nonmemica1.0.11 package

Create and Evaluate NONMEM Models in a Project Context

absolute

Check if File Path is Absolute

as_nms_canonical

Coerce to 'nms_canonical'

as_nms_nonmem

Coerce to 'nms_nonmem'

as_nms_pmx

Coerce to 'nms_pmx'

as_nms_psn

Coerce to 'nms_psn'

as.best.default

Convert Vector to Best of Numeric or Character

as.best

Convert to Best of Numeric or Character

as.bootstrap.bootstrap

Create Bootstrap from Bootstrap

as.bootstrap.numeric

Create Bootstrap from Numeric

as.bootstrap

Create a Bootstrap Table

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.character.problem

Coerce Problem to Character

as.data.frame.halfmatrix

Coerce Half Matrix to Data Frame

as.halfmatrix.default

Coerce to Half Matrix by Default

as.halfmatrix.halfmatrix

Coerce Half Matrix to Half Matrix

as.halfmatrix

Coerce to Half Matrix

as.init.init

Coerce init to init

as.init.numeric

Coerces numeric to init

as.init

Coerce to init

as.inits.list

Coerce list to inits

as.inits.numeric

Coerce numeric to inits

as.inits

Coerce to inits

as.items.character

Convert to Items from Character

as.items

Convert to Items

as.list.model

Coerce model to list

as.matrices.inits

Coerce to Matrices from Inits

as.matrices

Coerce to List of Matrices

as.matrices.records

Coerce to List of Matrices from Records

as.matrix.halfmatrix

Coerce Half Matrix to Matrix

as.model.character

Coerce character to model

as.model.numeric

Coerce to Model from Numeric

as.model

Coerce to NONMEM Control Object

as.omega.model

Extract Omegas from Model

as.omega

Extract Omegas

as.problem

Parse the Run Record

as.sigma.model

Extract Sigmas from Model

as.sigma

Extract Sigmas

as.tab.model

Extract Tables from Model

as.tab

Extract Tables

as.theta.model

Extract Thetas from Model

as.theta

Extract Thetas

as.xml_document.character

Create xml_document From Character

as.xml_document.numeric

Coerce numeric to xml_document

as.xml_document

Create an xml_document in a Project Context

but.default

Identify the Distinctive Feature of a Model

but

Identify a Distinctive Feature

cash-.init

Select init element

cash-set-.init

Set init element

comments.inits

Extract Comments from Inits

comments.items

Extract Comments from Items

comments.model

Extract Comments from Model

comments

Extract Comments

comwidth.character

Calculate Comment Widths for Character

comwidth.inits

Calculate Comment Widths for Inits

comwidth.items

Calculate Comment Widths for Items

comwidth

Calculate Comment Widths Calculates comment widths.

comwidthOne.character

Calculate Comment Widths for One Element of Character

comwidthOne

Calculate Comment Widths for One Element

contains

Check Whether Text Contains Pattern

datafile.character

Identify the Datafile for a Model

datafile.numeric

Identify Datafile from Numeric

datafile

Identify Datafile

definitions.definitions

Create Model Item Definitions from definitions

definitions.numeric

Create Model Item Definitions from Number.

definitions

Harvest Model Item Definitions

depends.default

Identify Model Dependencies

depends

Identify What Something Depends On

enclose

Enclose in Arbitrary Characters

errors.character

Get Errors for Character

errors.numeric

Get Errors for Numeric

errors

Get Errors

estimates.character

Get Estimates for Character

estimates.numeric

Get Estimates for Numeric

estimates

Get Estimates

fixed-set-.init

Set fixed init value

fixed-set-.inits

Set fixed attribute of inits

fixed-set-.model

Set fixed attribute of model

fixed-set

Set value of fixed attribute

fixed.init

Check if init is fixed

fixed.model

Check If Model is Fixed

fixed

Check if something is fixed

format.init

Format init

format.inits

Format inits

format.items

Format Items

format.model

Format model

generalize

Generalize a Nonmissing Value

grapes-contains-grapes

Check Whether x contains y

half.matrix

Find Half of Matrix

half

Find Half of Something

ignored

Extract Index for Ignored Records

initDex.model

Identify Indices of Initial Estimates in model

initDex

Identify Indices of Initial Estimates

initial-set-.model

Set Upper Bounds for Model Initial Estimates

initial-set

Set Initial Value

initial.model

Get Model Initial Estimates

initial

Get Initial Value

initSubscripts.model

Identify Subscripts of Initial Estimates in model

initSubscripts

Identify Subscripts

is.defined

Check Whether Elements are Defined

is.square.matrix

Test If Matrix is Square

is.square

Test If Something is Square

like.default

Identify the Relevant Reference Model

like

Identify What Something is Like

likebut

Modify a Model

locf

Impute Missing Vector Values

lower-set-.model

Set Lower Bounds for Model Initial Estimates

lower-set

Set Lower Value

lower.model

Get Lower Bounds for Model Initial Estimates

lower

Get Lower Value

maxWidths.list

Calculate Maximum Widths for List

maxWidths

Calculate Maximum Widths

meta.character

Get Metadata for Character

meta.numeric

Get Metadata for Numeric

meta

Get Metadata

metaplot_character

Metaplot Character, Standard Evaluation

metaplot.character

Metaplot Character

metaplot.numeric

Metaplot Numeric

metasuperset

Retrieve Model Outputs with Metadata

modeldir

Identify the Directory for a Model

modelfile

Identify the Modelfile for a Model

modelpath.character

Resolve A Path to a Model-related File for Character

modelpath.numeric

Resolve A Path to a Model-related File for Numeric

modelpath

Resolve A Path to a Model-related File

ninput.character

Calculate Number of Inputs for Character

ninput.numeric

Calculate Number of Inputs for Numeric

ninput

Calculate Number of Inputs

nms_canonical.character

Generate Canonical Names for Character

nms_canonical.model

Generate Canonical Names for Model

nms_canonical.nms_nonmem

Convert NONMEM Parameter Names to Canonical

nms_canonical.nms_pmx

Convert Parameter Names to NONMEM

nms_canonical.numeric

Generate Canonical Names for Numeric

nms_canonical

Generate Canonical Names

nms_nonmem.character

Generate NONMEM Names for Character

nms_nonmem.model

Generate NONMEM Names for Model

nms_nonmem.nms_canonical

Convert Canonical Parameter Names to NONMEM

nms_nonmem.nms_pmx

Convert pmxTools Names to NONMEM

nms_nonmem.numeric

Generate NONMEM Names for Numeric

nms_nonmem

Generate NONMEM Names

nms_pmx.nms_canonical

Convert Canonical Names to pmxTools

nms_pmx.nms_nonmem

Convert NONMEM Names to pmxTools

nms_pmx

Convert Parameter Names to pmxTools

nms_psn.character

Generate PsN-style Names for Character

nms_psn.model

Generate PsN-style Names for Model

nms_psn.numeric

Generate PsN-style Names for Numeric

nms_psn

Generate PsN-style Names

nonmemica

Create and Evaluate NONMEM Models in a Project Context

num_parameters.default

Get the Number of Declared Parameters for a NONMEM Model

num_parameters

Get the Number of Parameters

offdiag.halfmatrix

Isolate Off-diagonal of Half Matrix

offdiag

Isolate Off-diagonal

ord.halfmatrix

Calculate Order for Half Matrix

ord.inits

Identify the order of an inits

ord.items

Identify the Order of an Items Object

ord.matrix

Calculate Order for Matrix

ord

Calculate Order

padded

Pad Numeric with Zeros

parameters.character

Get Parameters for Character

parameters.numeric

Get Parameters for Numeric

parameters

Get Parameters

parens

Enclose in Parentheses

partab.character

Create a Parameter Table from Model Name

partab.numeric

Create Model Parameter Table from Number.

partab

Create Parameter Table

pool

Compare Sets

prettycom.character

Pretty-print a Comment for Character

prettycom

Pretty-print a Comment

print.halfmatrix

Print Half Matrix

print.init

Print init

print.inits

Print inits

print.items

Print Items

print.model

Print model

problem_

Identify the Single Model Problem Statement

problem.character

Identify the Model Problem Statement for Character

problem.numeric

Identify the Model Problem Statement for Numeric

problem

Identify the Model Problem Statement

psn_nested

PsN Model File is Nested

psn_options

Set PsN Options

read.model

Read model

relativizePath

Relativize a Path

resolve

Resolve File Path

rosetta

Translate Parameter Names

row_col

Create Indexed Model Parameter Table from Xml_document

runhead

Find Positions in a Vector that Differ from Previous

runlog.character

Create a Runlog for Character

runlog.numeric

Create a Runlog for Numeric

runlog

Create a Runlog

safe_join.data.frame

Join Data Frames Safely

safe_join

Join Data Safely

shuffle

Move the Columns of a Data Frame Relative to Each Other

specfile.character

Identify the Data Specification File for a Model

specfile.numeric

Identify Specfile from Numeric

specfile

Identify Specfile

sub-.inits

Subset inits

sub-.model

Subset model

sub-sub-.model

Select model Element

superset.character

Coerce to Superset from Character

superset.numeric

Coerce to Superset from Numeric

superset

Coerce to Superset

superspec.character

Create Specification for Model Inputs and Outputs From Character

superspec.numeric

Create Specification for Model Inputs and Outputs From Numeric

superspec

Create Specification for Model Inputs and Outputs

tad

Calculate Time Since Most Recent Dose

text2decimal

Convert Text to Decimal

tod

Calculate Time of Most Recent Dose

tweak.default

Tweak a Model by Default

tweak.init

Tweak Init

tweak.inits

Tweak inits

tweak.model

Tweak Model

tweak

Tweak Something

updated.character

Create the Updated Version of Character

updated.numeric

Create the Updated Version of Numeric

updated

Create the Updated Version of Something

upper-set-.model

Set Upper Bounds for Model Initial Estimates

upper-set

Set Upper Value

upper.model

Get Upper Bounds for Model Initial Estimates

upper

Get Upper Value

val_name

Create Model Parameter Table from Xml_document

write.model

Write model

xpath.default

Evaluate xpath Expression in Default Context

xpath

Evaluate Xpath Expression

xpath.xml_document

Evaluate xpath Expression in Document Context

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

  • Maintainer: Tim Bergsma
  • License: GPL-3
  • Last published: 2024-10-25