metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting
Version 5.57

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 <billk@metrumrg.com>
LicenseGPL
Version5.57
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("metrumrg", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

as.nmctl: Create, Manipulate, Read, and Write NONMEM Control Streams
AUC: Calculate AUC Using the Trapezoidal Method
justUnits: Extract Substring of Wiki Math
omegacor: Extract NONMEM Covariance or Correlation Matrices
specification: Create a Data Specification Corresponding to a Particular...
summary.nm: Analyze an NM Object
supp: Merge CDISC Supplemental Data
See all...

All man pages Function index File listing

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
as.best: Coerce data unambiguously to numeric or character
as.comment: Create and Manipulate Comment Objects
as.data.frame.block: 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
as.unilog.run: 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
inner.data.frame: 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
is.one.nonalpha: 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
ltable.data.frame: 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
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
NONR: Run NONMEM
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...
resample.data.frame: 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
safe.call: 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,...
tabular.data.frame: 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

Functions

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/CLNR.R
R/NONR.R
R/PLOTR.R
R/Tmax.R
R/accept.R
R/addl.R
R/as.best.R
R/as.comment.R
R/as.data.frame.block.R
R/as.define.R
R/as.digest.R
R/as.digest.data.frame.R
R/as.document.R
R/as.filename.R
R/as.flag.R
R/as.init.R
R/as.keyed.R
R/as.nm.R
R/as.nmctl.R
R/as.second.R
R/as.xml.R
R/attribute.R
R/bin.R
R/bounds.R
R/bracket.R
R/bundleRead.R
R/cast.R
R/check.subjects.R
R/colname.R
R/combinations.R
R/compute.cwres.R
R/constant.R
R/contains.R
R/convertLines.R
R/covariatePlots.R
R/css.R
R/cv.R
R/diagnosticPlots.R
R/electronicAppendix.R
R/findNonmemCommand.R
R/first.R
R/fixedwidth.R
R/ftable2data.frame.R
R/glue.R
R/hash.R
R/ibw.R
R/inner.data.frame.R
R/is.diagonal.R
R/iterations.R
R/latest.R
R/latex.R
R/locf.R
R/lookup.R
R/map.R
R/menu.define.R
R/metaMerge.R
R/metaSub.character.R
R/metrumrgURL.R
R/monotonic.R
R/nasum.R
R/nest.R
R/nmtrantab.define.R
R/omegacor.R
R/ops.keyed.R
R/panel.densitystrip.R
R/panel.hist.R
R/panel.stratify.R
R/parameter2wiki.R
R/params.R
R/parens.R
R/partab.R
R/percent.R
R/plot.nm.R
R/prev.R
R/qstat.R
R/random.R
R/read.cwres.data.R
R/reapply.R
R/resample.data.frame.R
R/rig.R
R/rlog.R
R/runCommand.R
R/runNonmem.R
R/runlog.R
R/safeQuote.R
R/sets.R
R/shuffle.R
R/simpar.R
R/snap.R
R/sortedInstall.R
R/spec.R
R/stableMerge.R
R/static.R
R/superset.R
R/supp.R
R/svnProp.R
R/tabular.data.frame.R
R/temporal.R
R/timeline.R
R/totitle.R
R/variants.R
R/wikimath.R
R/xpath2frame.R
R/xyplot.ext.R
R/zzz.R
inst
inst/CITATION
inst/example
inst/example/misc
inst/example/misc/8.ctl
inst/example/misc/epilog.R
inst/example/misc/metrumrgRunLogNM6.for
inst/example/misc/metrumrgboot.for
inst/example/project
inst/example/project/data
inst/example/project/data/derived
inst/example/project/data/derived/phase1.csv
inst/example/project/data/source
inst/example/project/data/source/dem.csv
inst/example/project/data/source/dose.csv
inst/example/project/data/source/pk.csv
inst/example/project/nonmem
inst/example/project/nonmem/1005
inst/example/project/nonmem/1005/1005.cat
inst/example/project/nonmem/1005/1005.coi
inst/example/project/nonmem/1005/1005.cor
inst/example/project/nonmem/1005/1005.cov
inst/example/project/nonmem/1005/1005.cpu
inst/example/project/nonmem/1005/1005.ctl
inst/example/project/nonmem/1005/1005.ext
inst/example/project/nonmem/1005/1005.grd
inst/example/project/nonmem/1005/1005.log.xml
inst/example/project/nonmem/1005/1005.lst
inst/example/project/nonmem/1005/1005.msf
inst/example/project/nonmem/1005/1005.pdf
inst/example/project/nonmem/1005/1005.phi
inst/example/project/nonmem/1005/1005.shk
inst/example/project/nonmem/1005/1005.shm
inst/example/project/nonmem/1005/1005.tab
inst/example/project/nonmem/1005/1005.xml
inst/example/project/nonmem/1005/1005_ETAS.msf
inst/example/project/nonmem/1005/1005_RMAT.msf
inst/example/project/nonmem/1005/1005_SMAT.msf
inst/example/project/nonmem/1005/1005par.tab
inst/example/project/nonmem/1005/INTER
inst/example/project/nonmem/1005bootlog.csv
inst/example/project/nonmem/ctl
inst/example/project/nonmem/ctl/1001.ctl
inst/example/project/nonmem/ctl/1002.ctl
inst/example/project/nonmem/ctl/1003.ctl
inst/example/project/nonmem/ctl/1004.ctl
inst/example/project/nonmem/ctl/1005.ctl
inst/example/project/nonmem/ctl/1006.ctl
inst/example/project/nonmem/ctl/1105.ctl
inst/example/project/nonmem/ctl/template.pnm
inst/example/project/nonmem/sim
inst/example/project/nonmem/sim/1.ctl
inst/example/project/nonmem/sim/10.ctl
inst/example/project/nonmem/sim/2.ctl
inst/example/project/nonmem/sim/3.ctl
inst/example/project/nonmem/sim/4.ctl
inst/example/project/nonmem/sim/5.ctl
inst/example/project/nonmem/sim/6.ctl
inst/example/project/nonmem/sim/7.ctl
inst/example/project/nonmem/sim/8.ctl
inst/example/project/nonmem/sim/9.ctl
inst/example/project/script
inst/example/project/script/Sweave.sty
inst/example/project/script/assemble.Rnw
inst/example/project/script/assemble.pdf
inst/example/project/script/assemble.tex
inst/example/project/script/covplot-covplot.pdf
inst/example/project/script/covplot.Rnw
inst/example/project/script/covplot.pdf
inst/example/project/script/covplot.tex
inst/example/project/script/logo.png
inst/example/project/script/model-covplot.pdf
inst/example/project/script/model-qq.pdf
inst/example/project/script/model-qqdensity.pdf
inst/example/project/script/model-qqdetail.pdf
inst/example/project/script/model.Rnw
inst/example/project/script/model.pdf
inst/example/project/script/model.tex
inst/example/project/script/parameters.Rnw
inst/example/project/script/parameters.pdf
inst/example/project/script/parameters.tex
inst/example/project/script/settings.sty
inst/example/project/script/simpar.Rnw
inst/example/project/script/simpar.pdf
inst/example/project/script/simpar.tex
inst/example/tabular
inst/example/tabular/Sweave.sty
inst/example/tabular/logo.png
inst/example/tabular/tabular.Rnw
inst/example/tabular/tabular.pdf
inst/example/tabular/tabular.tex
inst/example/wikimath
inst/example/wikimath/Sweave.sty
inst/example/wikimath/logo.png
inst/example/wikimath/wikimath-figure.pdf
inst/example/wikimath/wikimath.Rnw
inst/example/wikimath/wikimath.pdf
inst/example/wikimath/wikimath.tex
man
man/AUC.Rd
man/CLNR.Rd
man/NONR.Rd
man/PLOTR.Rd
man/Tmax.Rd
man/Tmin.Rd
man/accept.Rd
man/acceptance.Rd
man/addl.Rd
man/align.decimal.Rd
man/as.best.Rd
man/as.comment.Rd
man/as.data.frame.block.Rd
man/as.define.Rd
man/as.init.Rd
man/as.keyed.Rd
man/as.nm.Rd
man/as.nmctl.Rd
man/as.pxml.Rd
man/as.second.Rd
man/as.spec.Rd
man/as.unilog.run.Rd
man/as.xml.Rd
man/attribute.Rd
man/aug.Rd
man/backtrans.Rd
man/bin.Rd
man/bounds.Rd
man/bracket.Rd
man/breaks.Rd
man/bundleRead.Rd
man/c.temporal.Rd
man/cast-methods.Rd
man/check.subjects.Rd
man/closers.Rd
man/codes.Rd
man/colname.Rd
man/combinations.Rd
man/command.Rd
man/compileflag.Rd
man/compiler.Rd
man/compute.cwres.Rd
man/config.Rd
man/constant.Rd
man/contains.Rd
man/convertLines.Rd
man/css.Rd
man/cv.Rd
man/dataFormat.Rd
man/dataSynthesis.Rd
man/diagnosticPlots.Rd
man/digest.Rd
man/electronicAppendix.Rd
man/encode.Rd
man/episcript.Rd
man/extensions.Rd
man/extract.Rd
man/filename.Rd
man/findNonmemCommand.Rd
man/first.Rd
man/fixProblem.Rd
man/fixedwidth.Rd
man/flag.Rd
man/ftable2data.frame.Rd
man/getCovs.Rd
man/getCwres.Rd
man/getPars.Rd
man/getTabs.Rd
man/getdname.Rd
man/glue.Rd
man/groupnames.Rd
man/half.matrix.Rd
man/hash.Rd
man/helpAdminister.Rd
man/helpBrowse.Rd
man/helpClasses.Rd
man/helpDataFrame.Rd
man/helpList.Rd
man/helpMatrix.Rd
man/helpModel.Rd
man/helpPharmacometric.Rd
man/helpPrepare.Rd
man/helpQuantify.Rd
man/helpReport.Rd
man/helpSimulate.Rd
man/helpStrategic.Rd
man/helpVector.Rd
man/helpVisualize.Rd
man/ibw.Rd
man/index.Rd
man/inner.data.frame.Rd
man/is.alpha.Rd
man/is.defined.Rd
man/is.diagonal.Rd
man/is.latex.token.Rd
man/is.one.nonalpha.Rd
man/is.square.matrix.Rd
man/isSubversioned.Rd
man/isSubversionedFile.Rd
man/iterations.Rd
man/justUnits.Rd
man/keyed-class.Rd
man/latest.Rd
man/latex.args.Rd
man/latex.options.Rd
man/locf.Rd
man/lookup.Rd
man/ltable.data.frame.Rd
man/map.Rd
man/matches.Rd
man/melt.keyed.Rd
man/metaMerge.Rd
man/metaSub.character.Rd
man/metrumrg-package.Rd
man/metrumrgURL.Rd
man/monotonic.Rd
man/naInContext.Rd
man/nasum.Rd
man/ncomma.Rd
man/nest.Rd
man/nix.Rd
man/nm.pl.Rd
man/nmPlots.Rd
man/nmVersion.Rd
man/omegacor.Rd
man/ops.Rd
man/ord.matrix.Rd
man/packageCheck.Rd
man/panel.densitystrip.Rd
man/panel.hist.Rd
man/panel.stratify.Rd
man/parameter2wiki.Rd
man/params.Rd
man/parens.Rd
man/partab.Rd
man/percent.Rd
man/plot.nm.Rd
man/plotFileName.Rd
man/pool.Rd
man/posmat.Rd
man/prev.Rd
man/purge.dir.Rd
man/purge.files.Rd
man/qstat.Rd
man/qsub.Rd
man/random.Rd
man/reapply.Rd
man/resample.data.frame.Rd
man/rinvchisq.Rd
man/riwish.Rd
man/rlog.Rd
man/row2tabular.Rd
man/runCommand.Rd
man/runNonmem.Rd
man/runlog.Rd
man/runstate.Rd
man/safe.call.Rd
man/safeQuote.Rd
man/setCwres.Rd
man/sets.Rd
man/shuffle.Rd
man/simblock.Rd
man/simpar.Rd
man/snap.Rd
man/sortedInstall.Rd
man/spaces.Rd
man/specfile.Rd
man/specification.Rd
man/sqrtm.Rd
man/stableMerge.Rd
man/star.Rd
man/static.Rd
man/strain.Rd
man/summary.nm.Rd
man/superset.Rd
man/supp.Rd
man/svnIsText.Rd
man/svnMarkAsNonText.Rd
man/svnMarkAsText.Rd
man/svnMimeType.Rd
man/svnPropGet.Rd
man/svnPropGetFile.Rd
man/svnPropSet.Rd
man/svnPropSetFile.Rd
man/svnSetMimeType.Rd
man/synthesis.Rd
man/tabular.data.frame.Rd
man/tabularformat.Rd
man/tagvalue.Rd
man/temporal.Rd
man/text2decimal.Rd
man/toSAS.Rd
man/totitle.Rd
man/tweak.Rd
man/variants.Rd
man/wikiparse.Rd
man/win.Rd
man/wrap.Rd
man/xpath.Rd
man/xpath2frame.Rd
man/xyplot.ext.Rd
metrumrg documentation built on May 21, 2017, 3:29 a.m.

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