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

[Up] [Top]

Documentation for package ‘metrumrg’ version 5.55

Help Pages

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.spec Create and Manipulate spec Objects
as.spec.character Create and Manipulate spec Objects
as.spec.data.frame Create and Manipulate spec Objects
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.spec Create and Manipulate spec Objects
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.timeline 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
codes Recover Metadata from spec Objects and their Components
codes.default Recover Metadata from spec Objects and their Components
codes.spec Recover Metadata from spec Objects and their Components
colname Change Selected Names
colname<- Change Selected Names
combinations Display Combinations of Column Values
combinations.data.frame 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 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
decodes Recover Metadata from spec Objects and their Components
decodes.default Recover Metadata from spec Objects and their Components
decodes.spec Recover Metadata from spec Objects and their Components
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.
encode Encode Factor-like Levels and Labels as a Simple String
encode.character Encode Factor-like Levels and Labels as a Simple String
encode.default Encode Factor-like Levels and Labels as a Simple String
encode.list Encode Factor-like Levels and Labels as a Simple String
encoded Recover Metadata from spec Objects and their Components
encoded.default Recover Metadata from spec Objects and their Components
encoded.spec Recover Metadata from spec Objects and their Components
episcript Run an Epilog Script in a Pre-populated Environment
explicitPath Clean Up a Control Stream
extfile Clean Up a Control Stream
extract Extract a Parenthetically-grouped Substring of a Regular Expression
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
guidetext Recover Metadata from spec Objects and their Components
guidetext.spec Recover Metadata from spec Objects and their Components

-- 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 --

labels.spec Recover Metadata from spec Objects and their Components
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 --

makePreamble Convert a Data Frame to a Latex Tabular Environment, Latex Document, or PDF
map Map One Set of Values to Another
matches Test the Correspondence between a Table and a Specification
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
metaMerge Recursively Merge Multiple Tables
metaMerge.character Recursively Merge Multiple Tables
metaMerge.data.frame Recursively Merge Multiple Tables
metaMerge.default Recursively Merge Multiple Tables
metaMerge.list Recursively Merge Multiple Tables
metaMerge.NULL 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
monotonic Determine Whether a Vector is Monotonic
monotonic.default Determine Whether a Vector is Monotonic
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
nondecreasing Determine Whether a Vector is Monotonic
nondecreasing.default Determine Whether a Vector is Monotonic
nonincreasing Determine Whether a Vector is Monotonic
nonincreasing.default Determine Whether a Vector is Monotonic
NONR 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
read.spec Create and Manipulate spec Objects
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.timeline 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.timeline 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
specfile Determine the Expected Path to a Specification File
specification Create a Data Specification Corresponding to a Particular Data Set
specification.comment Create a Data Specification Corresponding to a Particular Data Set
specification.data.frame Create a Data Specification Corresponding to a Particular Data Set
specification.default Create a Data Specification Corresponding to a Particular Data Set
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.spec Create and Manipulate spec Objects
Summary.timepoint Temporal Classes with Selective Defaults
superset Augment NONMEM Input with Table Output
supp Merge CDISC Supplemental Data
supp.data.frame Merge CDISC Supplemental Data
supp.keyed 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, 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
write.spec Create and Manipulate spec Objects

-- X --

xlog Extract Indexed Values from XML
xmlValue.XMLAttributeValue Extract Indexed Values from XML
xpath Extract Value of an xpath Expression from and XML File
xpath2frame Extract Indexed Values from XML
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
%matches% Test the Correspondence between a Table and a Specification
%matches%.character Test the Correspondence between a Table and a Specification
%matches%.data.frame Test the Correspondence between a Table and a Specification
%matches%.keyed Test the Correspondence between a Table and a Specification
%matches%.spec Test the Correspondence between a Table and a Specification
%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
[.timeline 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
[[.timeline Support for timepoint Classes
[[.uniKey Create and Manipulate Keyed Data Frames