Pharmacometric tools for data preparation, modeling, simulation, and reporting

Documentation for package ‘metrumrg’ version 5.36

DESCRIPTION file.

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A B C D E F G H I J K L M N O P Q R S T U V W X Z misc

metrumrg-package

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

-- A --

accept	Document Acceptance of an R Installation
acceptance	List the History of Acceptance.
acr	Calculate One-Compartment Model Properties
addl	Calculate a NONMEM ADDL data item from explicit records.
addl.data.frame	Calculate a NONMEM ADDL data item from explicit records.
addl.default	Calculate a NONMEM ADDL data item from explicit records.
after	Identify Elements Within Cells Meeting Some Instance of a Condition
aggregate.keyed	Create and Manipulate Keyed Data Frames
align.decimal	Format Numeric Vectors Specially
and.keyed	Operator Syntax for Joining Keyed Data Frames
as.best	Coerce data unambiguously to numeric or character
as.best.data.frame	Coerce data unambiguously to numeric or character
as.best.default	Coerce data unambiguously to numeric or character
as.best.digest	Diagnose Static Data Relationships
as.character.comment	Create and Manipulate Comment Objects
as.character.flag	Create and Manipulate Flags
as.character.init	Work with Initial Estimates as Objects
as.character.initList	Work with Initial Estimates as Objects
as.character.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
as.character.timepoint	Support for timepoint Classes
as.character.uniKey	Create and Manipulate Keyed Data Frames
as.chartime	Support for timepoint Classes
as.chartime.numeric	Support for timepoint Classes
as.comment	Create and Manipulate Comment Objects
as.comment.comment	Create and Manipulate Comment Objects
as.comment.default	Create and Manipulate Comment Objects
as.conditioned	Visualize Static Data Relationships
as.conditioned.digest	Visualize Static Data Relationships
as.conditioned.isolated	Visualize Static Data Relationships
as.conditioned.keyed	Visualize Static Data Relationships
as.csv.filename	Create Replicate Data Sets by Stratified Sampling
as.csv.filename.character	Create Replicate Data Sets by Stratified Sampling
as.data.frame.block	Convert a Block of Lines to Data Frame
as.data.frame.comment	Create and Manipulate Comment Objects
as.data.frame.flag	Create and Manipulate Flags
as.data.frame.keyed	Create and Manipulate Keyed Data Frames
as.day	Interconvert Nominal Time Units
as.day.day	Interconvert Nominal Time Units
as.day.duration	Interconvert Nominal Time Units
as.day.hour	Interconvert Nominal Time Units
as.day.month	Interconvert Nominal Time Units
as.day.numeric	Interconvert Nominal Time Units
as.day.week	Interconvert Nominal Time Units
as.day.year	Interconvert Nominal Time Units
as.digest	Diagnose Static Data Relationships
as.digest.data.frame	Diagnose Static Data Relationships
as.digest.digest	Diagnose Static Data Relationships
as.digest.keyed	Diagnose Static Data Relationships
as.digest.nm	Diagnose Static Data Relationships
as.document	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.document.character	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.document.data.frame	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.file.runlog	Convert Model Metadata to Various Formats
as.filename	Create Replicate Text files with Systematic Substitutions
as.filename.character	Create Replicate Text files with Systematic Substitutions
as.flag	Create and Manipulate Flags
as.flag.default	Create and Manipulate Flags
as.flag.flag	Create and Manipulate Flags
as.halfmatrix	Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.halfmatrix.default	Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.halfmatrix.halfmatrix	Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.hour	Interconvert Nominal Time Units
as.hour.day	Interconvert Nominal Time Units
as.hour.duration	Interconvert Nominal Time Units
as.hour.hour	Interconvert Nominal Time Units
as.hour.minute	Interconvert Nominal Time Units
as.hour.numeric	Interconvert Nominal Time Units
as.hour.second	Interconvert Nominal Time Units
as.init	Work with Initial Estimates as Objects
as.init.init	Work with Initial Estimates as Objects
as.init.numeric	Work with Initial Estimates as Objects
as.initList	Work with Initial Estimates as Objects
as.initList.character	Work with Initial Estimates as Objects
as.initList.initList	Work with Initial Estimates as Objects
as.initList.list	Work with Initial Estimates as Objects
as.initList.numeric	Work with Initial Estimates as Objects
as.isolated	Visualize Static Data Relationships
as.isolated.digest	Visualize Static Data Relationships
as.isolated.isolated	Visualize Static Data Relationships
as.isolated.keyed	Visualize Static Data Relationships
as.keyed	Create and Manipulate Keyed Data Frames
as.keyed.data.frame	Create and Manipulate Keyed Data Frames
as.keyed.nm	Diagnose Static Data Relationships
as.list.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
as.ltable	Convert a Data Frame to a Latex Table
as.matrix.halfmatrix	Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.mDate	Temporal Classes with Selective Defaults
as.mDate.character	Temporal Classes with Selective Defaults
as.mDate.Date	Temporal Classes with Selective Defaults
as.mDate.dates	Temporal Classes with Selective Defaults
as.mDate.mDate	Temporal Classes with Selective Defaults
as.mDate.numeric	Temporal Classes with Selective Defaults
as.mDate.sasdate	Temporal Classes with Selective Defaults
as.mDateTime	Temporal Classes with Selective Defaults
as.mDateTime.character	Temporal Classes with Selective Defaults
as.mDateTime.chron	Temporal Classes with Selective Defaults
as.mDateTime.mDate	Temporal Classes with Selective Defaults
as.mDateTime.mDateTime	Temporal Classes with Selective Defaults
as.mDateTime.numeric	Temporal Classes with Selective Defaults
as.mDateTime.POSIXct	Temporal Classes with Selective Defaults
as.mDateTime.POSIXlt	Temporal Classes with Selective Defaults
as.minute	Interconvert Nominal Time Units
as.minute.duration	Interconvert Nominal Time Units
as.minute.hour	Interconvert Nominal Time Units
as.minute.minute	Interconvert Nominal Time Units
as.minute.numeric	Interconvert Nominal Time Units
as.minute.second	Interconvert Nominal Time Units
as.month	Interconvert Nominal Time Units
as.month.day	Interconvert Nominal Time Units
as.month.duration	Interconvert Nominal Time Units
as.month.month	Interconvert Nominal Time Units
as.month.numeric	Interconvert Nominal Time Units
as.moot	Modify Assembly of nm Objects
as.motif	Visualize Static Data Relationships
as.motif.digest	Visualize Static Data Relationships
as.motif.keyed	Visualize Static Data Relationships
as.motif.motif	Visualize Static Data Relationships
as.motif.nm	Visualize Static Data Relationships
as.mTime	Temporal Classes with Selective Defaults
as.mTime.character	Temporal Classes with Selective Defaults
as.mTime.mTime	Temporal Classes with Selective Defaults
as.mTime.numeric	Temporal Classes with Selective Defaults
as.mTime.times	Temporal Classes with Selective Defaults
as.nm	Create and Manipulate nm Objects
as.nm.data.frame	Create and Manipulate nm Objects
as.nm.default	Create and Manipulate nm Objects
as.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
as.nmctl.character	Create, Manipulate, Read, and Write NONMEM Control Streams
as.numeric.chartime	Support for timepoint Classes
as.pdf	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.pdf.character	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.pdf.data.frame	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.pdf.document	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.pxml	Convert a Param File to XML
as.pxml.ext	Convert a Param File to XML
as.rigged	Modify Assembly of nm Objects
as.roles	Visualize Static Data Relationships
as.roles.digest	Visualize Static Data Relationships
as.roles.keyed	Visualize Static Data Relationships
as.runlog.file	Convert Model Metadata to Various Formats
as.runlog.unilog	Convert Model Metadata to Various Formats
as.second	Interconvert Nominal Time Units
as.second.day	Interconvert Nominal Time Units
as.second.duration	Interconvert Nominal Time Units
as.second.hour	Interconvert Nominal Time Units
as.second.minute	Interconvert Nominal Time Units
as.second.numeric	Interconvert Nominal Time Units
as.second.second	Interconvert Nominal Time Units
as.tabular	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
as.unilog.lst	Convert Model Metadata to Various Formats
as.unilog.pxml	Convert Model Metadata to Various Formats
as.unilog.run	Create a Run Log for NONMEM7 using NONMEM6 Format
as.unilog.runlog	Convert Model Metadata to Various Formats
as.vector.keyed	Binary Operators for Set Relations
as.vector.uniKey	Create and Manipulate Keyed Data Frames
as.week	Interconvert Nominal Time Units
as.week.day	Interconvert Nominal Time Units
as.week.duration	Interconvert Nominal Time Units
as.week.numeric	Interconvert Nominal Time Units
as.week.week	Interconvert Nominal Time Units
as.xml	Represent an Object as XML
as.xml.character	Represent an Object as XML
as.xml.data.frame	Represent an Object as XML
as.xml.default	Represent an Object as XML
as.year	Interconvert Nominal Time Units
as.year.day	Interconvert Nominal Time Units
as.year.duration	Interconvert Nominal Time Units
as.year.numeric	Interconvert Nominal Time Units
as.year.year	Interconvert Nominal Time Units
at	Identify Elements Within Cells Meeting Some Instance of a Condition
attribute	Encode an Attribute for an XML Open Tag
AUC	Calculate AUC Using the Trapezoidal Method
auc	Calculate One-Compartment Model Properties
aug	Augment a List-like Object
autolog.pl	Build Commands to Invoke NONMEM

-- B --

backtrans	Back-transform Columns in a Data Frame
badAmt	Analyze an NM Object
badAmt.nm	Analyze an NM Object
badDv	Analyze an NM Object
badDv.nm	Analyze an NM Object
badII	Analyze an NM Object
badII.nm	Analyze an NM Object
bakfor	Impute Missing Vector Values
before	Identify Elements Within Cells Meeting Some Instance of a Condition
bin	Calculate Bin Sizes and Limits for a Vector
bmi	Calculate Various Clinical Indicators
bounds	Calculate Normal Quantiles at Boundaries of Probability Intervals
bracket	Create an XML Tag
breaks	Identify Boundaries Between Sets of Elements
bsa	Calculate Various Clinical Indicators
bundleRead	Read Data Files from a Directory into a List

-- C --

c.comment	Create and Manipulate Comment Objects
c.flag	Create and Manipulate Flags
c.timepoint	Support for timepoint Classes
c.uniKey	Create and Manipulate Keyed Data Frames
cast-method	Methods for Function 'cast' in Package 'reshape'
cast-methods	Methods for Function 'cast' in Package 'reshape'
cavg	Calculate One-Compartment Model Properties
check.subjects	Summarize Columns of Subject Data
clear	Lookup Alternate Versions of Parameter Codes
CLNR	Delete Files and Directories
closers	Calculate Closing Text for Nested Script Levels
cmax	Calculate One-Compartment Model Properties
cmin	Calculate One-Compartment Model Properties
colname	Change Selected Names
colname<-	Change Selected Names
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 installation.
constant	Test for Nested Factors
constant.default	Test for Nested Factors
contains	Test a Character Vector for Occurences of a Pattern
convertLines	Convert Line Endings
covariatePlots	Create Diagnostic Plots
covplot	Display Distributions with Respect to Reference Values
crcl	Calculate Various Clinical Indicators
CreateParametersForSimulation	Create Parameters for Simulation with Uncertainty
crosses	Test for Nested Factors
css	Calculate One-Compartment Model Properties
ctl2xml	Lookup Alternate Versions of Parameter Codes
cv	Compute Coefficient of Variation for Normal and Log-Normal Data.
cvLognormal	Compute Coefficient of Variation for Normal and Log-Normal Data.
cvNormal	Compute Coefficient of Variation for Normal and Log-Normal Data.
cwresPlots	Create Diagnostic Plots

-- D --

dataFormat	Integrate NONMEM Data for Plotting
dataSynthesis	Build a Standard Plotting Data Set for a Given NONR Run
deranged	Modify Assembly of nm Objects
deranged.data.frame	Modify Assembly of nm Objects
deranged.keyed	Modify Assembly of nm Objects
diagnosticPlots	Create Diagnostic Plots
digest	Diagnose Static Data Relationships
distance	Identify Elements Within Cells Meeting Some Instance of a Condition
divide.keyed	Operator Syntax for Joining Keyed Data Frames
dupKeys	Create and Manipulate Keyed Data Frames
dupKeys.default	Create and Manipulate Keyed Data Frames
dupKeys.nm	Analyze an NM Object
duration	Interconvert Nominal Time Units
dynamic	Return the static portion of an object.
dynamic.data.frame	Return the static portion of an object.
dynamic.keyed	Return the static portion of an object.

-- E --

electronicAppendix	Make an FDA-style Electronic Appendix from a Subversioned Directory.
episcript	Run an Epilog Script in a Pre-populated Environment
explicitPath	Clean Up a Control Stream
extfile	Clean Up a Control Stream
extractPath	Clean Up a Control Stream

-- F --

f	Create and Manipulate Flags
falseAmt	Analyze an NM Object
falseAmt.nm	Analyze an NM Object
falseDv	Analyze an NM Object
falseDv.nm	Analyze an NM Object
filename	Construct a Canonical File Name
findNonmemCommand	Find Paths to Available Nonmem Commands
first	Identify Elements Within Cells Meeting Some Instance of a Condition
fixed	Work with Initial Estimates as Objects
fixed.init	Work with Initial Estimates as Objects
fixed.initList	Work with Initial Estimates as Objects
fixed<-	Work with Initial Estimates as Objects
fixed<-.init	Work with Initial Estimates as Objects
fixed<-.initList	Work with Initial Estimates as Objects
fixedwidth	Apply Fixed-width Formatting to a Data Frame
fixedwidth.data.frame	Apply Fixed-width Formatting to a Data Frame
fixFile	Clean Up a Control Stream
fixProblem	Clean Up a Control Stream
follow	Detect State of a Run Using File Existence Criteria
forbak	Impute Missing Vector Values
format.comment	Create and Manipulate Comment Objects
format.duration	Interconvert Nominal Time Units
format.flag	Create and Manipulate Flags
format.init	Work with Initial Estimates as Objects
format.initList	Work with Initial Estimates as Objects
format.legacy	Visualize Static Data Relationships
format.mDate	Temporal Classes with Selective Defaults
format.mDateTime	Temporal Classes with Selective Defaults
format.mTime	Temporal Classes with Selective Defaults
format.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
format.uniKey	Create and Manipulate Keyed Data Frames
ftable2data.frame	Convert ftable to data.frame

-- G --

getCovs	Return Non-commented Non-duplicated Rows of a NONMEM Data Set
getCwres	Return the Conditional Weighted Residuals Pertinent to a Given Run
getdname	Extract the Path and File from the DATA Block in the Control Stream Associated with a Filename
getdname.default	Extract the Path and File from the DATA Block in the Control Stream Associated with a Filename
getdname.nmctl	Extract the Path and File from the DATA Block in the Control Stream Associated with a Filename
getPars	Return the Non-duplicated (ID) Rows Corresponding to the Specified Filename
getTabs	Return the Observation Rows (EVID==0) Corresponding to the Specified Filename
glue	Paste Items with No Space
groupnames	Construct a Single Vector of Group Names from Possibly Multiple Indices to the Plotting Data Set

-- H --

half	Interconvert Between a Symmetric Matrix and a Triangular Matrix
half.matrix	Interconvert Between a Symmetric Matrix and a Triangular Matrix
hash	Supply Comment Characters with Output
head.digest	Diagnose Static Data Relationships
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
hidden	Create and Manipulate Comment Objects
hidden.data.frame	Create and Manipulate Comment Objects
hide	Create and Manipulate Comment Objects
hide.data.frame	Create and Manipulate Comment Objects

-- I --

ibw	Calculate Various Clinical Indicators
ignored	Augment NONMEM Input with Table Output
ind.cwres	Compute the Conditional Weighted Residuals
index	Visualize Static Data Relationships
index.conditioned	Visualize Static Data Relationships
index.digest	Visualize Static Data Relationships
index.isolated	Visualize Static Data Relationships
index.keyed	Visualize Static Data Relationships
index.nm	Visualize Static Data Relationships
init	Work with Initial Estimates as Objects
initList	Work with Initial Estimates as Objects
inner	Limit Data to Inner Quantiles by Imputing NA.
inner.data.frame	Limit Data to Inner Quantiles by Imputing NA.
is.alpha	Test For Alphabetic Content
is.cwres.readable.file	Compute the Conditional Weighted Residuals
is.defined	Test Whether Values are Defined
is.diagonal	Analyze Parameter Labels
is.fixed	Analyze Parameter Labels
is.iiv	Analyze Parameter Labels
is.latex.token	Determine if String is Valid Latex Command or Environment
is.offdiagonal	Analyze Parameter Labels
is.one.nonalpha	Check That Each Element is a Single Non-letter
is.random	Analyze Parameter Labels
is.residual	Analyze Parameter Labels
is.square	Test Whether a Matrix is Square
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 from Covariance to Correlation

-- J --

justUnits

Extract Substring of Wiki Math

-- K --

ke	Calculate One-Compartment Model Properties
key	Create and Manipulate Keyed Data Frames
key<-	Create and Manipulate Keyed Data Frames
keyed-class	Class '"keyed"'

-- L --

last	Identify Elements Within Cells Meeting Some Instance of a Condition
latest	Identify the Latest Variants of Each File as Distinguished by Enclosing Subdirectories
latex.args	Format Latex Command Arguments
latex.options	Format Latex Command Options
lbm	Calculate Various Clinical Indicators
left.keyed	Operator Syntax for Joining Keyed Data Frames
legacy	Visualize Static Data Relationships
legacy<-	Visualize Static Data Relationships
lhs	Extract Substring of Wiki Math
locf	Impute Missing Vector Values
lookup	Lookup Alternate Versions of Parameter Codes
lookup.one	Lookup Alternate Versions of Parameter Codes
lower	Calculate Normal Quantiles at Boundaries of Probability Intervals
ltable	Convert a Data Frame to a Latex Table
ltable.data.frame	Convert a Data Frame to a Latex Table
lyse	Return the static portion of an object.
lyse.data.frame	Return the static portion of an object.
lyse.keyed	Return the static portion of an object.

-- M --

map	Map One Set of Values to Another
maxChar	Check Some Properties of Vectors
mDate	Temporal Classes with Selective Defaults
mDateTime	Temporal Classes with Selective Defaults
melt.keyed	Melt a Keyed Data Frame
merge.keyed	Create and Manipulate Keyed Data Frames
merge.nm	Create and Manipulate nm Objects
metaMerge	Recursively Merge Multiple Tables
metaMerge.character	Recursively Merge Multiple Tables
metaMerge.default	Recursively Merge Multiple Tables
metaMerge.list	Recursively Merge Multiple Tables
metaSub	Create Replicate Text files with Systematic Substitutions
metaSub.character	Create Replicate Text files with Systematic Substitutions
metaSub.filename	Create Replicate Text files with Systematic Substitutions
metrumrg	Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting
metrumrgURL	View a metrumrg Package File
minus.keyed	Operator Syntax for Joining Keyed Data Frames
minus.moot	Modify Assembly of nm Objects
moot	Modify Assembly of nm Objects
moot.nm	Modify Assembly of nm Objects
motif	Visualize Static Data Relationships
msffile	Clean Up a Control Stream
mTime	Temporal Classes with Selective Defaults

-- N --

naInContext	Display Missing Values in Context
naKeys	Create and Manipulate Keyed Data Frames
naKeys.default	Create and Manipulate Keyed Data Frames
naKeys.nm	Analyze an NM Object
name	Change Selected Names
name<-	Change Selected Names
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
nm	Create and Manipulate nm Objects
nm.data-class	Compute the Conditional Weighted Residuals
nm.pl	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
nocb	Impute Missing Vector Values
NONR	Run NONMEM
NONR72	Run NONMEM
noPk	Analyze an NM Object
noPk.nm	Analyze an NM Object
nospace	Extract Substring of Wiki Math
not.keyed	Operator Syntax for Joining Keyed Data Frames
noUnits	Extract Substring of Wiki Math
nth	Identify Elements Within Cells Meeting Some Instance of a Condition
nxt	Check Some Properties of Vectors

-- O --

offdiag	Interconvert Between a Symmetric Matrix and a Triangular Matrix
offdiag.halfmatrix	Interconvert Between a Symmetric Matrix and a Triangular Matrix
omegacor	Convert NONMEM Omega Covariance Matrix to Correlation Matrix
on.diagonal	Analyze Parameter Labels
only	Identify Elements Within Cells Meeting Some Instance of a Condition
Ops.keyed	Operator Syntax for Joining Keyed Data Frames
ord	Give the Order of a Symmetric Matrix or Half Matrix
ord.halfmatrix	Give the Order of a Symmetric Matrix or Half Matrix
ord.matrix	Give the Order of a Symmetric Matrix or Half Matrix

-- P --

packageCheck	Load a Package and Run Package-level Examples for Testing Purposes
padded	Format Numeric Vectors Specially
panel.bar	Plot Histograms Flexibly
panel.covplot	Display Distributions with Respect to Reference Values
panel.cuts	Display Distributions with Respect to Reference Values
panel.densitystrip	Display Distributions with Respect to Reference Values
panel.hist	Plot Histograms Flexibly
panel.ref	Display Distributions with Respect to Reference Values
panel.stratify	Handle Each Level of a Stripplot Separately
parameter2wiki	Convert Parameter Labels to Wikimath
params	List Documented Parameters
parens	Wrap Text in Parentheses
parfile	Clean Up a Control Stream
partab	Construct a Parameter Table
percent	Calculate Percent.
plot.conditioned	Visualize Static Data Relationships
plot.digest	Visualize Static Data Relationships
plot.isolated	Visualize Static Data Relationships
plot.keyed	Visualize Static Data Relationships
plot.nm	Plot An Object of Class nm
plotfilename	Make a Name for a Diagnostic Plot File
PLOTR	Create Diagnostic Plots for a NONMEM Run
plus.keyed	Operator Syntax for Joining Keyed Data Frames
plus.rigged	Modify Assembly of nm Objects
pool	Test Set Relations Among Two Vectors
posmat	Coerce a Matrix to be Positive Definite
predoseDv	Analyze an NM Object
predoseDv.nm	Analyze an NM Object
prev	Check Some Properties of Vectors
print.comment	Create and Manipulate Comment Objects
print.duration	Interconvert Nominal Time Units
print.flag	Create and Manipulate Flags
print.halfmatrix	Interconvert Between a Symmetric Matrix and a Triangular Matrix
print.init	Work with Initial Estimates as Objects
print.initList	Work with Initial Estimates as Objects
print.keyed.summary	Create and Manipulate Keyed Data Frames
print.nm.summary	Analyze an NM Object
print.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
print.timepoint	Support for timepoint Classes
print.uniKey	Create and Manipulate Keyed Data Frames
progress	Detect State of a Run Using File Existence Criteria
purge.dir	Purge a Directory
purge.files	Purge Files
purgeRunDir	Generate a Combined Run Log from Multiple NONMEM Runs

-- Q --

qstat	Invoke SGE qstat
qsub	Build Commands to Invoke SGE qsub

-- R --

raised.keyed	Operator Syntax for Joining Keyed Data Frames
random	Select Random Members of an Object
random.data.frame	Select Random Members of an Object
read.cwres.data	Compute the Conditional Weighted Residuals
read.nm	Create and Manipulate nm Objects
read.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
reapply	Apply a Function Across Cells of an Indexed Vector, Giving an Identically-indexed Result
rep.comment	Create and Manipulate Comment Objects
rep.flag	Create and Manipulate Flags
rep.timepoint	Support for timepoint Classes
rep.uniKey	Create and Manipulate Keyed Data Frames
resample	Create Replicate Data Sets by Stratified Sampling
resample.csv.filename	Create Replicate Data Sets by Stratified Sampling
resample.data.frame	Create Replicate Data Sets by Stratified Sampling
resample.filename	Create Replicate Data Sets by Stratified Sampling
resolve	Clean Up a Control Stream
rhs	Extract Substring of Wiki Math
rig	Modify Assembly of nm Objects
rig.nm	Modify Assembly of nm Objects
rinvchisq	Generate Inverse Chi-square Distribution
riwish	Generate Inverse Wishart Distribution
rlog	Generate a Combined Run Log from Multiple NONMEM Runs
roles	Visualize Static Data Relationships
row2tabular	Format Vector for Latex Tabular Row
runCommand	Issue the System Call That Invokes NONMEM
runhead	Check Some Properties of Vectors
runlog	Convert Model Metadata to Various Formats
runNonmem	Process a Request for NONMEM Invocation
runstate	Detect State of a Run Using File Existence Criteria

-- S --

safe.call	Call a Function Safely
safeQuote	Single-quote Conditionally
scavenge	Clean Up a Control Stream
seq.timepoint	Support for timepoint Classes
setCwres	Append Conditional Weighted Residuals to an Appropriate File
shuffle	Move the Columns of a Data Frame Relative to Each Other
sigmacor	Convert NONMEM Omega Covariance Matrix to Correlation Matrix
simblock	Generate Random Effect Deviates for Simulation
simpar	Create Parameters for Simulation with Uncertainty
snap	Coerce Values to Nearest of Candidates
sort.keyed	Create and Manipulate Keyed Data Frames
sortedInstall	Install Local Source Packages Sorted by Dependency
spaces	Generate a String of Spaces
splom.conditioned	Visualize Static Data Relationships
splom.digest	Visualize Static Data Relationships
splom.keyed	Visualize Static Data Relationships
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.
static.data.frame	Return the static portion of an object.
static.keyed	Return the static portion of an object.
strain	Reduce x to Those Elements that Occur in Options
summary.hidden.data.frame	Create and Manipulate Comment Objects
summary.keyed	Create and Manipulate Keyed Data Frames
summary.nm	Analyze an NM Object
Summary.timepoint	Temporal Classes with Selective Defaults
superset	Augment NONMEM Input with Table Output
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, Picking Up Novel Columns

-- T --

tabfile	Clean Up a Control Stream
tabular	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
tabular.data.frame	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
tabularformat	Create the Format String for Latex Tabular Environment
tagvalue	Convert List to Tag and Value Format
tex2pdf	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
text2decimal	Convert Mixed Text to Decimal
timeline	Temporal Classes with Selective Defaults
timepoint	Temporal Classes with Selective Defaults
times.keyed	Operator Syntax for Joining Keyed Data Frames
titleCase	Convert Text to Title Case
Tmax	Calculate Tmax
tmax	Calculate One-Compartment Model Properties
Tmin	Calculate Tmin
tos	Extract Substring of Wiki Math
totitle	Convert Text to Title Case
transform.keyed	Create and Manipulate Keyed Data Frames
TruncateParametersForSimulation	Create Parameters for Simulation with Uncertainty
tweak	Adjust Values
tweak.init	Adjust Values
tweak.initList	Adjust Values
tweak.nmctl	Adjust Values

-- U --

uniKey	Create and Manipulate Keyed Data Frames
uniKey.keyed	Create and Manipulate Keyed Data Frames
unilog	Convert Model Metadata to Various Formats
unilogcor	Convert NONMEM Omega Covariance Matrix to Correlation Matrix
unique.comment	Create and Manipulate Comment Objects
unique.timepoint	Temporal Classes with Selective Defaults
unique.uniKey	Create and Manipulate Keyed Data Frames
unitDensity	Display Distributions with Respect to Reference Values
unitHist	Plot Histograms Flexibly
unsorted	Create and Manipulate Keyed Data Frames
unsorted.keyed	Create and Manipulate Keyed Data Frames
upper	Calculate Normal Quantiles at Boundaries of Probability Intervals

-- V --

variants	Locate Variants of a File in Distinctive Subdirectories
viewtex	Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF

-- W --

wiki2label	Parse Wikimath
wiki2latex	Parse Wikimath
wiki2parameter	Parse Wikimath
wiki2plotmath	Parse Wikimath
wikimath	Parse Wikimath
wikiparse	Parse Wikimath
wikitab	Construct a Parameter Table
win	Identify Windows Platforms
wrap	Wrap Text in a Latex Environment
write.nm	Create and Manipulate nm Objects
write.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams

-- X --

xpath	Extract Value of an xpath Expression from and XML File
xtfrm.comment	Create and Manipulate Comment Objects
xtfrm.flag	Create and Manipulate Flags
xtfrm.timepoint	Temporal Classes with Selective Defaults
xtfrm.uniKey	Create and Manipulate Keyed Data Frames
xyplotExt	Plot the Parameter Search History for a NONMEM 7 Run

-- Z --

zeroAmt	Analyze an NM Object
zeroAmt.nm	Analyze an NM Object
zeroDv	Analyze an NM Object
zeroDv.nm	Analyze an NM Object

-- misc --

$.init	Work with Initial Estimates as Objects
$<-.init	Work with Initial Estimates as Objects
%&%	Binary Operators for Set Relations
%&%.default	Binary Operators for Set Relations
%+%	Binary Operators for Set Relations
%+%.default	Binary Operators for Set Relations
%-%	Binary Operators for Set Relations
%-%.default	Binary Operators for Set Relations
%contains%	Test a Character Vector for Occurences of a Pattern
%crossed.on%	Test for Nested Factors
%crosses%	Test for Nested Factors
%n%	Binary Operators for Set Relations
%nested.in%	Test for Nested Factors
%nests%	Test for Nested Factors
%u%	Binary Operators for Set Relations
+.timeline	Temporal Classes with Selective Defaults
-.timeline	Temporal Classes with Selective Defaults
[.comment	Create and Manipulate Comment Objects
[.conditioned	Visualize Static Data Relationships
[.digest	Diagnose Static Data Relationships
[.flag	Create and Manipulate Flags
[.initList	Work with Initial Estimates as Objects
[.keyed	Create and Manipulate Keyed Data Frames
[.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
[.timepoint	Support for timepoint Classes
[.uniKey	Create and Manipulate Keyed Data Frames
[<-.timepoint	Support for timepoint Classes
[[.comment	Create and Manipulate Comment Objects
[[.flag	Create and Manipulate Flags
[[.nmctl	Create, Manipulate, Read, and Write NONMEM Control Streams
[[.timepoint	Support for timepoint Classes
[[.uniKey	Create and Manipulate Keyed Data Frames