nonmem-class: Class nonmem: contain and describe all nonmem output

In PKreport: A reporting pipeline for checking population pharmacokinetic model assumption

Description

This is a class representation for nonmem output.

Objects from the Class

Objects can be created by calls of the form new("nonmem", output.lst, output.tab, output.dir, delim, ...).

This creates a nonmem object containing all nonmem output.

Slots

file.cov:

Object of class "list". This list includes title (character) and data (data.frame) for cov file.

file.cor:

Object of class "list" . This list includes title (character) and data (data.frame) for cor file.

file.coi:

Object of class "list". This list includes title (character) and data (data.frame) for coi file.

file.phi:

Object of class "list". This list includes title (character) and data (data.frame) for phi file.

file.lst:

Object of class "character". This character vector contains the information from NONMEM lst file.

method:

Object of class "character". This character vector matches \#METH tag in lst file and contains the estimation method.

analysis:

Object of class "list" . This list matches text between \#TERM tag and \#TERE tag in lst file and contains the analysis information.

objt:

Object of class "character". This character vector matches \#OBJT tag in lst file and describes the objective function.

objv:

Object of class "character". This character vector matches \#OBJV tag in lst file and describes the objective function value.

objs:

Object of class "character". This character vector matches \#OBJT tag in lst file and describes the objective function standard deviation.

tabid:

Object of class "character". This character vector is from the first line of tab file and describes the title of tab file.

tabdata:

Object of class "data.frame". This data frame matches data in tab file and describes the title of tab file.

Methods

Class-specific methods

non.lst(nonmem):

Access lst content in the file.lst slot.

non.lst.meth(nonmem):

Access method section (\#meth tag) in the file.lst slot.

non.lst.term(nonmem):

Access analysis section (\#TERM, \#TERE tag) in the file.lst slot.

non.lst.objt(nonmem):

Access objective function (\#OBJT tag) in the file.lst slot.

non.lst.objv(nonmem):

Access objective function value (\#OBJV tag) in the file.lst slot.

non.lst.objs(nonmem):

Access objective function standard deviation (\#OBJS tag) in the file.lst slot.

non.tab(nonmem):

Access tab content in the file.tab slot.

non.cov(nonmem):

Access cov content in the file.cov slot.

non.cor(nonmem):

Access cor content in the file.cor slot.

non.coi(nonmem):

Access coi content in the file.coi slot.

non.phi(nonmem):

Access phi content in the file.phi slot.

non.select(nonmem, lines, sep):

Select the lines in the lst file.

Standard generic methods

initialize(object, output.lst, output.tab, output.dir):

Object instantiation. output.lst: the file name for lst file from NONMEM 7; output.tab: the filename for tab file from any NONMEM version; output.dir(optional): the output directory including cor, cov, coi and phi files from NONMEM 7. output.lst and output.dir only works for NONMEM 7.

nonmem instances are created through new("nonmem", ...). The arguments to new should include output.lst and output.tab. If output.dir is missing, NULL will be assigned to proper slots.

Author(s)

Xiaoyong Sun

Examples

showClass("nonmem")

Example output

Loading required package: lattice
Loading required package: ggplot2
Class "nonmem" [package "PKreport"]

Slots:
                                                                        
Name:    file.cov   file.cor   file.coi   file.phi   file.lst     method
Class:       list       list       list       list  character  character
                                                                        
Name:    analysis       objt       objv       objs      tabid    tabdata
Class:       list  character  character  character  character data.frame

PKreport documentation built on May 2, 2019, 10:15 a.m.