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nonmemica (version 0.7.9)

Create and Evaluate NONMEM Models in a Project Context

Description

Systematically creates and modifies NONMEM(R) control streams. Harvests NONMEM output, builds run logs, creates derivative data, generates diagnostics. NONMEM (ICON Development Solutions ) is software for nonlinear mixed effects modeling. See 'package?nonmemica'.

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Version

Install

install.packages('nonmemica')

Monthly Downloads

730

Version

0.7.9

License

GPL-3

Maintainer

Tim Bergsma

Last Published

November 30th, 2017

Functions in nonmemica (0.7.9)

as.character.items

Coerce Items to Character
absolute

Check if File Path is Absolute
as.character.model

Coerce NONMEM Control Object to character
as.file

Coerce to file
as.best

Convert to Best of Numeric or Character
as.bootstrap

Create a Bootstrap Table
as.character.init

Coerce init to character
as.character.inits

Coerce inits to character
as.bootstrap.numeric

Create Bootstrap from Numeric
as.docx

Coerce to docx
as.init

Coerce to init
as.init.numeric

Coerces numeric to init
as.matrices.inits

Coerce to Matrices from Inits
as.items.character

Convert to Items from Character
as.flextable

Coerce to flextable
as.inits

Coerce to inits
as.matrices

Coerce to List of Matrices
as.items

Convert to Items
as.inits.numeric

Coerce numeric to inits
as.model.numeric

Coerce to Model from Numeric
$<-.init

Set init element
as.omega

Extract Omegas
comments

Extract Comments
as.omega.model

Extract Omegas from Model
as.tab.model

Extract Tables from Model
as.theta

Extract Thetas
as.sigma

Extract Sigmas
as.theta.model

Extract Thetas from Model
comwidth

Calculate Comment Widths Calculates comment widths.
as.xml_document

Create an xml_document in a Project Context
comwidth.character

Calculate Comment Widths for Character
as.sigma.model

Extract Sigmas from Model
datafile.character

Identify the Datafile for a Model
as.tab

Extract Tables
datafile.numeric

Identify Datafile from Numeric
estimates.numeric

Get Estimates for Numeric
but.default

Identify the Distinctive Feature of a Model
fixed<-.init

Set fixed init value
$.init

Select init element
fixed.model

Check If Model is Fixed
as.list.model

Coerce model to list
contains

Check Whether Text Contains Pattern
as.matrices.records

Coerce to List of Matrices from Records
datafile

Identify Datafile
as.model

Coerce to NONMEM Control Object
as.xml_document.numeric

Coerce numeric to xml_document
comwidth.inits

Calculate Comment Widths for Inits
but

Identify a Distinctive Feature
comwidth.items

Calculate Comment Widths for Items
errors.character

Get Errors for Character
definitions

Harvest Model Item Definitions
errors.numeric

Get Errors for Numeric
definitions.numeric

Create Model Item Definitions from Number.
fold.character

Fold Character
comwidthOne

Calculate Comment Widths for One Element
initSubscripts

Identify Subscripts
comwidthOne.character

Calculate Comment Widths for One Element of Character
initSubscripts.model

Identify Subscripts of Initial Estimates in model
estimates

Get Estimates
estimates.character

Get Estimates for Character
fixed<-.inits

Set fixed attribute of inits
fixed<-

Set value of fixed attribute
fixed<-.model

Set fixed attribute of model
fixed

Check if something is fixed
like.default

Identify the Relevant Reference Model
initDex

Identify Indices of Initial Estimates
likebut

Modify a Model
initDex.model

Identify Indices of Initial Estimates in model
meta.character

Get Metadata for Character
meta.numeric

Get Metadata for Numeric
enclose

Enclose in Arbitrary Characters
errors

Get Errors
modelpath

Resolve A Path to a Model-related File
format.init

Format init
modelpath.character

Resolve A Path to a Model-related File for Character
initial<-.model

Set Upper Bounds for Model Initial Estimates
initial<-

Set Initial Value
nms_psn

Generate PsN-style Names
is.defined

Check Whether Elements are Defined
nms_psn.character

Generate PsN-style Names for Character
format.inits

Format inits
lower<-

Set Lower Value
generalize

Generalize a Nonmissing Value
lower

Get Lower Value
%contains%

Check Whether x contains y
maxWidths.list

Calculate Maximum Widths for List
like

Identify What Something is Like
metaplot_character

Metaplot Character, Standard Evaluation
meta

Get Metadata
metasuperset

Retrieve Model Outputs in Meta Format
modeldir

Identify the Directory for a Model
depends

Identify What Something Depends On
nms_canonical

Generate Canonical Names
depends.default

Identify Model Dependencies
nms_canonical.character

Generate Canonical Names for Character
fold.numeric

Fold Numeric
nms_nonmem

Generate NONMEM-style Names
modelfile

Identify the Modelfile for a Model
nms_psn.model

Generate PsN-style Names for Model
nms_nonmem.character

Generate NONMEM-style Names for Character
nms_psn.numeric

Generate PsN-style Names for Numeric
parameters.numeric

Get Parameters for Numeric
ord.items

Identify the Order of an Items Object
parens

Enclose in Parentheses
nonmemica

Create and Evaluate NONMEM Models in a Project Context
partab

Create Parameter Table
num_parameters

Get the Number of Parameters
padded

Pad Numeric with Zeros
partab.numeric

Create Model Parameter Table from Number.
fold_character

Fold Character with Standard Evaluation
print.init

Print init
format.items

Format Items
print.inits

Print inits
format.model

Format model
locf

Impute Missing Vector Values
runhead

Find Positions in a Vector that Differ from Previous
lower<-.model

Set Lower Bounds for Model Initial Estimates
runlog

Create a Runlog
metaplot.character

Metaplot Character
[.inits

Subset inits
[.model

Subset model
metaplot.numeric

Metaplot Numeric
tod

Calculate Time of Most Recent Dose
modelpath.numeric

Resolve A Path to a Model-related File for Numeric
tweak

Tweak Something
ninput

Calculate Number of Inputs
pool

Compare Sets
nms_canonical.model

Generate Canonical Names for Model
read.model

Read model
nms_canonical.numeric

Generate Canonical Names for Numeric
relativizePath

Relativize a Path
parameters

Get Parameters
partab.character

Create a Parameter Table from Model Name
parameters.character

Get Parameters for Character
problem.numeric

Identify the Model Problem Statement for Numeric
prettycom

Pretty-print a Comment
problem_

Identify the Single Model Problem Statement
prettycom.character

Pretty-print a Comment for Character
updated.numeric

Create the Updated Version of Numeric
problem

Identify the Model Problem Statement
upper<-.model

Set Upper Bounds for Model Initial Estimates
upper<-

Set Upper Value
problem.character

Identify the Model Problem Statement for Character
specfile.character

Identify the Data Specification File for a Model
runlog.character

Create a Runlog for Character
specfile.numeric

Identify Specfile from Numeric
upper

Get Upper Value
superspec

Create Specification for Model Inputs and Outputs
unfold.character

Unfold Character
superspec.character

Create Specification for Model Inputs and Outputs From Character
unfold.numeric

Unfold Numeric
superset.numeric

Coerce to Superset from Numeric
tweak.inits

Tweak inits
write.model

Write model
tweak.model

Tweak Model
xpath

Evaluate Xpath Expression
upper.model

Get Upper Bounds for Model Initial Estimates
shuffle

Move the Columns of a Data Frame Relative to Each Other
val_name

Create Model Parameter Table from Xml_document
specfile

Identify Specfile
runlog.numeric

Create a Runlog for Numeric
superset.character

Coerce to Superset from Character
tad1

A NONMEM-like Dataset
text2decimal

Convert Text to Decimal
initial

Get Initial Value
maxWidths

Calculate Maximum Widths
initial.model

Get Model Initial Estimates
ninput.character

Calculate Number of Inputs for Character
lower.model

Get Lower Bounds for Model Initial Estimates
ninput.numeric

Calculate Number of Inputs for Numeric
updated

Create the Updated Version of Something
nms_nonmem.model

Generate NONMEM-style Names for Model
updated.character

Create the Updated Version of Character
nms_nonmem.numeric

Generate NONMEM-style Names for Numeric
ord.inits

Identify the order of an inits
num_parameters.default

Get the Number of Declared Parameters for a NONMEM Model
superset

Coerce to Superset
print.items

Print Items
superspec.numeric

Create Specification for Model Inputs and Outputs From Numeric
print.model

Print model
resolve

Resolve File Path
tweak.default

Tweak a Model by Default
row_col

Create Indexed Model Parameter Table from Xml_document
[[.model

Select model Element
tad

Calculate Time Since Most Recent Dose
tweak.init

Tweak Init