helpList: metrumrg: Defined Functions
In metrumresearchgroup/metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting
Description
Exhaustive list of functions defined by metrumrg.
Details
metrumrg
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[.comment subset a comment
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[.conditioned subset a conditioned object
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[.digest subset a digest object
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[.flag subset a flag
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[.initList subset initList
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[.keyed subset a keyed data frame
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[.nmctl subset a control stream object
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[.timeline subset a timeline object
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[.uniKey subset a uniKey object
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[[.comment select element from a comment
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[[.flag select element from a flag
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[[.nmctl select element from a control stream object
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[[.timeline select element from a timeline object
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[[.uniKey select element from a uniKey object
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[<-.timepoint assign to a timepoint object
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%+% generic set union binary operator
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%&% generic set intersection binary operator
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%-% generic set difference binary operator
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%u% generic set union binary operator
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%n% generic set intersection binary operator
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%+%.default vector set union
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%&%.default vector set intersection
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%-%.default vector set difference
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%contains% test whether x contains y
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%crossed.on% test whether a is crossed on b
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%crosses% test whether a crosses b
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%matches% generic
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%matches%.character test whether data (file name) matches spec
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%matches%.data.frame test whether data.frame matches spec
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%matches%.keyed test whether keyed data.frame matches spec
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%matches%.spec test whether spec matches data
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%nested.in% test whether a is nested in b
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%nests% test whether a nests b
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$.init select init element
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$<-.init assign init element
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+.timeline add timepoints and durations
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-.timeline subtract timepoints and durations
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accept document the acceptance of an R installation
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acceptance display the acceptance documentation for an R installation
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acr calculate accumulation ratio
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addl.data.frame collapse dose records by means of ADDL notation
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addl.default calculate the ADDL data item (NONMEM) from explicit dose records
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addl calculate addl
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after test whether elements occur after some condition is TRUE
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aggregate.keyed aggregate a keyed data frame
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align.decimal align numeric column in latex table on the decimal
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as.best.data.frame coerce a data.frame to unambigous numeric or character columns
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as.best.default coerce a vector unambiguously to numeric or character
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as.best.digest coerce a digest to unambiguous numeric or character
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as.best generic
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as.character.comment convert comment to character
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as.character.flag convert flag to character
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as.character.init convert init to character
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as.character.initList convert initList to character
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as.character.nmctl convert nmctl to character
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as.character.timepoint convert timepoint to character
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as.character.uniKey convert uniKey to character
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as.chartime.numeric convert numeric to time
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as.chartime convert to time (generic, internal)
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as.comment.comment convert comment to comment
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as.comment.default convert default to comment
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as.comment convert to comment
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as.conditioned.digest convert a digest to conditioned
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as.conditioned.isolated convert isolated to conditioned
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as.conditioned.keyed convert keyed to conditioned
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as.conditioned split a data frame per levels of conditioning variables
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as.csv.filename.character convert character to csv.filename
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as.csv.filename convert to csv.filename
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as.data.frame.block convert a block of lines to data frame
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as.data.frame.comment convert comment to data frame
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as.data.frame.flag convert flag to data frame
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as.day.day coerce day to day
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as.day.hour coerce hour to day
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as.day.month coerce month to day
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as.day.duration coerce duration to day
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as.day.numeric coerce numeric to day
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as.day.week coerce week to day
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as.day.year coerce year to day
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as.day coerce to day
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as.define create a define object
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as.define.spec convert spec to a define object
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as.digest.data.frame convert data.frame to digest
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as.digest.digest convert digest to digest
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as.digest.keyed convert keyed to digest
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as.digest.nm convert nm to digest
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as.digest resolve static components of an object hierarchy
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as.document convert to latex document
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as.document.character convert tex fragments to latex document
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as.document.data.frame convert data.frame to latex document
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as.document.define convert define object to document
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as.file.runlog convert to convert runlog to file
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as.filename.character convert character to filename
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as.filename convert to filename
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as.flag.default convert default to flag
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as.flag.flag convert flag to flag
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as.flag convert to flag
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as.halfmatrix.default convert a vector to halfmatrix
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as.halfmatrix.halfmatrix preserve halfmatrix
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as.halfmatrix generic
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as.hour.day coerce day to hour
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as.hour.hour coerce hour to hour
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as.hour.minute coerce minute to hour
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as.hour.duration coerce duration to hour
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as.hour.numeric coerce numeric to hour
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as.hour.second coerce second to hour
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as.hour coerce to hour
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as.init.init convert init to init
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as.init.numeric convert numeric to init
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as.init convert to init
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as.initList.character convert character to initList
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as.initList.initList convert initList to initList
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as.initList.list convert list (of init) to initList
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as.initList.numeric convert numeric to initList
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as.initList convert to initList (generic)
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as.isolated.digest convert digest to isolated
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as.isolated.isolated convert isolated to isolated
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as.isolated.keyed convert keyed to isolated
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as.isolated split a data frame column-wise into members with only one non-key column
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as.keyed.data.frame convert data frame to keyed
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as.keyed.nm convert nm to isolated
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as.keyed convert to keyed
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as.list.nmctl convert nmctl to list
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as.matrix.halfmatrix convert a vector to a symmetric matrix
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as.mDate.character convert character to mDate
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as.mDate.Date convert Date to mDate
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as.mDate.dates convert dates (chron) to mDate
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as.mDate.mDate convert mDate to mDate
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as.mDate.numeric convert numeric to mDate
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as.mDate.sasdate convert SAS date to mDate
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as.mDate convert to mDate
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as.mDateTime.character convert character to mDateTime
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as.mDateTime.chron convert chron to mDateTime
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as.mDateTime.mDate convert mDate to mDateTime
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as.mDateTime.mDateTime convert mDateTime to mDateTime
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as.mDateTime.numeric convert numeric to mDateTime
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as.mDateTime.POSIXct convert POSIXct to mDateTime
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as.mDateTime.POSIXlt convert POSIXlt to mDateTime
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as.mDateTime convert to mDateTime
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as.minute.hour coerce hour to minute
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as.minute.minute coerce minute to minute
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as.minute.duration coerce duration to minute
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as.minute.numeric coerce numeric to minute
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as.minute.second coerce second to minute
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as.minute coerce to minute
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as.month.day coerce day to month
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as.month.month coerce month to month
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as.month.duration coerce duration to month
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as.month.numeric coerce numeric to month
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as.month coerce to month
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as.motif.digest create motif for digest
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as.motif.keyed create motif for keyed
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as.motif.motif create motif from motif
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as.motif.nm create motif for nm
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as.motif create default motif for various objects
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as.mTime.character convert character to mTime
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as.mTime.mTime convert mTime to mTime
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as.mTime.numeric convert numeric to mTime
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as.mTime.times convert times (chron) to mTime
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as.mTime convert to mTime
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as.nm.data.frame convert data frame to nm
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as.nm convert to nm (NMTRAN-ready NONMEM data set)
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as.nmctl.character convert character to nmctl
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as.nmctl convert to nmctl
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as.numeric.chartime convert chartime to numeric
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as.pdf.character convert tex fragments to pdf
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as.pdf.data.frame convert data.frame to pdf
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as.pdf convert to pdf
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as.pdf.define convert define object to pdf
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as.pdf.document convert latex document to pdf
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as.pxml.ext convert a param file to XML
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as.roles.digest create roles for digest
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as.roles.keyed create roles for keyed
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as.roles create default roles for parts of objects
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as.runlog.file convert file to runlog
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as.runlog.unilog convert unilog to runlog
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as.second.day coerce day to second
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as.second.hour coerce hour to second
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as.second.minute coerce minute to second
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as.second.duration coerce duration to second
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as.second.numeric coerce numeric to second
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as.second.second coerce second to second
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as.second coerce to second (time unit)
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as.spec generic
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as.spec.data.frame convert data.frame to spec
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as.spec.character convert file name to spec
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as.tabular convert to a latex tabular environment
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as.unilog.lst convert nonmem output (.lst) to unilog
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as.unilog.pxml convert nonmem output (.ext) to unilog
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as.unilog.run convert run to unilog
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as.unilog.runlog convert runlog to unilog
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as.week.day coerce day to week
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as.vector.keyed coerce keyed to vector
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as.vector.spec coerce spec to vector
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as.vector.uniKey coerce uniKey to vector
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as.week.duration coerce duration to week
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as.week.numeric coerce numeric to week
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as.week.week coerce week to week
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as.week coerce to week
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as.xml.character convert character to XML
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as.xml.data.frame convert data.frame to XML
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as.xml.default convert arbitrary object to XML
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as.xml convert object to XML
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as.year.day coerce day to year
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as.year.numeric coerce numeric to year
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as.year.year coerce year to year
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as.year coerce to year
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at test whether elements occur where some condition is TRUE
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attribute encode an attribute for an XML open tag
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auc calculate area under the curve
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AUC calculate the area under the curve for each subject over the time interval for dv using the trapezoidal rule
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aug add named elements to an object
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autolog.pl prepare command lines for autolog.pl.
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backtrans backtransform cols in x, returning x
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badAmt.nm AMT is NA where EVID is 1
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badAmt generic
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badDv.nm DV is NA where EVID is 0
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badDv generic
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badII.nm II is greater than 0 where ADDL is NA or 0 (unless SS > 0)
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badII generic
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bakfor impute NAs using last observation carried forward after next observation carried backward
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before test whether elements occur before some condition is TRUE
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bin calculate bin limits for x and place each value in a bin, returning the number of values in each bin
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bmi calculate body mass index
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bounds calculate normal quantiles at bounding probabilities
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bracket create an XML tag
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breaks calculate breaks between grouped elements
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bsa calculate body surface area
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bundleRead read filtered directory contents into a list
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c.comment combine comment
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c.flag combine flag
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c.timeline combine timeline
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c.uniKey combine uniKey
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cast,keyed-method cast a keyed data.frame, restoring key and output classes
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cavg calculate average concentration
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check.subjects check for missing data, numeric data, ranges, etc.
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clean.spec clean up spec storage format
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clear drop regular patterns from a character vector
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CLNR delete files and directories and log what was deleted to a text file in the project
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closers set closing positions for wikmath nests
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cmax calculate maximum steady-state concentration
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cmin calculate minimum steady-state concentration
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codes generic
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codes.default extract codes from an encoded vector
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codes.spec extract codes from a spec guide
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colname<- change identified column names
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command generate a latex command
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combinations show sorted unique rows
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compileflag calculate compiler flag for qsub
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compiler extract compiler specification from configuration file
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compute.cwres compute conditional weighted residuals
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config calculate path to configuration file
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constant.default test whether values of x are contant within an index
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constant generic
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contains test a character vector for occurences of a pattern
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convertLines convert line endings
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covariatePlots create diagnostic plots for covariates
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crcl calculate creatinine clearance
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crosses test whether a crosses b
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css calculate steady-state concentration
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ctl2xml isolate xml comments from a control stream
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cvLognormal calculate coefficient of variation for log-normal data
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cvNormal calculate coefficient of variation for normal data
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cwresPlots create conditional weighted residual diagnostic plots
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dataFormat combine NONMEM predictions, parameter estimates, and covariates into a standard format
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dataSynthesis build a standard plotting data set for a given NONR run
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decodes generic
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decodes.default extract decodes from an encoded vector
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decodes.spec extract decodes from a spec guide
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deranged.data.frame instantiate records implied by range data
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deranged.keyed instantiate records implied by range data
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deranged generic
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diagnosticPlots create standard diagnostic plots
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digest alias for as.digest
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distance calculate element positions relative to the n^th TRUE element positions (usually, within levels of an index)
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dupKeys.default give a logical index to duplicated rows of a keyed data frame, AND the rows of which they are duplicates
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dupKeys.nm default behavior, after stripping comments
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dupKeys generic
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dynamic.data.frame return the dynamic portion of a data frame
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dynamic.keyed return the dynamic portion of a keyed data frame
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dynamic generic
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electronicAppendix create an FDA-style electronic appendix from a subversioned directory
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encode generic
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encode.list encode levels and labels in simple strings
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encode.character encode levels and labels in simple strings
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encode.default encode levels and labels in simple strings
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encoded generic
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encoded.default test whether a vector is encoded
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encoded.spec test whether the guide column of a spec is encoded
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episcript run a script in an environment that defines the passed arguments
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explicitPath add separators to control stream paths that have none
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extfile extract arbitrary file specification from a control stream
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extract extract numbered parenthetical substrings of regular expressions
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extractPath isolate file path from surrounding text (MSF, TAB files).
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f alias for as.flag
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falseAmt.nm AMT defined where EVID is not 1
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falseAmt generic
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falseDv.nm DV is defined where EVID is not 0
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falseDv generic
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filename generate standard file name (internal)
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findNonmemCommand find available NONMEM executables
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first repeat, for each element, the first element where a condition is TRUE (usually, within levels of an index)
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fixed.init find out if an init is fixed
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fixed.initList find out if elements of an initList are fixed
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fixed find out if something is fixed (generic)
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fixed<-.init set the value of 'fixed' for an init
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fixed<-.initList set the values of 'fixed' for elements of an initList
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fixed<- set the value of 'fixed'
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fixedwidth.data.frame convert a data.frame to fixed-width format
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fixedwidth convert to fixed-width format
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fixFile rewrite run name in control stream file specifications
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fixProblem rewrite run name in control stream PROBLEM statement
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follow follow progress of NONMEM runs
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forbak impute NAs using last observation carried forward and then next observation carried backward
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format.comment format comment
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format.flag format flag
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format.init format init
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format.initList format initList
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format.legacy pretty-print legacy information (conditioned objects)
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format.mDate format mDate
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format.mDateTime format mDateTime
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format.mTime format mTime
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format.nmctl format nmctl
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format.duration format duration
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format.uniKey format uniKey
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ftable2data.frame convert ftable to data.frame as displayed
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getCovs return non-commented non-duplicated rows of a NONMEM data set (internal)
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getCwres return the conditional weighted residuals pertinent to a given run (internal, expects cwtab1.deriv)
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getdname extract the path and file from the DATA block in the control stream associated with filename (internal)
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getPars return the non-duplicated (ID) rows corresponding to the specified filename (internal)
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getTabs return the observation rows (EVID==0) corresponding to the specified filename (internal)
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glue paste with no separator
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groupnames construct a single vector of group names from possibly multiple indices to the plotting data set (internal)
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guidetext generic
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guidetext.spec extract guide text from a spec
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half.matrix vectorize the lower triangular portion of a symmetric matrix
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half generic
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hash prepend a character to each line of output
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head.digest show head of each table in a digest
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hidden.data.frame show commented rows of a data frame
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hidden generic
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hide.data.frame comment out the specified rows of a data frame, appending a flag that suggests the reason
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hide generic
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ibw calculate ideal body weight
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ignored check which rows of an input data set were ignored by NONMEM
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ind.cwres compute conditional weighted residuals (internal)
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index.conditioned index a conditioned object
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index.digest index a digest
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index.isolated index an isolated object
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index.keyed index a keyed data frame
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index.nm index an nm object
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index create an index plot
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inner.data.frame reduce columns to inner quantiles by imputing NA
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inner generic
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is.alpha test whether text is letters-only
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is.cwres.readable.file compute conditional weighted residuals (internal)
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is.defined test whether elements are defined
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is.diagonal test whether parameter label represents matrix diagonal element
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is.fixed detect thetas in parameter labels
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is.iiv detect omegas in parameter labels
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is.latex.token test whether text is valid latex command or environment
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is.offdiagonal test whether parameter label represents matrix offdiagonal element
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is.one.nonalpha test whether text is singular non-letter
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is.random detect omegas and sigmas in parameter labels
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is.residual detect sigmas in parameter labels
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is.square.matrix test whether a matrix is square
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is.square generic
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isSubversioned check if files are subversioned
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isSubversionedFile check if one file is subversioned
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iterations retrieve iteration statistics from NONMEM output file
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justUnits extract units from wikimath
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ke calculate elimination constant
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key return the key of a keyed data frame
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key<- assign a key
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labels.spec extract labels from a spec
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last repeat, for each element, the last element where a condition is TRUE (usually, within levels of an index)
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latest identify the latest of each set of variants
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latex.args format latex arguments
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latex.options format latex options
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lbm calculate lean body mass
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legacy extract legacy from a conditioned object
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legacy<- assign legacy for a conditioned object
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lhs extract left-hand side of wikimath
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locf impute NA using last observation carried forward
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lookup.one translate among parameter attributes (scalar)
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lookup translate among parameter attributes (vector)
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lower calculate normal quantiles at lower probability of interval
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ltable.data.frame convert a data.frame to a latex table
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ltable.matrix convert a matrix to a latex table
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ltable.table convert a (2D) table object to a latex table
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ltable convert to a latex table
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lyse.data.frame return the static and dynamic portions of a data frame
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lyse.keyed return the static and dynamic portions of a keyed data frame
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lyse generic
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makePreamble construct a preamble for a latex document
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map map one set of values to another
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maxChar return the number of printed characters for the widest element of x
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melt.keyed melt keyed data frames, restoring key
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merge.keyed merge keyed data frames, preserving attributes
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metaMerge.character recursively merge based on a vector of file names
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metaMerge.default merge two groomed objects
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metaMerge.list recursively merge elements of a list
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metaMerge generic
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metaSub.character systematically substitute elements in a character vector
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metaSub.filename systematically substitute elements in a text file
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metaSub generic
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metrumrgURL view a file in the metrumrg package
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monotonic generic
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monotonic.default check whether the values in a vector are monotonic
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nondecreasing generic
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nondecreasing.default check whether the values in a vector are nondecreasing
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nonincreasinggeneric
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nonincreasing.default check whether the values in a vector are nonincreasing
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motif alias for as.motif
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msffile extract msffile specification from a control stream
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naInContext display rows of data with missing values, as well as other rows with the same key
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naKeys.default detect rows for which one or more key fields is NA
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naKeys.nm default behavior, after stripping comments
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naKeys generic
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name<- change identified object names
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nasum diagnose missingness
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ncomma report names as comma-delimited
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nest nest an XML fragment in a parent element
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nix identify Unix-like platforms (internal)
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nm.pl prepare command lines for nm.pl
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nm give a zero-row data frame with suitable columns and column classes; i.e. a template for NMTRAN data sets
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nmPlots a list of functions that plot nm objects
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nmVersion extract NONMEM version specification from configuration file
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nocb impute NA with next observation carried backward
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NONR run NONMEM and create diagnostic plots
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noPk.nm rows where EVID is never 0 within SUBJ
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noPk generic
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nospace drop spaces from text
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noUnits drop units from wikimath
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nth repeat, for each element, the n^th element where a condition is TRUE (usually, within levels of an index)
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nxt calculate the next element for each element of x
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offdiag.halfmatrix select just the off-diagonal elements of a halfmatrix
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offdiag generic
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omegacor convert omega covariance in NONMEM output to correlation matrix
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omegacov convert omega covariance in NONMEM output to covariance matrix
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only repeat, for each element, the only element where a condition is TRUE (usually, within levels of an index)
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Ops.keyed use concise syntax to join data frames
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ord.halfmatrix compute the order of a half matrix
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ord.matrix compute the order of a symmetric matrix
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ord generic
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packageCheck load a package and run package-level examples
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padded pad a numeric with leading zeros
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panel.bar for each level, plot vertical (or horizontal) bars corresponding to x (y).
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panel.covplot plot distributions with respect to reference values; i.e. combine panel.cuts, panel.densitystrip, and panel.ref
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panel.cuts for each level, plot percent observations in each vertical category defined by cuts
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panel.densitystrip for each level, plot a filled polygon representing smoothed density of the distribution
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panel.hist for each level, plot a histogram
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panel.ref plot a reference region in a stripplot
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panel.stratify handle strips (levels) of data one at a time
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parameter2wiki convert parameter labels to wikmath
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params list documented model parameters
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parens wrap text in parentheses
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parfile extract parfile specification from a control stream
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partab construct a model parameter table
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percent convert to percent
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plot.conditioned plot a conditioned object
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plot.digest plot a digest
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plot.isolated plot isolated
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plot.keyed plot keyed
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plot.nm generate standard plots for an nm object using nmPlots
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plotfilename make a name for a diagnostic plot file
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PLOTR create diagnostic plots for NONMEM runs
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pool test for unique and shared elments among two vectors
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posmat coerce a matrix to be positive definite
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predoseDv.nm DV is defined before the first record within SUBJ where EVID is 1
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predoseDv generic
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prev calculate the previous element for each element of x
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print.comment print comment
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print.flag print flag
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print.halfmatrix print halfmatrix
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print.init print init
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print.initList print initList
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print.keyed.summary print keyed summary
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print.nm.summary print nm summary
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print.nmctl print nmctl
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print.duration print duration
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print.timepoint print timepoint
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print.uniKey print uniKey
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progress summarize progress of NONMEM runs
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purge.dir purge a directory (internal)
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purge.files purge files (internal)
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purgeRunDir delete certain files from run directories
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qstat invoke SGE qstat
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qsub prepare commandlines for qsub
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read.cwres.data compute conditional weighted residuals (internal)
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read.nm read a csv file and try to transform to nm
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read.nmctl read a NONMEM control stream, converting to modifiable object
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read.spec read a spec
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reapply apply a function across cells of an indexed vector, giving an identically-indexed result
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rep.comment repeat comment
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rep.flag repeat flag
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rep.timeline repeat timeline
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rep.uniKey repeat uniKey
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resample.csv.filename create replicate data sets by stratified sampling with replacement, after reading csv file
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resample.data.frame create replicate data sets by stratified sampling with replacement
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resample.filename create replicate data sets by stratified sampling with replacement, after reading file
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resample generic
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respecify update a data specification
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respecify.character update a data specification by filename
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respecify.spec update a data specification explicitly
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resolve reinterpret relative file paths with respect to specified directory.
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rhs extract right-hand side of wikimath
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rinvchisq generate inverse chi-square distribution
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riwish generate inverse Wishart distribution
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rlog generate a combined run log for multiple NONMEM runs
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roles alias for as.roles
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row2tabular convert a vector to a latex tabular row
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runCommand issue the system call that invokes NONMEM (internal)
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runhead determine whether each element is the start of a run
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runlog create a zero-row runlog
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runNonmem process a request for NONMEM invocation
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runstate determine the status of a run
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safe.call call a function, passing only those extra arguments that the function accepts
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safeQuote single-quote unquoted text that contains space
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scavenge find an expression in lines of text
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seq.timeline generate timeline sequence
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setCwres append conditional weighted residuals to an appropriate file
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shuffle move columns in a data frame
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sigmacor convert sigma covariance in NONMEM output to correlation matrix
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sigmacov convert sigma covariance in NONMEM output to covariance matrix
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simblock generate deviates of the elements of a variance-covariance matrix
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simpar generate deviates of a set of model parameters for simulation
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snap coerce values to nearest of candidates
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sort.keyed sort a keyed data frame
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spaces create a string of spaces
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specification generic
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specification.comment pre-format a comment for specification
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specification.data.frame develop a draft specification for a data.frame
-
specification.default pre-format a vector for specification
-
specfile for a run and project, guess a path to a data specification file
-
splom.conditioned scatterplot for conditioned
-
splom.digest scatterplot for digest
-
splom.keyed scatterplot for keyed
-
sqrtm support compute.cwres
-
stableMerge produce a left join, with strict error checking
-
star replace asterisk in x with y (internal)
-
static.data.frame return the static portion of a data frame
-
static.keyed return the static portion of a keyed data frame
-
static generic
-
strain reduce x to those elements that occur in options (internal)
-
Summary.timepoint group generic summary for objects of class 'timepoint'
-
summary.hidden.data.frame summarize hidden rows of a data frame
-
summary.keyed summarize a keyed data frame
-
summary.nm summarize an nm object
-
summary.spec summarize a spec object
-
superset combine all NONMEM input with all output
-
supp generic
-
supp.data.frame supplement a CDISC data.frame
-
supp.keyed supplement a CDISC keyed data.frame
-
svnIsText check if subversioned files are text rather than binary
-
svnMarkAsNonText tell Subversion to treat files as binary
-
svnMarkAsText tell Subversion to treat files as text
-
svnMimeType get the Subversion mime-type for files
-
svnPropGet get a Subversion property for files
-
svnPropGetFile get a Subversion property for one file
-
svnPropSet set a subversion property on files
-
svnPropSetFile set a Subversion property on a file
-
svnSetMimeType set Subversion mime type on file
-
synthesis sequentially left-join an arbitrary number of data frames, picking up novel columns (internal)
-
tabfile extract tabfile specification from a control stream
-
tabular.data.frame convert a data.frame to a latex tabular environment
-
tabular convert to a latex tabular environment
-
tabular.define convert define object to tabular
-
tabular.matrix convert matrix to tabular
-
tabular.table convert a (2D) table object to tabular
-
tabularformat generate a format string for a latex tabular environment
-
tagvalue convert a list to a string of delimited tag-value pairs
-
tex2pdf convert tex files to pdf
-
text2decimal convert mixed text to decimal
-
titleCase convert mixed case to title case, strictly by default
-
Tmax calculate the time associated with the maximum concentration for each subject
-
tmax calculate the time of the maximum concentration
-
Tmin calculate the time associated with the minimum concentration for each subject
-
toSAS.mDate encode mDate in SAS format for writing
-
toSAS.mDateTime encode mDateTime in SAS format for writing
-
toSAS.mTime encode mTime in SAS format for writing
-
tos extract thetas, omegas, and sigmas from wikimath
-
totitle convert mixed case to title case, not strictly by default
-
transform.keyed transform a keyed data frame, preserving class
-
tweak.init randomly adjust an initial parameter value
-
tweak.initList randomly adjust a list of initial parameter values
-
tweak.nmctl randomly adjust the initial fixed effect parameters in a control stream
-
tweak randomly adjust a value
-
uniKey.keyed create a single character vector from all the key columns
-
uniKey generic
-
unilog create a zero-row unilog
-
unilogcor convert omega or sigma covariance in NONMEM output to correlation matrix
-
unilogcov convert omega or sigma covariance in NONMEM output to covariance matrix
-
unique.comment find unique elements of a comment vector
-
unique.timepoint find unique elements of a timepoint vector
-
unique.uniKey find unique elements of a uniKey vector
-
unitDensity calculate univariate density with maximum equal to 1
-
unitHist calculate univariate histogram architecture with maximum height equal to 1
-
unsorted generic
-
unsorted.keyed detect rows that would move on sort
-
upper calculate normal quantiles at upper probability of interval
-
variants locate variants of a file in distinctive subdirectories
-
viewtex view (as pdfs) files that contain fragmentary tex code (e.g. tables)
-
wiki2label convert wikimath to a label, e.g. CL/F
-
wiki2latex convert wikimath to latex
-
wiki2parameter convert wikimath to a parameter, e.g. THETA1
-
wiki2plotmath convert wikimath to plotmath
-
wikiparse parse wikimath
-
wikitab extract wikimath specification from a control stream
-
win identify Windows platforms (internal)
-
wrap wrap text in a latex environment
-
write.nm write an nm object to file
-
write.nmctl write an nmctl object to file
-
write.spec write a spec object to file
-
xpath extract value of an xpath exrpession from an xml file
-
xtfrm.comment produce a numeric vector that sorts in the same order as comment
-
xtfrm.flag produce a numeric vector that sorts in the same order as flag
-
xtfrm.timepoint produce a numeric vector that sorts in the same order as timepoint
-
xtfrm.uniKey produce a character vector that sorts in the same order as uniKey
-
xyplotExt plot the parameter search history for a NONMEM7 run
-
zeroAmt.nm AMT is zero where EVID is 1
-
zeroAmt generic
-
zeroDv.nm DV is zero where EVID is zero
-
zeroDv generic
metrumresearchgroup/metrumrg documentation built on May 22, 2019, 7:51 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
Exhaustive list of functions defined by metrumrg.
Details
metrumrg
-
[.comment subset a comment
-
[.conditioned subset a conditioned object
-
[.digest subset a digest object
-
[.flag subset a flag
-
[.initList subset initList
-
[.keyed subset a keyed data frame
-
[.nmctl subset a control stream object
-
[.timeline subset a timeline object
-
[.uniKey subset a uniKey object
-
[[.comment select element from a comment
-
[[.flag select element from a flag
-
[[.nmctl select element from a control stream object
-
[[.timeline select element from a timeline object
-
[[.uniKey select element from a uniKey object
-
[<-.timepoint assign to a timepoint object
-
%+% generic set union binary operator
-
%&% generic set intersection binary operator
-
%-% generic set difference binary operator
-
%u% generic set union binary operator
-
%n% generic set intersection binary operator
-
%+%.default vector set union
-
%&%.default vector set intersection
-
%-%.default vector set difference
-
%contains% test whether x contains y
-
%crossed.on% test whether a is crossed on b
-
%crosses% test whether a crosses b
-
%matches% generic
-
%matches%.character test whether data (file name) matches spec
-
%matches%.data.frame test whether data.frame matches spec
-
%matches%.keyed test whether keyed data.frame matches spec
-
%matches%.spec test whether spec matches data
-
%nested.in% test whether a is nested in b
-
%nests% test whether a nests b
-
$.init select init element
-
$<-.init assign init element
-
+.timeline add timepoints and durations
-
-.timeline subtract timepoints and durations
-
accept document the acceptance of an R installation
-
acceptance display the acceptance documentation for an R installation
-
acr calculate accumulation ratio
-
addl.data.frame collapse dose records by means of ADDL notation
-
addl.default calculate the ADDL data item (NONMEM) from explicit dose records
-
addl calculate addl
-
after test whether elements occur after some condition is
TRUE -
aggregate.keyed aggregate a keyed data frame
-
align.decimal align numeric column in latex table on the decimal
-
as.best.data.frame coerce a data.frame to unambigous numeric or character columns
-
as.best.default coerce a vector unambiguously to numeric or character
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as.best.digest coerce a digest to unambiguous numeric or character
-
as.best generic
-
as.character.comment convert comment to character
-
as.character.flag convert flag to character
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as.character.init convert init to character
-
as.character.initList convert initList to character
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as.character.nmctl convert nmctl to character
-
as.character.timepoint convert timepoint to character
-
as.character.uniKey convert uniKey to character
-
as.chartime.numeric convert numeric to time
-
as.chartime convert to time (generic, internal)
-
as.comment.comment convert comment to comment
-
as.comment.default convert default to comment
-
as.comment convert to comment
-
as.conditioned.digest convert a digest to conditioned
-
as.conditioned.isolated convert isolated to conditioned
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as.conditioned.keyed convert keyed to conditioned
-
as.conditioned split a data frame per levels of conditioning variables
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as.csv.filename.character convert character to csv.filename
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as.csv.filename convert to csv.filename
-
as.data.frame.block convert a block of lines to data frame
-
as.data.frame.comment convert comment to data frame
-
as.data.frame.flag convert flag to data frame
-
as.day.day coerce day to day
-
as.day.hour coerce hour to day
-
as.day.month coerce month to day
-
as.day.duration coerce duration to day
-
as.day.numeric coerce numeric to day
-
as.day.week coerce week to day
-
as.day.year coerce year to day
-
as.day coerce to day
-
as.define create a define object
-
as.define.spec convert spec to a define object
-
as.digest.data.frame convert data.frame to digest
-
as.digest.digest convert digest to digest
-
as.digest.keyed convert keyed to digest
-
as.digest.nm convert nm to digest
-
as.digest resolve static components of an object hierarchy
-
as.document convert to latex document
-
as.document.character convert tex fragments to latex document
-
as.document.data.frame convert data.frame to latex document
-
as.document.define convert define object to document
-
as.file.runlog convert to convert runlog to file
-
as.filename.character convert character to filename
-
as.filename convert to filename
-
as.flag.default convert default to flag
-
as.flag.flag convert flag to flag
-
as.flag convert to flag
-
as.halfmatrix.default convert a vector to halfmatrix
-
as.halfmatrix.halfmatrix preserve halfmatrix
-
as.halfmatrix generic
-
as.hour.day coerce day to hour
-
as.hour.hour coerce hour to hour
-
as.hour.minute coerce minute to hour
-
as.hour.duration coerce duration to hour
-
as.hour.numeric coerce numeric to hour
-
as.hour.second coerce second to hour
-
as.hour coerce to hour
-
as.init.init convert init to init
-
as.init.numeric convert numeric to init
-
as.init convert to init
-
as.initList.character convert character to initList
-
as.initList.initList convert initList to initList
-
as.initList.list convert list (of init) to initList
-
as.initList.numeric convert numeric to initList
-
as.initList convert to initList (generic)
-
as.isolated.digest convert digest to isolated
-
as.isolated.isolated convert isolated to isolated
-
as.isolated.keyed convert keyed to isolated
-
as.isolated split a data frame column-wise into members with only one non-key column
-
as.keyed.data.frame convert data frame to keyed
-
as.keyed.nm convert nm to isolated
-
as.keyed convert to keyed
-
as.list.nmctl convert nmctl to list
-
as.matrix.halfmatrix convert a vector to a symmetric matrix
-
as.mDate.character convert character to mDate
-
as.mDate.Date convert Date to mDate
-
as.mDate.dates convert dates (chron) to mDate
-
as.mDate.mDate convert mDate to mDate
-
as.mDate.numeric convert numeric to mDate
-
as.mDate.sasdate convert SAS date to mDate
-
as.mDate convert to mDate
-
as.mDateTime.character convert character to mDateTime
-
as.mDateTime.chron convert chron to mDateTime
-
as.mDateTime.mDate convert mDate to mDateTime
-
as.mDateTime.mDateTime convert mDateTime to mDateTime
-
as.mDateTime.numeric convert numeric to mDateTime
-
as.mDateTime.POSIXct convert POSIXct to mDateTime
-
as.mDateTime.POSIXlt convert POSIXlt to mDateTime
-
as.mDateTime convert to mDateTime
-
as.minute.hour coerce hour to minute
-
as.minute.minute coerce minute to minute
-
as.minute.duration coerce duration to minute
-
as.minute.numeric coerce numeric to minute
-
as.minute.second coerce second to minute
-
as.minute coerce to minute
-
as.month.day coerce day to month
-
as.month.month coerce month to month
-
as.month.duration coerce duration to month
-
as.month.numeric coerce numeric to month
-
as.month coerce to month
-
as.motif.digest create motif for digest
-
as.motif.keyed create motif for keyed
-
as.motif.motif create motif from motif
-
as.motif.nm create motif for nm
-
as.motif create default motif for various objects
-
as.mTime.character convert character to mTime
-
as.mTime.mTime convert mTime to mTime
-
as.mTime.numeric convert numeric to mTime
-
as.mTime.times convert times (chron) to mTime
-
as.mTime convert to mTime
-
as.nm.data.frame convert data frame to nm
-
as.nm convert to nm (NMTRAN-ready NONMEM data set)
-
as.nmctl.character convert character to nmctl
-
as.nmctl convert to nmctl
-
as.numeric.chartime convert chartime to numeric
-
as.pdf.character convert tex fragments to pdf
-
as.pdf.data.frame convert data.frame to pdf
-
as.pdf convert to pdf
-
as.pdf.define convert define object to pdf
-
as.pdf.document convert latex document to pdf
-
as.pxml.ext convert a param file to XML
-
as.roles.digest create roles for digest
-
as.roles.keyed create roles for keyed
-
as.roles create default roles for parts of objects
-
as.runlog.file convert file to runlog
-
as.runlog.unilog convert unilog to runlog
-
as.second.day coerce day to second
-
as.second.hour coerce hour to second
-
as.second.minute coerce minute to second
-
as.second.duration coerce duration to second
-
as.second.numeric coerce numeric to second
-
as.second.second coerce second to second
-
as.second coerce to second (time unit)
-
as.spec generic
-
as.spec.data.frame convert data.frame to spec
-
as.spec.character convert file name to spec
-
as.tabular convert to a latex tabular environment
-
as.unilog.lst convert nonmem output (.lst) to unilog
-
as.unilog.pxml convert nonmem output (.ext) to unilog
-
as.unilog.run convert run to unilog
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as.unilog.runlog convert runlog to unilog
-
as.week.day coerce day to week
-
as.vector.keyed coerce keyed to vector
-
as.vector.spec coerce spec to vector
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as.vector.uniKey coerce uniKey to vector
-
as.week.duration coerce duration to week
-
as.week.numeric coerce numeric to week
-
as.week.week coerce week to week
-
as.week coerce to week
-
as.xml.character convert character to XML
-
as.xml.data.frame convert data.frame to XML
-
as.xml.default convert arbitrary object to XML
-
as.xml convert object to XML
-
as.year.day coerce day to year
-
as.year.numeric coerce numeric to year
-
as.year.year coerce year to year
-
as.year coerce to year
-
at test whether elements occur where some condition is
TRUE -
attribute encode an attribute for an XML open tag
-
auc calculate area under the curve
-
AUC calculate the area under the curve for each subject over the time interval for dv using the trapezoidal rule
-
aug add named elements to an object
-
autolog.pl prepare command lines for autolog.pl.
-
backtrans backtransform cols in x, returning x
-
badAmt.nm AMT is NA where EVID is 1
-
badAmt generic
-
badDv.nm DV is NA where EVID is 0
-
badDv generic
-
badII.nm II is greater than 0 where ADDL is NA or 0 (unless SS > 0)
-
badII generic
-
bakfor impute NAs using last observation carried forward after next observation carried backward
-
before test whether elements occur before some condition is
TRUE -
bin calculate bin limits for x and place each value in a bin, returning the number of values in each bin
-
bmi calculate body mass index
-
bounds calculate normal quantiles at bounding probabilities
-
bracket create an XML tag
-
breaks calculate breaks between grouped elements
-
bsa calculate body surface area
-
bundleRead read filtered directory contents into a list
-
c.comment combine comment
-
c.flag combine flag
-
c.timeline combine timeline
-
c.uniKey combine uniKey
-
cast,keyed-method cast a keyed data.frame, restoring key and output classes
-
cavg calculate average concentration
-
check.subjects check for missing data, numeric data, ranges, etc.
-
clean.spec clean up spec storage format
-
clear drop regular patterns from a character vector
-
CLNR delete files and directories and log what was deleted to a text file in the project
-
closers set closing positions for wikmath nests
-
cmax calculate maximum steady-state concentration
-
cmin calculate minimum steady-state concentration
-
codes generic
-
codes.default extract codes from an encoded vector
-
codes.spec extract codes from a spec guide
-
colname<- change identified column names
-
command generate a latex command
-
combinations show sorted unique rows
-
compileflag calculate compiler flag for qsub
-
compiler extract compiler specification from configuration file
-
compute.cwres compute conditional weighted residuals
-
config calculate path to configuration file
-
constant.default test whether values of x are contant within an index
-
constant generic
-
contains test a character vector for occurences of a pattern
-
convertLines convert line endings
-
covariatePlots create diagnostic plots for covariates
-
crcl calculate creatinine clearance
-
crosses test whether a crosses b
-
css calculate steady-state concentration
-
ctl2xml isolate xml comments from a control stream
-
cvLognormal calculate coefficient of variation for log-normal data
-
cvNormal calculate coefficient of variation for normal data
-
cwresPlots create conditional weighted residual diagnostic plots
-
dataFormat combine NONMEM predictions, parameter estimates, and covariates into a standard format
-
dataSynthesis build a standard plotting data set for a given NONR run
-
decodes generic
-
decodes.default extract decodes from an encoded vector
-
decodes.spec extract decodes from a spec guide
-
deranged.data.frame instantiate records implied by range data
-
deranged.keyed instantiate records implied by range data
-
deranged generic
-
diagnosticPlots create standard diagnostic plots
-
digest alias for as.digest
-
distance calculate element positions relative to the n^th
TRUEelement positions (usually, within levels of an index) -
dupKeys.default give a logical index to duplicated rows of a keyed data frame, AND the rows of which they are duplicates
-
dupKeys.nm default behavior, after stripping comments
-
dupKeys generic
-
dynamic.data.frame return the dynamic portion of a data frame
-
dynamic.keyed return the dynamic portion of a keyed data frame
-
dynamic generic
-
electronicAppendix create an FDA-style electronic appendix from a subversioned directory
-
encode generic
-
encode.list encode levels and labels in simple strings
-
encode.character encode levels and labels in simple strings
-
encode.default encode levels and labels in simple strings
-
encoded generic
-
encoded.default test whether a vector is encoded
-
encoded.spec test whether the guide column of a spec is encoded
-
episcript run a script in an environment that defines the passed arguments
-
explicitPath add separators to control stream paths that have none
-
extfile extract arbitrary file specification from a control stream
-
extract extract numbered parenthetical substrings of regular expressions
-
extractPath isolate file path from surrounding text (MSF, TAB files).
-
f alias for as.flag
-
falseAmt.nm AMT defined where EVID is not 1
-
falseAmt generic
-
falseDv.nm DV is defined where EVID is not 0
-
falseDv generic
-
filename generate standard file name (internal)
-
findNonmemCommand find available NONMEM executables
-
first repeat, for each element, the first element where a condition is
TRUE(usually, within levels of an index) -
fixed.init find out if an init is fixed
-
fixed.initList find out if elements of an initList are fixed
-
fixed find out if something is fixed (generic)
-
fixed<-.init set the value of 'fixed' for an init
-
fixed<-.initList set the values of 'fixed' for elements of an initList
-
fixed<- set the value of 'fixed'
-
fixedwidth.data.frame convert a data.frame to fixed-width format
-
fixedwidth convert to fixed-width format
-
fixFile rewrite run name in control stream file specifications
-
fixProblem rewrite run name in control stream PROBLEM statement
-
follow follow progress of NONMEM runs
-
forbak impute NAs using last observation carried forward and then next observation carried backward
-
format.comment format comment
-
format.flag format flag
-
format.init format init
-
format.initList format initList
-
format.legacy pretty-print legacy information (conditioned objects)
-
format.mDate format mDate
-
format.mDateTime format mDateTime
-
format.mTime format mTime
-
format.nmctl format nmctl
-
format.duration format duration
-
format.uniKey format uniKey
-
ftable2data.frame convert ftable to data.frame as displayed
-
getCovs return non-commented non-duplicated rows of a NONMEM data set (internal)
-
getCwres return the conditional weighted residuals pertinent to a given run (internal, expects cwtab1.deriv)
-
getdname extract the path and file from the DATA block in the control stream associated with filename (internal)
-
getPars return the non-duplicated (ID) rows corresponding to the specified filename (internal)
-
getTabs return the observation rows (EVID==0) corresponding to the specified filename (internal)
-
glue paste with no separator
-
groupnames construct a single vector of group names from possibly multiple indices to the plotting data set (internal)
-
guidetext generic
-
guidetext.spec extract guide text from a spec
-
half.matrix vectorize the lower triangular portion of a symmetric matrix
-
half generic
-
hash prepend a character to each line of output
-
head.digest show head of each table in a digest
-
hidden.data.frame show commented rows of a data frame
-
hidden generic
-
hide.data.frame comment out the specified rows of a data frame, appending a flag that suggests the reason
-
hide generic
-
ibw calculate ideal body weight
-
ignored check which rows of an input data set were ignored by NONMEM
-
ind.cwres compute conditional weighted residuals (internal)
-
index.conditioned index a conditioned object
-
index.digest index a digest
-
index.isolated index an isolated object
-
index.keyed index a keyed data frame
-
index.nm index an nm object
-
index create an index plot
-
inner.data.frame reduce columns to inner quantiles by imputing NA
-
inner generic
-
is.alpha test whether text is letters-only
-
is.cwres.readable.file compute conditional weighted residuals (internal)
-
is.defined test whether elements are defined
-
is.diagonal test whether parameter label represents matrix diagonal element
-
is.fixed detect thetas in parameter labels
-
is.iiv detect omegas in parameter labels
-
is.latex.token test whether text is valid latex command or environment
-
is.offdiagonal test whether parameter label represents matrix offdiagonal element
-
is.one.nonalpha test whether text is singular non-letter
-
is.random detect omegas and sigmas in parameter labels
-
is.residual detect sigmas in parameter labels
-
is.square.matrix test whether a matrix is square
-
is.square generic
-
isSubversioned check if files are subversioned
-
isSubversionedFile check if one file is subversioned
-
iterations retrieve iteration statistics from NONMEM output file
-
justUnits extract units from wikimath
-
ke calculate elimination constant
-
key return the key of a keyed data frame
-
key<- assign a key
-
labels.spec extract labels from a spec
-
last repeat, for each element, the last element where a condition is
TRUE(usually, within levels of an index) -
latest identify the latest of each set of variants
-
latex.args format latex arguments
-
latex.options format latex options
-
lbm calculate lean body mass
-
legacy extract legacy from a conditioned object
-
legacy<- assign legacy for a conditioned object
-
lhs extract left-hand side of wikimath
-
locf impute NA using last observation carried forward
-
lookup.one translate among parameter attributes (scalar)
-
lookup translate among parameter attributes (vector)
-
lower calculate normal quantiles at lower probability of interval
-
ltable.data.frame convert a data.frame to a latex table
-
ltable.matrix convert a matrix to a latex table
-
ltable.table convert a (2D) table object to a latex table
-
ltable convert to a latex table
-
lyse.data.frame return the static and dynamic portions of a data frame
-
lyse.keyed return the static and dynamic portions of a keyed data frame
-
lyse generic
-
makePreamble construct a preamble for a latex document
-
map map one set of values to another
-
maxChar return the number of printed characters for the widest element of x
-
melt.keyed melt keyed data frames, restoring key
-
merge.keyed merge keyed data frames, preserving attributes
-
metaMerge.character recursively merge based on a vector of file names
-
metaMerge.default merge two groomed objects
-
metaMerge.list recursively merge elements of a list
-
metaMerge generic
-
metaSub.character systematically substitute elements in a character vector
-
metaSub.filename systematically substitute elements in a text file
-
metaSub generic
-
metrumrgURL view a file in the metrumrg package
-
monotonic generic
-
monotonic.default check whether the values in a vector are monotonic
-
nondecreasing generic
-
nondecreasing.default check whether the values in a vector are nondecreasing
-
nonincreasinggeneric
-
nonincreasing.default check whether the values in a vector are nonincreasing
-
motif alias for as.motif
-
msffile extract msffile specification from a control stream
-
naInContext display rows of data with missing values, as well as other rows with the same key
-
naKeys.default detect rows for which one or more key fields is NA
-
naKeys.nm default behavior, after stripping comments
-
naKeys generic
-
name<- change identified object names
-
nasum diagnose missingness
-
ncomma report names as comma-delimited
-
nest nest an XML fragment in a parent element
-
nix identify Unix-like platforms (internal)
-
nm.pl prepare command lines for nm.pl
-
nm give a zero-row data frame with suitable columns and column classes; i.e. a template for NMTRAN data sets
-
nmPlots a list of functions that plot nm objects
-
nmVersion extract NONMEM version specification from configuration file
-
nocb impute NA with next observation carried backward
-
NONR run NONMEM and create diagnostic plots
-
noPk.nm rows where EVID is never 0 within SUBJ
-
noPk generic
-
nospace drop spaces from text
-
noUnits drop units from wikimath
-
nth repeat, for each element, the n^th element where a condition is
TRUE(usually, within levels of an index) -
nxt calculate the next element for each element of x
-
offdiag.halfmatrix select just the off-diagonal elements of a halfmatrix
-
offdiag generic
-
omegacor convert omega covariance in NONMEM output to correlation matrix
-
omegacov convert omega covariance in NONMEM output to covariance matrix
-
only repeat, for each element, the only element where a condition is
TRUE(usually, within levels of an index) -
Ops.keyed use concise syntax to join data frames
-
ord.halfmatrix compute the order of a half matrix
-
ord.matrix compute the order of a symmetric matrix
-
ord generic
-
packageCheck load a package and run package-level examples
-
padded pad a numeric with leading zeros
-
panel.bar for each level, plot vertical (or horizontal) bars corresponding to x (y).
-
panel.covplot plot distributions with respect to reference values; i.e. combine panel.cuts, panel.densitystrip, and panel.ref
-
panel.cuts for each level, plot percent observations in each vertical category defined by cuts
-
panel.densitystrip for each level, plot a filled polygon representing smoothed density of the distribution
-
panel.hist for each level, plot a histogram
-
panel.ref plot a reference region in a stripplot
-
panel.stratify handle strips (levels) of data one at a time
-
parameter2wiki convert parameter labels to wikmath
-
params list documented model parameters
-
parens wrap text in parentheses
-
parfile extract parfile specification from a control stream
-
partab construct a model parameter table
-
percent convert to percent
-
plot.conditioned plot a conditioned object
-
plot.digest plot a digest
-
plot.isolated plot isolated
-
plot.keyed plot keyed
-
plot.nm generate standard plots for an nm object using
nmPlots -
plotfilename make a name for a diagnostic plot file
-
PLOTR create diagnostic plots for NONMEM runs
-
pool test for unique and shared elments among two vectors
-
posmat coerce a matrix to be positive definite
-
predoseDv.nm DV is defined before the first record within SUBJ where EVID is 1
-
predoseDv generic
-
prev calculate the previous element for each element of x
-
print.comment print comment
-
print.flag print flag
-
print.halfmatrix print halfmatrix
-
print.init print init
-
print.initList print initList
-
print.keyed.summary print keyed summary
-
print.nm.summary print nm summary
-
print.nmctl print nmctl
-
print.duration print duration
-
print.timepoint print timepoint
-
print.uniKey print uniKey
-
progress summarize progress of NONMEM runs
-
purge.dir purge a directory (internal)
-
purge.files purge files (internal)
-
purgeRunDir delete certain files from run directories
-
qstat invoke SGE qstat
-
qsub prepare commandlines for qsub
-
read.cwres.data compute conditional weighted residuals (internal)
-
read.nm read a csv file and try to transform to nm
-
read.nmctl read a NONMEM control stream, converting to modifiable object
-
read.spec read a spec
-
reapply apply a function across cells of an indexed vector, giving an identically-indexed result
-
rep.comment repeat comment
-
rep.flag repeat flag
-
rep.timeline repeat timeline
-
rep.uniKey repeat uniKey
-
resample.csv.filename create replicate data sets by stratified sampling with replacement, after reading csv file
-
resample.data.frame create replicate data sets by stratified sampling with replacement
-
resample.filename create replicate data sets by stratified sampling with replacement, after reading file
-
resample generic
-
respecify update a data specification
-
respecify.character update a data specification by filename
-
respecify.spec update a data specification explicitly
-
resolve reinterpret relative file paths with respect to specified directory.
-
rhs extract right-hand side of wikimath
-
rinvchisq generate inverse chi-square distribution
-
riwish generate inverse Wishart distribution
-
rlog generate a combined run log for multiple NONMEM runs
-
roles alias for as.roles
-
row2tabular convert a vector to a latex tabular row
-
runCommand issue the system call that invokes NONMEM (internal)
-
runhead determine whether each element is the start of a run
-
runlog create a zero-row runlog
-
runNonmem process a request for NONMEM invocation
-
runstate determine the status of a run
-
safe.call call a function, passing only those extra arguments that the function accepts
-
safeQuote single-quote unquoted text that contains space
-
scavenge find an expression in lines of text
-
seq.timeline generate timeline sequence
-
setCwres append conditional weighted residuals to an appropriate file
-
shuffle move columns in a data frame
-
sigmacor convert sigma covariance in NONMEM output to correlation matrix
-
sigmacov convert sigma covariance in NONMEM output to covariance matrix
-
simblock generate deviates of the elements of a variance-covariance matrix
-
simpar generate deviates of a set of model parameters for simulation
-
snap coerce values to nearest of candidates
-
sort.keyed sort a keyed data frame
-
spaces create a string of spaces
-
specification generic
-
specification.comment pre-format a comment for specification
-
specification.data.frame develop a draft specification for a data.frame
-
specification.default pre-format a vector for specification
-
specfile for a run and project, guess a path to a data specification file
-
splom.conditioned scatterplot for conditioned
-
splom.digest scatterplot for digest
-
splom.keyed scatterplot for keyed
-
sqrtm support
compute.cwres -
stableMerge produce a left join, with strict error checking
-
star replace asterisk in x with y (internal)
-
static.data.frame return the static portion of a data frame
-
static.keyed return the static portion of a keyed data frame
-
static generic
-
strain reduce x to those elements that occur in options (internal)
-
Summary.timepoint group generic summary for objects of class 'timepoint'
-
summary.hidden.data.frame summarize hidden rows of a data frame
-
summary.keyed summarize a keyed data frame
-
summary.nm summarize an nm object
-
summary.spec summarize a spec object
-
superset combine all NONMEM input with all output
-
supp generic
-
supp.data.frame supplement a CDISC data.frame
-
supp.keyed supplement a CDISC keyed data.frame
-
svnIsText check if subversioned files are text rather than binary
-
svnMarkAsNonText tell Subversion to treat files as binary
-
svnMarkAsText tell Subversion to treat files as text
-
svnMimeType get the Subversion mime-type for files
-
svnPropGet get a Subversion property for files
-
svnPropGetFile get a Subversion property for one file
-
svnPropSet set a subversion property on files
-
svnPropSetFile set a Subversion property on a file
-
svnSetMimeType set Subversion mime type on file
-
synthesis sequentially left-join an arbitrary number of data frames, picking up novel columns (internal)
-
tabfile extract tabfile specification from a control stream
-
tabular.data.frame convert a data.frame to a latex tabular environment
-
tabular convert to a latex tabular environment
-
tabular.define convert define object to tabular
-
tabular.matrix convert matrix to tabular
-
tabular.table convert a (2D) table object to tabular
-
tabularformat generate a format string for a latex tabular environment
-
tagvalue convert a list to a string of delimited tag-value pairs
-
tex2pdf convert tex files to pdf
-
text2decimal convert mixed text to decimal
-
titleCase convert mixed case to title case, strictly by default
-
Tmax calculate the time associated with the maximum concentration for each subject
-
tmax calculate the time of the maximum concentration
-
Tmin calculate the time associated with the minimum concentration for each subject
-
toSAS.mDate encode mDate in SAS format for writing
-
toSAS.mDateTime encode mDateTime in SAS format for writing
-
toSAS.mTime encode mTime in SAS format for writing
-
tos extract thetas, omegas, and sigmas from wikimath
-
totitle convert mixed case to title case, not strictly by default
-
transform.keyed transform a keyed data frame, preserving class
-
tweak.init randomly adjust an initial parameter value
-
tweak.initList randomly adjust a list of initial parameter values
-
tweak.nmctl randomly adjust the initial fixed effect parameters in a control stream
-
tweak randomly adjust a value
-
uniKey.keyed create a single character vector from all the key columns
-
uniKey generic
-
unilog create a zero-row unilog
-
unilogcor convert omega or sigma covariance in NONMEM output to correlation matrix
-
unilogcov convert omega or sigma covariance in NONMEM output to covariance matrix
-
unique.comment find unique elements of a comment vector
-
unique.timepoint find unique elements of a timepoint vector
-
unique.uniKey find unique elements of a uniKey vector
-
unitDensity calculate univariate density with maximum equal to 1
-
unitHist calculate univariate histogram architecture with maximum height equal to 1
-
unsorted generic
-
unsorted.keyed detect rows that would move on sort
-
upper calculate normal quantiles at upper probability of interval
-
variants locate variants of a file in distinctive subdirectories
-
viewtex view (as pdfs) files that contain fragmentary tex code (e.g. tables)
-
wiki2label convert wikimath to a label, e.g. CL/F
-
wiki2latex convert wikimath to latex
-
wiki2parameter convert wikimath to a parameter, e.g. THETA1
-
wiki2plotmath convert wikimath to plotmath
-
wikiparse parse wikimath
-
wikitab extract wikimath specification from a control stream
-
win identify Windows platforms (internal)
-
wrap wrap text in a latex environment
-
write.nm write an nm object to file
-
write.nmctl write an nmctl object to file
-
write.spec write a spec object to file
-
xpath extract value of an xpath exrpession from an xml file
-
xtfrm.comment produce a numeric vector that sorts in the same order as comment
-
xtfrm.flag produce a numeric vector that sorts in the same order as flag
-
xtfrm.timepoint produce a numeric vector that sorts in the same order as timepoint
-
xtfrm.uniKey produce a character vector that sorts in the same order as uniKey
-
xyplotExt plot the parameter search history for a NONMEM7 run
-
zeroAmt.nm AMT is zero where EVID is 1
-
zeroAmt generic
-
zeroDv.nm DV is zero where EVID is zero
-
zeroDv generic
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