: Data Classes

helpDataFrame: metrumrg: Working with Data Frames

helpList: metrumrg: Defined Functions

helpMatrix: metrumrg: Working with Matrices

helpModel: metrumrg: Modeling

helpPharmacometric: metrumrg: Pharmacometrics

helpPrepare: metrumrg: Data Preparation

helpQuantify: metrumrg: Statistics

helpReport: metrumrg: Reporting

helpSimulate: metrumrg: Simulation

helpStrategic: metrumrg: Strategic Data Manipulation

helpVector: metrumrg: Working with Vectors

helpVisualize: metrumrg: Plotting

ibw: Calculate Various Clinical Indicators

index: Visualize Static Data Relationships Limit Data to Inner Quantiles by Imputing NA.

is.alpha: Test For Alphabetic Content

is.defined: Test Whether Values are Defined

is.diagonal: Analyze Parameter Labels

is.latex.token: Determine if String is Valid Latex Command or Environment Check That Each Element is a Single Non-letter

is.square.matrix: Test Whether a Matrix is Square

isSubversioned: Check Whether Files Are Subversioned

isSubversionedFile: Check If Single file Is Subversioned

iterations: Harvest Iteration Statistics from NONMEM Output and Convert...

justUnits: Extract Substring of Wiki Math

keyed-class: Class '"keyed"'

latest: Identify the Latest Variants of Each File as Distinguished by...

latex.args: Format Latex Command Arguments

latex.options: Format Latex Command Options

locf: Impute Missing Vector Values

lookup: Lookup Alternate Versions of Parameter Codes Convert a Data Frame to a Latex Table

map: Map One Set of Values to Another

matches: Test the Correspondence between a Table and a Specification

melt.keyed: Melt a Keyed Data Frame

metaMerge: Recursively Merge Multiple Tables

metaSub.character: Create Replicate Text files with Systematic Substitutions

metrumrg-package: Pharmacometric Tools for Data Preparation, Modeling,...

metrumrgURL: View a metrumrg Package File

monotonic: Determine Whether a Vector is Monotonic

naInContext: Display Missing Values in Context

nasum: Count Number of 'NA' Values in List Items

ncomma: Report Names as Comma-delimited

nest: Nest an XML Fragment in a Parent Element

nix: Identify Unix-like Platforms Build Commands to Invoke NONMEM

nmPlots: An Extensible List of Diagnostic Plots for nm Objects

nmVersion: Extract the NONMEM Version from an NMQual Configuration File


omegacor: Extract NONMEM Covariance or Correlation Matrices

ops: Operator Syntax for Joining Keyed Data Frames

ord.matrix: Give the Order of a Symmetric Matrix or Half Matrix

packageCheck: Load a Package and Run Package-level Examples for Testing...

panel.densitystrip: Display Distributions with Respect to Reference Values

panel.hist: Plot Histograms Flexibly

panel.stratify: Handle Each Level of a Stripplot Separately

parameter2wiki: Convert Parameter Labels to Wikimath

params: List Documented Parameters

parens: Wrap Text in Parentheses

partab: Construct a Parameter Table

percent: Calculate Percent.

plotFileName: Make a Name for a Diagnostic Plot File

plot.nm: Plot An Object of Class nm

PLOTR: Create Diagnostic Plots for a NONMEM Run

pool: Test Set Relations Among Two Vectors

posmat: Coerce a Matrix to be Positive Definite

prev: Check Some Properties of Vectors

purge.dir: Purge a Directory

purge.files: Purge Files

qstat: Invoke SGE qstat

qsub: Build Commands to Invoke SGE qsub

random: Select Random Members of an Object

reapply: Apply a Function Across Cells of an Indexed Vector, Giving an... Create Replicate Data Sets by Stratified Sampling

rinvchisq: Generate Inverse Chi-square Distribution

riwish: Generate Inverse Wishart Distribution

rlog: Generate a Combined Run Log from Multiple NONMEM Runs

row2tabular: Format Vector for Latex Tabular Row

runCommand: Issue the System Call That Invokes NONMEM

runlog: Convert Model Metadata to Various Formats

runNonmem: Process a Request for NONMEM Invocation

runstate: Detect State of a Run Using File Existence Criteria Call a Function Safely

safeQuote: Single-quote Conditionally

setCwres: Append Conditional Weighted Residuals to an Appropriate File

sets: Binary Operators for Set Relations

shuffle: Move the Columns of a Data Frame Relative to Each Other

simblock: Generate Random Effect Deviates for Simulation

simpar: Create Parameters for Simulation with Uncertainty

snap: Coerce Values to Nearest of Candidates

sortedInstall: Install Local Source Packages Sorted by Dependency

spaces: Generate a String of Spaces

specfile: Determine the Expected Path to a Specification File

specification: Create a Data Specification Corresponding to a Particular...

sqrtm: Help Calculate CWRES

stableMerge: Execute a Stable Left Join

star: Replace Asterisk in x With y

static: Return the static portion of an object.

strain: Reduce x to Those Elements that Occur in Options

summary.nm: Analyze an NM Object

superset: Augment NONMEM Input with Table Output

supp: Merge CDISC Supplemental Data

svnIsText: Check Whether Subversioned Files are Text.

svnMarkAsNonText: Mark Subversioned Files as Non-text.

svnMarkAsText: Mark Subversioned Files as Text

svnMimeType: Determine Mime Type for Multiple Files

svnPropGet: Get Subversion Property for a Vector of Files

svnPropGetFile: Get Subversion Property for a Single File

svnPropSet: Set a Property on a Vector of Subversioned Files

svnPropSetFile: Set a Property on a Subversioned File

svnSetMimeType: Set Subversion Mime Type

synthesis: Sequentially Left-join an Arbitrary Number of Data Frames,... Convert a Data Frame to a Latex Tabular Environment, Latex...

tabularformat: Create the Format String for Latex Tabular Environment

tagvalue: Convert List to Tag and Value Format

temporal: Temporal Classes with Selective Defaults

text2decimal: Convert Mixed Text to Decimal

Tmax: Calculate Tmax

Tmin: Calculate Tmin

toSAS: Convert Timepoint to SAS Format

totitle: Convert Text to Title Case

tweak: Adjust Values

variants: Locate Variants of a File in Distinctive Subdirectories

wikiparse: Parse Wikimath

win: Identify Windows Platforms

wrap: Wrap Text in a Latex Environment

xpath: Extract Value of an xpath Expression from and XML File

xpath2frame: Extract Indexed Values from XML

xyplot.ext: Plot the Parameter Search History for a NONMEM 7 Run


\%-\% Man page
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accept Man page
acceptance Man page
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glue Man page
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helpDataFrame Man page
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helpMatrix Man page
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helpPrepare Man page
helpQuantify Man page
helpReport Man page
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ibw Man page
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zeroDv Man page
zeroDv.nm Man page


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