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nonmemica (version 0.7.4)

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

0.7.4

License

GPL-3

Maintainer

Tim Bergsma

Last Published

July 10th, 2017

Functions in nonmemica (0.7.4)

as.bootstrap

Create a Bootstrap Table
as.bootstrap.numeric

Create Bootstrap from Numeric
as.docx

Coerce to docx
as.file

Coerce to file
absolute

Check if File Path is Absolute
as.best

Convert to Best of Numeric or Character
as.character.init

Coerce init to character
as.character.inits

Coerce inits to character
as.character.items

Coerce Items to Character
as.character.model

Coerce NONMEM Control Object to character
as.matrices

Coerce to List of Matrices
as.matrices.inits

Coerce to Matrices from Inits
as.model.numeric

Coerce to Model from Numeric
as.items.character

Convert to Items from Character
as.list.model

Coerce model to list
as.sigma.model

Extract Sigmas from Model
as.flextable

Coerce to flextable
as.init

Coerce to init
as.matrices.records

Coerce to List of Matrices from Records
as.model

Coerce to NONMEM Control Object
as.tab

Extract Tables
as.xml_document.numeric

Coerce numeric to xml_document
but

Identify a Distinctive Feature
comwidth.inits

Calculate Comment Widths for Inits
as.theta.model

Extract Thetas from Model
as.xml_document

Create an xml_document in a Project Context
contains

Check Whether Text Contains Pattern
datafile

Identify Datafile
as.omega

Extract Omegas
$<-.init

Set init element
comments

Extract Comments
definitions

Harvest Model Item Definitions
as.inits.numeric

Coerce numeric to inits
as.items

Convert to Items
as.tab.model

Extract Tables from Model
as.theta

Extract Thetas
comwidth.items

Calculate Comment Widths for Items
errors.character

Get Errors for Character
errors.numeric

Get Errors for Numeric
definitions.numeric

Create Model Item Definitions from Number.
depends

Identify What Something Depends On
depends.default

Identify Model Dependencies
format.init

Format init
fold.numeric

Fold Numeric
fold_character

Fold Character with Standard Evaluation
format.model

Format model
comwidth

Calculate Comment Widths Calculates comment widths.
comwidth.character

Calculate Comment Widths for Character
datafile.character

Identify the Datafile for a Model
datafile.numeric

Identify Datafile from Numeric
format.items

Format Items
estimates.numeric

Get Estimates for Numeric
fixed<-.init

Set fixed init value
fixed.model

Check If Model is Fixed
fold.character

Fold Character
%contains%

Check Whether x contains y
initDex

Identify Indices of Initial Estimates
lower.model

Get Lower Bounds for Model Initial Estimates
maxWidths

Calculate Maximum Widths
metasuperset

Retrieve Model Outputs in Meta Format
modeldir

Identify the Directory for a Model
nms_nonmem

Generate NONMEM-style Names
nms_nonmem.character

Generate NONMEM-style Names for Character
format.inits

Format inits
initial<-

Set Initial Value
initial

Get Initial Value
initial.model

Get Model Initial Estimates
as.init.numeric

Coerces numeric to init
as.inits

Coerce to inits
as.omega.model

Extract Omegas from Model
as.sigma

Extract Sigmas
is.defined

Check Whether Elements are Defined
metaplot.numeric

Metaplot Numeric
metaplot_character

Metaplot Character, Standard Evaluation
nms_nonmem.model

Generate NONMEM-style Names for Model
enclose

Enclose in Arbitrary Characters
errors

Get Errors
fixed<-.inits

Set fixed attribute of inits
but.default

Identify the Distinctive Feature of a Model
$.init

Select init element
comwidthOne

Calculate Comment Widths for One Element
comwidthOne.character

Calculate Comment Widths for One Element of Character
ord.items

Identify the Order of an Items Object
padded

Pad Numeric with Zeros
parameters

Get Parameters
parameters.character

Get Parameters for Character
lower<-

Set Lower Value
lower

Get Lower Value
meta

Get Metadata
meta.character

Get Metadata for Character
fixed<-.model

Set fixed attribute of model
initDex.model

Identify Indices of Initial Estimates in model
initSubscripts

Identify Subscripts
likebut

Modify a Model
estimates

Get Estimates
estimates.character

Get Estimates for Character
fixed<-

Set value of fixed attribute
fixed

Check if something is fixed
initSubscripts.model

Identify Subscripts of Initial Estimates in model
initial<-.model

Set Upper Bounds for Model Initial Estimates
like

Identify What Something is Like
lower<-.model

Set Lower Bounds for Model Initial Estimates
modelfile

Identify the Modelfile for a Model
modelpath

Resolve A Path to a Model-related File
nms_canonical.model

Generate Canonical Names for Model
like.default

Identify the Relevant Reference Model
meta.numeric

Get Metadata for Numeric
metaplot.character

Metaplot Character
nms_canonical

Generate Canonical Names
nms_canonical.character

Generate Canonical Names for Character
nms_psn.model

Generate PsN-style Names for Model
nms_psn.numeric

Generate PsN-style Names for Numeric
prettycom

Pretty-print a Comment
modelpath.character

Resolve A Path to a Model-related File for Character
modelpath.numeric

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

Create and Evaluate NONMEM Models in a Project Context
num_parameters

Get the Number of Parameters
prettycom.character

Pretty-print a Comment for Character
read.model

Read model
relativizePath

Relativize a Path
runhead

Find Positions in a Vector that Differ from Previous
runlog

Create a Runlog
nms_nonmem.numeric

Generate NONMEM-style Names for Numeric
num_parameters.default

Get the Number of Declared Parameters for a NONMEM Model
ord.inits

Identify the order of an inits
partab.numeric

Create Model Parameter Table from Number.
superset.numeric

Coerce to Superset from Numeric
tad

Calculate Time Since Most Recent Dose
updated.numeric

Create the Updated Version of Numeric
upper<-.model

Set Upper Bounds for Model Initial Estimates
pool

Compare Sets
print.init

Print init
print.inits

Print inits
partab

Create Parameter Table
partab.character

Create a Parameter Table from Model Name
problem

Identify the Model Problem Statement
problem.character

Identify the Model Problem Statement for Character
nms_canonical.numeric

Generate Canonical Names for Numeric
nms_psn

Generate PsN-style Names
nms_psn.character

Generate PsN-style Names for Character
parameters.numeric

Get Parameters for Numeric
upper.model

Get Upper Bounds for Model Initial Estimates
val_name

Create Model Parameter Table from Xml_document
parens

Enclose in Parentheses
print.items

Print Items
specfile

Identify Specfile
specfile.character

Identify the Data Specification File for a Model
specfile.numeric

Identify Specfile from Numeric
[.inits

Subset inits
tad1

A NONMEM-like Dataset
text2decimal

Convert Text to Decimal
print.model

Print model
tweak.default

Tweak a Model by Default
tweak.init

Tweak Init
runlog.character

Create a Runlog for Character
runlog.numeric

Create a Runlog for Numeric
[.model

Subset model
[[.model

Select model Element
problem.numeric

Identify the Model Problem Statement for Numeric
problem_

Identify the Single Model Problem Statement
resolve

Resolve File Path
row_col

Create Indexed Model Parameter Table from Xml_document
superset

Coerce to Superset
superset.character

Coerce to Superset from Character
unfold.character

Unfold Character
unfold.numeric

Unfold Numeric
tod

Calculate Time of Most Recent Dose
tweak

Tweak Something
tweak.inits

Tweak inits
updated

Create the Updated Version of Something
updated.character

Create the Updated Version of Character
upper<-

Set Upper Value
upper

Get Upper Value
write.model

Write model
xpath

Evaluate Xpath Expression
tweak.model

Tweak Model