Package 'pmxcode' reference manual

Title:	Create Pharmacometric Models
Description:	Provides a user interface to create or modify pharmacometric models for various modeling and simulation software platforms.
Authors:	Sebastien Bihorel [cre, aut]
Maintainer:	Sebastien Bihorel <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.4
Built:	2024-11-20 06:23:21 UTC
Source:	CRAN

Auto indent mrgsolve code

Description

Auto indent mrgsolve code

Usage

align_annotations(code)
align_annotations(code)

Arguments

code

Code lines containing comments to align across

Auto indent NONMEM code tags

Description

Auto indent NONMEM code tags

Usage

align_tags(code)
align_tags(code)

Arguments

code

Code lines containing comments to align across

Multi-argument version of isTruthy

Description

See shiny::isTruthy for details.

Usage

areTruthy(...)
areTruthy(...)

Arguments

...

Any object

Value

TRUE if all objects are "truthy", FALSE if at least one is not.

Check covariate definition table

Description

Check covariate definition table

Usage

check_covariate_table(table = NULL, check_step = FALSE)
check_covariate_table(table = NULL, check_step = FALSE)

Arguments

`table`	a data.frame with expected columns
`check_step`	a logical indicator to check content of Step column or not

Check if covariate definition table contains rows with incomplete data

Description

Check if covariate definition table contains rows with incomplete data

Usage

check_incomplete_covariate_table(table)
check_incomplete_covariate_table(table)

Arguments

table

a data.frame with expected columns

Convert reference code for univariate model creation

Description

Convert reference code for univariate model creation

Usage

convert_reference_code(code)
convert_reference_code(code)

Arguments

code

A character string containing NONMEM code

Generate univariate model code

Description

Generate univariate model code

Usage

create_univariate_models(
  code,
  referenceName,
  nThetas,
  table,
  style,
  prefix,
  startNumber,
  path
)
create_univariate_models(
  code,
  referenceName,
  nThetas,
  table,
  style,
  prefix,
  startNumber,
  path
)

Arguments

`code`	A character string containing the code of the reference NONMEM model
`referenceName`	The name of the reference model file
`nThetas`	The number of THETA parameters in the reference NONMEM model
`table`	The table of covariate relationship definition
`style`	Either PsN or standard
`prefix`	If standard style, the prefix to start the name of the univariable model file with
`startNumber`	If PsN style, the number to start univariate model run files
`path`	The directory in which the univariate models will be saved and run

Determines if a file path exists

Description

Determines if a file path exists

Usage

file_exists(file)
file_exists(file)

Arguments

file

a path to a file

Creation of model code

Description

Creation of model code

Usage

get_code(
  input = NULL,
  template = NULL,
  vars,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  isPREDPP,
  varianceTable,
  covarianceBlock,
  rvTable,
  parm_lib,
  model_lib,
  rv_lib,
  scaling,
  replacement = TRUE
)
get_code(
  input = NULL,
  template = NULL,
  vars,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  isPREDPP,
  varianceTable,
  covarianceBlock,
  rvTable,
  parm_lib,
  model_lib,
  rv_lib,
  scaling,
  replacement = TRUE
)

Arguments

`input`	Internal parameter for `shiny`
`template`	Text template
`vars`	Reactive object - List of variables in data file
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`isODE`	Reactive object - is model coded with ODEs?
`isLINMAT`	Reactive object - is model coded as linear matrix?
`isPREDPP`	Reactive object - is mode coded with $PK?
`varianceTable`	Variance- table
`covarianceBlock`	Variance-covariance matrix
`rvTable`	Reactive object - residual variability matrix
`parm_lib`	Library of parameters
`model_lib`	Library for $MODEL replacement
`rv_lib`	Library for residual variability replacement
`scaling`	Library for scaling
`replacement`	Logical value indicating with replacement is required

Convert of covariance matrix into a 0/1 correlation map table

Description

Convert of covariance matrix into a 0/1 correlation map table

Usage

get_correlation_table(x, na_zero = FALSE)
get_correlation_table(x, na_zero = FALSE)

Arguments

`x`	A covariance matrix
`na_zero`	Logical indicating whether NA should be replaced by 0's

Value

A matrix of 0 and 1

Get lines of code for derived parameters

Description

Get lines of code for derived parameters

Usage

get_derived_parms_code(
  input,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  parms,
  parm_lib
)
get_derived_parms_code(
  input,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  parms,
  parm_lib
)

Arguments

`input`	Internal parameter for `shiny`
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`isODE`	Reactive object - is model coded with ODEs?
`isLINMAT`	Reactive object - is model coded as linear matrix?
`parms`	Parameter selection
`parm_lib`	Library of parameters

Get line of code for individual parameter value

Description

Get line of code for individual parameter value

Usage

get_individual_parm_code(parms, varianceTable, iparm, ieta, mu)
get_individual_parm_code(parms, varianceTable, iparm, ieta, mu)

Arguments

`parms`	Parameter selection
`varianceTable`	Variability selection
`iparm`	Index of parameter in parms data frame
`ieta`	Index of ETA associated with parameter
`mu`	A logical indicator for mu transformation

Get compartment intialization block

Description

Get compartment intialization block

Usage

get_init_code(input, advan, trans, nPKcmts, nPDcmts, parm_lib)
get_init_code(input, advan, trans, nPKcmts, nPDcmts, parm_lib)

Arguments

`input`	Internal parameter for `shiny`
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`nPKcmts`, `nPDcmts`	Number of compartments for PK and PD model components
`parm_lib`	Library of parameters

Get line of code for individual parameter value

Description

Get line of code for individual parameter value

Usage

get_mrg_individual_parm_code(parms, iparm, eparm)
get_mrg_individual_parm_code(parms, iparm, eparm)

Arguments

`parms`	Parameter selection
`iparm`	Index of parameter in parms data frame
`eparm`	Parameter associated with IIV in ordered categorical models

Get mrgsolve model parameter code lines as list

Description

Get mrgsolve model parameter code lines as list

Usage

get_mrg_parms_code(input, parms, mu)
get_mrg_parms_code(input, parms, mu)

Arguments

`input`	Internal parameter for `shiny`
`parms`	Parameter selection
`mu`	A logical indicator for mu transformation

Creation of mrgsolve code

Description

Creation of mrgsolve code

Usage

get_mrgsolve_code(
  input = NULL,
  template = NULL,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  isPREDPP,
  varianceTable,
  covarianceBlock,
  rvTable,
  parm_lib,
  model_lib,
  rv_lib,
  scaling,
  replacement = TRUE
)
get_mrgsolve_code(
  input = NULL,
  template = NULL,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  isPREDPP,
  varianceTable,
  covarianceBlock,
  rvTable,
  parm_lib,
  model_lib,
  rv_lib,
  scaling,
  replacement = TRUE
)

Arguments

`input`	Internal parameter for `shiny`
`template`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`isODE`	Reactive object - is model coded with ODEs?
`isLINMAT`	Reactive object - is model coded as linear matrix?
`isPREDPP`	Reactive object - is mode coded with $PK?
`varianceTable`	Variance- table
`covarianceBlock`	Variance-covariance matrix
`rvTable`	Reactive object - residual variability matrix
`parm_lib`	Library of parameters
`model_lib`	Library for $MODEL replacement
`rv_lib`	Library for residual variability replacement
`scaling`	Library for scaling
`replacement`	Logical value indicating with replacement is required

Get the number of PK and PD compartments

Description

Get the number of PK and PD compartments

Usage

get_ncmts(input, new, model_lib, isPRED, isPREDPP)
get_ncmts(input, new, model_lib, isPRED, isPREDPP)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`model_lib`	Library for $MODEL replacement
`isPRED`	Reactive object - is model coded with $PRED?
`isPREDPP`	Reactive object - is mode coded with $PK?

Get NONMEM code blocks

Description

Process a character string containing NONMEM model code and returns a character vector in which each element contain a particular $ block

Usage

get_nonmem_blocks(code)
get_nonmem_blocks(code)

Arguments

code

A character string containing the control stream

Creation of NONMEM code

Description

Creation of NONMEM code

Usage

get_nonmem_code(
  input = NULL,
  template = NULL,
  vars,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  isPREDPP,
  varianceTable,
  covarianceBlock,
  rvTable,
  parm_lib,
  model_lib,
  rv_lib,
  scaling,
  replacement = TRUE
)
get_nonmem_code(
  input = NULL,
  template = NULL,
  vars,
  advan,
  trans,
  isPRED,
  isODE,
  isLINMAT,
  isPREDPP,
  varianceTable,
  covarianceBlock,
  rvTable,
  parm_lib,
  model_lib,
  rv_lib,
  scaling,
  replacement = TRUE
)

Arguments

`input`	Internal parameter for `shiny`
`template`	Text template
`vars`	Reactive object - List of variables in data file
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`isODE`	Reactive object - is model coded with ODEs?
`isLINMAT`	Reactive object - is model coded as linear matrix?
`isPREDPP`	Reactive object - is mode coded with $PK?
`varianceTable`	Variance- table
`covarianceBlock`	Variance-covariance matrix
`rvTable`	Reactive object - residual variability matrix
`parm_lib`	Library of parameters
`model_lib`	Library for $MODEL replacement
`rv_lib`	Library for residual variability replacement
`scaling`	Library for scaling
`replacement`	Logical value indicating with replacement is required

Get NONMEM model parameter code lines as list

Description

Get NONMEM model parameter code lines as list

Usage

get_parms_code(input, parms, varianceTable, mu)
get_parms_code(input, parms, varianceTable, mu)

Arguments

`input`	Internal parameter for `shiny`
`parms`	Parameter selection
`varianceTable`	Variability selection
`mu`	A logical indicator for mu transformation

Get lines of preamble code for transit compartment absorption model and delayed dosing records

Description

Get lines of preamble code for transit compartment absorption model and delayed dosing records

Usage

get_preamble_code(input, parms, vars)
get_preamble_code(input, parms, vars)

Arguments

`input`	Internal parameter for `shiny`
`parms`	Parameter selection
`vars`	Character vector of variable names

Get code lines for scaling and bioavailability

Description

Get code lines for scaling and bioavailability

Usage

get_scaling_code(input, advan, trans, parm_lib, scaling)
get_scaling_code(input, advan, trans, parm_lib, scaling)

Arguments

`input`	Internal parameter for `shiny`
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`parm_lib`	Library of parameters
`scaling`	Library for scaling

Get number of THETA parameters

Description

Get number of THETA parameters

Usage

get_theta_number(code)
get_theta_number(code)

Arguments

code

A character string containing the control stream

Convert covariate handsontable data to R data.frame without factor

Description

Convert covariate handsontable data to R data.frame without factor

Usage

hot_to_r_raw(...)
hot_to_r_raw(...)

Arguments

...

passed to rhandsontable::hot_to_r

Determine if a square matrix is of type block, band or error

Description

Determine if a square matrix is of type block, band or error

Usage

is_EDB(x)
is_EDB(x)

Arguments

`x`	A square matrix

Value

Either "error", "band", or "block"

New model module

Description

New model module

Usage

new_model_server(session, input, output, resources)
new_model_server(session, input, output, resources)

Arguments

`input`, `output`, `session`	Internal parameters for `shiny`.
`resources`	A list of internal resources

Opposite of areTruthy

Description

Opposite of areTruthy

Usage

notTruthy(...)
notTruthy(...)

Arguments

...

Any object

Value

TRUE if at least one object is not "truthy", FALSE if all are.

Replacement of @ABBREVIATED tag

Description

Replacement of @ABBREVIATED tag

Usage

replace_abbreviated(input, new, vars)
replace_abbreviated(input, new, vars)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`vars`	Character vector of variable names

Replacement of @DATA tag

Description

Replacement of @DATA tag

Usage

replace_data(input, new)
replace_data(input, new)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template

Replace @DES tag

Description

Replace @DES tag

Usage

replace_des(input, new, advan, trans, isODE, vars, nPKcmts, nPDcmts, parm_lib)
replace_des(input, new, advan, trans, isODE, vars, nPKcmts, nPDcmts, parm_lib)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isODE`	Reactive object - is model coded with ODEs?
`vars`	Reactive object - List of variables in data file
`nPKcmts`	Number of PK compartments in the model
`nPDcmts`	Number of PD compartments in the model
`parm_lib`	Library of parameters

Replace @ERROR tag

Description

Replace @ERROR tag

Usage

replace_error(
  input,
  new,
  advan,
  trans,
  isPRED,
  nPKcmts,
  nPDcmts,
  parm_lib,
  rv_lib
)
replace_error(
  input,
  new,
  advan,
  trans,
  isPRED,
  nPKcmts,
  nPDcmts,
  parm_lib,
  rv_lib
)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`nPKcmts`	Number of PK compartments in the model
`nPDcmts`	Number of PD compartments in the model
`parm_lib`	Library of parameters
`rv_lib`	Library for residual variability replacement

Replacement of @INPUT tag

Description

Replacement of @INPUT tag

Usage

replace_input(input, new, vars)
replace_input(input, new, vars)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`vars`	Character vector of variable names

Replace @MODEL tag

Description

Replace @MODEL tag

Usage

replace_model(input, new, model_lib, isPRED, isPREDPP)
replace_model(input, new, model_lib, isPRED, isPREDPP)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`model_lib`	Library for $MODEL replacement
`isPRED`	Reactive object - is model coded with $PRED?
`isPREDPP`	Reactive object - is mode coded with $PK?

Replacement of @CAPTURE tag

Description

Replacement of @CAPTURE tag

Usage

replace_mrg_capture(input, new, parms)
replace_mrg_capture(input, new, parms)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`parms`	Parameter selection

Replacement of @CMT tag

Description

Replacement of @CMT tag

Usage

replace_mrg_cmt(input, new, model_lib, isPRED)
replace_mrg_cmt(input, new, model_lib, isPRED)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`model_lib`	Library for $MODEL replacement
`isPRED`	Reactive object - is model coded with $PRED?

Replacement of @GLOBAL tag

Description

Replacement of @GLOBAL tag

Usage

replace_mrg_global(input, new, advan, trans, nPKcmts, parm_lib)
replace_mrg_global(input, new, advan, trans, nPKcmts, parm_lib)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`nPKcmts`	Number of compartments for PK
`parm_lib`	Library of parameters

Replace @MAIN or @PRED tags

Description

Replace @MAIN or @PRED tags

Usage

replace_mrg_main_pred(
  input,
  new,
  preamble_code,
  parms_code,
  derived_parms_code,
  scaling_code,
  init_code,
  isPRED,
  parms,
  parm_lib,
  rv_lib
)
replace_mrg_main_pred(
  input,
  new,
  preamble_code,
  parms_code,
  derived_parms_code,
  scaling_code,
  init_code,
  isPRED,
  parms,
  parm_lib,
  rv_lib
)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`preamble_code`	Preamble code
`parms_code`	Typical and individual parameter code
`derived_parms_code`	Derived parameter code
`scaling_code`	Dose scaling and bioavailability code
`init_code`	Compartment initialization code
`isPRED`	Reactive object - is model coded with $PRED?
`parms`	Parameter selection
`parm_lib`	Library of parameters
`rv_lib`	Library for residual variability replacement

Replacement of @ODE tag

Description

Replacement of @ODE tag

Usage

replace_mrg_ode(input, new, advan, trans, isODE, nPKcmts, nPDcmts, parm_lib)
replace_mrg_ode(input, new, advan, trans, isODE, nPKcmts, nPDcmts, parm_lib)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isODE`	Reactive object - is model coded with ODEs?
`nPKcmts`	Number of PK compartments in the model
`nPDcmts`	Number of PD compartments in the model
`parm_lib`	Library of parameters

Replacement of @OMEGA tag

Description

Replacement of @OMEGA tag

Usage

replace_mrg_omega(input, new, parms, blocks, nmextImport)
replace_mrg_omega(input, new, parms, blocks, nmextImport)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`parms`	Parameter selection
`blocks`	Variance - covariance matrix
`nmextImport`	A logical indicating whether NONMEM ext file content should be imported

Replacement of @PARAM tag

Description

Replacement of @PARAM tag

Usage

replace_mrg_param(input, new, parms, nmextImport)
replace_mrg_param(input, new, parms, nmextImport)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`parms`	Parameter selection
`nmextImport`	A logical indicating whether NONMEM ext file content should be imported

Replacement of @PLUGIN tag

Description

Replacement of @PLUGIN tag

Usage

replace_mrg_plugin(input, new)
replace_mrg_plugin(input, new)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template

Replacement of @SIGMA tag

Description

Replacement of @SIGMA tag

Usage

replace_mrg_sigma(input, new, rvTable, nmextImport)
replace_mrg_sigma(input, new, rvTable, nmextImport)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`rvTable`	Residual variability selection
`nmextImport`	A logical indicating whether NONMEM ext file content should be imported

Replacement of @TABLE tag

Description

Replacement of @TABLE tag

Usage

replace_mrg_table(
  input,
  new,
  advan,
  trans,
  isPRED,
  nPKcmts,
  nPDcmts,
  parm_lib,
  rv_lib
)
replace_mrg_table(
  input,
  new,
  advan,
  trans,
  isPRED,
  nPKcmts,
  nPDcmts,
  parm_lib,
  rv_lib
)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`nPKcmts`	Number of PK compartments in the model
`nPDcmts`	Number of PD compartments in the model
`parm_lib`	Library of parameters
`rv_lib`	Library for residual variability replacement

Replacement of @NMEXT tag

Description

Replacement of @NMEXT tag

Usage

replace_nmext(input, new, nmextImport = FALSE)
replace_nmext(input, new, nmextImport = FALSE)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`nmextImport`	A logical indicating whether NONMEM ext file content should be imported

Replacement of @OMEGA tag

Description

Replacement of @OMEGA tag

Usage

replace_omega(new, parms, varianceTable, blocks)
replace_omega(new, parms, varianceTable, blocks)

Arguments

`new`	Text template
`parms`	Parameter selection
`varianceTable`	Variability selection
`blocks`	Variance - covariance matrix

Replacement of @PATH tag

Description

Replacement of @PATH tag

Usage

replace_path(input, new)
replace_path(input, new)

Arguments

`input`	Internal parameter for `shiny`.
`new`	Text template

Replace @PK and @PRED tags

Description

Replace @PK and @PRED tags

Usage

replace_pk_pred(
  input,
  new,
  preamble_code,
  parms_code,
  derived_parms_code,
  scaling_code,
  init_code,
  isPRED,
  parms,
  varianceTable,
  parm_lib,
  rv_lib,
  mu
)
replace_pk_pred(
  input,
  new,
  preamble_code,
  parms_code,
  derived_parms_code,
  scaling_code,
  init_code,
  isPRED,
  parms,
  varianceTable,
  parm_lib,
  rv_lib,
  mu
)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`preamble_code`	Preamble code
`parms_code`	Typical and individual parameter code
`derived_parms_code`	Derived parameter code
`scaling_code`	Dose scaling and bioavailability code
`init_code`	Compartment initialization code
`isPRED`	Reactive object - is model coded with $PRED?
`parms`	Parameter selection
`varianceTable`	Variability selection
`parm_lib`	Library of parameters
`rv_lib`	Library for residual variability replacement
`mu`	A logical indicator for mu transformation

Replacement of @PRIOR tag

Description

Replacement of @PRIOR tag

Usage

replace_prior(input, new, parms, varianceTable, estimations)
replace_prior(input, new, parms, varianceTable, estimations)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`parms`	Parameter selection
`varianceTable`	Variability selection
`estimations`	Table of estimation tasks

Replacement of @PROB1 and @PROB2 tags

Description

Replacement of @PROB1 and @PROB2 tags

Usage

replace_problem(input, new)
replace_problem(input, new)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template

Replacement of @PURPOSE tag

Description

Replacement of @PURPOSE tag

Usage

replace_purpose(input, new, varianceTable)
replace_purpose(input, new, varianceTable)

Arguments

`input`	Internal parameter for `shiny`.
`new`	Text template
`varianceTable`	Variance- table

Replacement of @SIGMA tag

Description

Replacement of @SIGMA tag

Usage

replace_sigma(new, input, rvTable)
replace_sigma(new, input, rvTable)

Arguments

`new`	Text template
`input`	Internal parameter for `shiny`
`rvTable`	Residual variability selection

Replacement of @SUBROUTINE tag

Description

Replacement of @SUBROUTINE tag

Usage

replace_subroutine(input, new, advan, trans, isPRED, isODE, isLINMAT)
replace_subroutine(input, new, advan, trans, isPRED, isODE, isLINMAT)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`advan`	Reactive object - NONMEM ADVAN value
`trans`	Reactive object - NONMEM TRANS value
`isPRED`	Reactive object - is model coded with $PRED?
`isODE`	Reactive object - is model coded with ODEs?
`isLINMAT`	Reactive object - is model coded as linear matrix?

Replace @TABLE tag

Description

Replace @TABLE tag

Usage

replace_table(input, new, vars)
replace_table(input, new, vars)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`vars`	Reactive object - List of variables in data file

Replace $TAGs tag

Description

Replace $TAGs tag

Usage

replace_tags(input, new)
replace_tags(input, new)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template

Replace @TASK tag

Description

Replace @TASK tag

Usage

replace_task(input, new, estimations, isODE)
replace_task(input, new, estimations, isODE)

Arguments

`input`	Internal parameter for `shiny`
`new`	Text template
`estimations`	Table of estimation tasks
`isODE`	Reactive object - is model coded with ODEs?

Replacement of @THETA tag

Description

Replacement of @THETA tag

Usage

replace_theta(new, parms)
replace_theta(new, parms)

Arguments

`new`	Text template
`parms`	Parameter selection

Load resource files

Description

Load resource files

Usage

resources()
resources()

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_app(
  onStart = NULL,
  options = list(launch.browser = TRUE),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)
run_app(
  onStart = NULL,
  options = list(launch.browser = TRUE),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)

Arguments

`onStart`	A function that will be called before the app is actually run. This is only needed for `shinyAppObj`, since in the `shinyAppDir` case, a `global.R` file can be used for this purpose.
`options`	Named options that should be passed to the `runApp` call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify `width` and `height` parameters which provide a hint to the embedding environment about the ideal height/width for the app.
`enableBookmarking`	Can be one of `"url"`, `"server"`, or `"disable"`. The default value, `NULL`, will respect the setting from any previous calls to `enableBookmarking()`. See `enableBookmarking()` for more information on bookmarking your app.
`uiPattern`	A regular expression that will be applied to each `GET` request to determine whether the `ui` should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.
`...`	arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.

Value

Starts the PMXcode Shiny application

Examples

## Not run: 
if( interactive() ){
  pmxcode::run_app()
}

## End(Not run)
## Not run: 
if( interactive() ){
  pmxcode::run_app()
}

## End(Not run)

Format variables by lines of 10.

Description

Format variables by lines of 10.

Usage

tenvars(x)
tenvars(x)

Arguments

`x`	Character vectors of variables

Package 'pmxcode'

Help Index

Auto indent mrgsolve code

Description

Usage

Arguments

Auto indent NONMEM code tags

Description

Usage

Arguments

Multi-argument version of isTruthy

Description

Usage

Arguments

Value

Check covariate definition table

Description

Usage

Arguments

Check if covariate definition table contains rows with incomplete data

Description

Usage

Arguments

Convert reference code for univariate model creation

Description

Usage

Arguments

Generate univariate model code

Description

Usage

Arguments

Determines if a file path exists

Description

Usage

Arguments

Creation of model code

Description

Usage

Arguments

Convert of covariance matrix into a 0/1 correlation map table

Description

Usage

Arguments

Value

Get lines of code for derived parameters

Description

Usage

Arguments

Get line of code for individual parameter value

Description

Usage

Arguments

Get compartment intialization block

Description

Usage

Arguments

Get line of code for individual parameter value

Description

Usage

Arguments

Get mrgsolve model parameter code lines as list

Description

Usage

Arguments

Creation of mrgsolve code

Description

Usage

Arguments

Get the number of PK and PD compartments

Description

Usage

Arguments

Get NONMEM code blocks

Description

Usage

Arguments

Creation of NONMEM code

Description

Usage

Arguments