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

## Documentation for package ‘metrumrg’ version 5.3

- DESCRIPTION file.

## 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
after | Identify Elements Within Cells Meeting Some Instance of a Condition
aggregate.keyed | Create and Manipulate Keyed Data Frames
align.decimal | Format a Vector Aligning on Decimal
and.keyed | Operator Syntax for Joining Keyed Data Frames
as.character.comment | Create and Manipulate Comment Objects
as.character.flag | Create and Manipulate Flags
as.character.nmctl | Create, Manipulate, Read, and Write NONMEM Control Streams
as.character.temporal | Support for temporal Classes
as.chartime | Support for temporal Classes
as.chartime.numeric | Support for temporal 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.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.document | 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.document.tabular | 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.keyed | Create and Manipulate Keyed Data Frames
as.keyed.data.frame | Create and Manipulate Keyed Data Frames
as.list.nmctl | Create, Manipulate, Read, and Write NONMEM Control Streams
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.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.moot | Modify Assembly of nm Objects
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.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 temporal Classes
as.pdf | 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.pdf.tabular | 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.runlog.file | Convert Model Metadata to Various Formats
as.runlog.unilog | Convert Model Metadata to Various Formats
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.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
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
bracket | Create an XML Tag
breaks | Identify Boundaries Between Sets of Elements
bsa | Calculate Various Clinical Indicators

## -- C --

c.comment | Create and Manipulate Comment Objects
c.flag | Create and Manipulate Flags
c.temporal | Support for temporal Classes
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
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
ctl | A Sample NONMEM(r) Control Stream
ctl2xml | Lookup Alternate Versions of Parameter Codes
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
distance | Identify Elements Within Cells Meeting Some Instance of a Condition
dupKeys | Create and Manipulate Keyed Data Frames
dupKeys.default | Create and Manipulate Keyed Data Frames
dupKeys.nm | Analyze an NM 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
first | Identify Elements Within Cells Meeting Some Instance of a Condition
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
forbak | Impute Missing Vector Values
format.comment | Create and Manipulate Comment Objects
format.flag | Create and Manipulate Flags
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
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
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
helpAdminister | metrumrg: Administrative
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
ind.cwres | Compute the Conditional Weighted Residuals
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.latex.token | Determine if String is Valid Latex Command or Environment
is.one.nonalpha | Check That Each Element is a Single Non-letter
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

## -- 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
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
ltable | Convert a Data Frame to a Latex Table
ltable.data.frame | Convert a Data Frame to a Latex Table

## -- M --

map | Map One Set of Values to Another
maxChar | Check Some Properties of Vectors
merge.keyed | Create and Manipulate Keyed Data Frames
merge.nm | Create and Manipulate nm Objects
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
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
msffile | Clean Up a Control Stream

## -- 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~~
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
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
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
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
params | List Documented Parameters
parens | Wrap Text in Parentheses
parfile | Clean Up a Control Stream
partab | Construct a Parameter Table
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
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.flag | Create and Manipulate Flags
print.halfmatrix | Interconvert Between a Symmetric Matrix and a Triangular Matrix
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.temporal | Support for temporal Classes
purge.dir | Purge a Directory
purge.files | Purge Files

## -- Q --

qsub | Build Commands to Invoke SGE qsub

## -- R --

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.temporal | Support for temporal Classes
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
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 Existance Criteria

## -- S --

safe.call | Call a Function Safely
safeQuote | Single-quote Conditionally ~~
scavenge | Clean Up a Control Stream
seq.temporal | Support for temporal 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
spaces | Generate a String of Spaces
sqrtm | Help Calculate CWRES
stableMerge | Execute a Stable Left Join
star | Replace Asterisk in x With y
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
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
temporal | Temporal Classes with Selective Defaults
text2decimal | Convert Mixed Text to Decimal
Tmax | Calculate Tmax
tmax | Calculate One-Compartment Model Properties
Tmin | Calculate Tmin
tos | Extract Substring of Wiki Math
transform.keyed | Create and Manipulate Keyed Data Frames
TruncateParametersForSimulation | Create Parameters for Simulation with Uncertainty

## -- 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.temporal | Temporal Classes with Selective Defaults
unitDensity | Display Distributions with Respect to Reference Values
unitHist | Plot Histograms Flexibly

## -- V --

variants | Locate Variants of a File in Distinctive Subdirectories

## -- 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 --

xtfrm.comment | Create and Manipulate Comment Objects
xtfrm.flag | Create and Manipulate Flags
xtfrm.temporal | Temporal Classes with Selective Defaults
xyplot.ext | 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 --

%contains% | Test a Character Vector for Occurences of a Pattern
%nested.in% | Test for Nested Factors
%nests% | Test for Nested Factors
[.comment | Create and Manipulate Comment Objects
[.flag | Create and Manipulate Flags
[.keyed | Create and Manipulate Keyed Data Frames
[.nmctl | Create, Manipulate, Read, and Write NONMEM Control Streams
[.temporal | Support for temporal Classes
[<-.temporal | Support for temporal Classes
[[.comment | Create and Manipulate Comment Objects
[[.flag | Create and Manipulate Flags
[[.nmctl | Create, Manipulate, Read, and Write NONMEM Control Streams
[[.temporal | Support for temporal Classes