'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

Documentation for package ‘ggPMX’ version 1.3.0

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-- A --

abbrev	Give the whole abbreviation definition
add_draft	Add draft layer annotation

-- C --

check_shrink

Performs checks of names in shrink list

-- D --

distrib	creates a graphic distribution object
dummy	Eta Covariates plots

-- E --

eta_cov	This creates an ETA covariance matrix which can be used to define the co-relation between the parameters and its shrinkage..
eta_cov_plot	Eta Covariates plots
eta_distribution_plot	Eta distribution plots
eta_pairs	This creates an eta correlation which defines the relationship between parameters
eval_sym_parent_env	Try to evaluate a symbol in the parent frame (on error return the symbol)

-- G --

getPmxOption	Get ggPMX Option
get_abbrev	Get abbreviation definition by key
get_cats	Get category covariates
get_conts	Get continuous covariates
get_covariates	Get covariates variables
get_data	Get controller data set
get_occ	Get controller occasional covariates
get_plot	Get plot object
get_plot_config	Get the plot config by name
get_strats	Get extra stratification variables
gtable_remove_grobs	Remove named elements from gtable

-- I --

individual	This function can be used to obtain individual prediction and compare with observed data and population prediction for each individual separately
input_finegrid	Merge input and fingrid data sets
is.pmx_gpar	Check if an object is a pmx_gpar class

-- L --

load_config	Obtain the data source config
load_data_set	Load data set
load_source	Load all/or some source data set
l_left_join	Merge 2 lists

-- N --

n_pages

Determine the number of pages in a paginated facet plot

-- P --

param_table	Creates parameter kable
parse_mlxtran	Parse MONOLIX mlxtran file
pk_occ	Creates pmx controller using monlix data having Occasional variable
pk_pd	Creates pkpd pmx controller using package internal data
plots	Get plots description
plot_names	Get plot names
plot_pmx	This is a generic plot method that produces all plots by default described in pmx model evaluation guidance.
plot_pmx.distrib	Plot EBE distribution
plot_pmx.eta_cov	This plots an ETA covariance matrix which can be used to define the co-relation between the parameters and its shrinkage
plot_pmx.eta_pairs	Plot random effect correlation plot
plot_pmx.individual	This function can be used to plot individual prediction and compare with observed data and population prediction for each individual separately
plot_pmx.pmx_dens	This function plots EBE versus covariates using qq plots
plot_pmx.pmx_gpar	The ggPMX base plot function
plot_pmx.pmx_param_history	S3 method for plots of class pmx_param_history
plot_pmx.pmx_qq	This function plot EBE versus covariates using qq plots
plot_pmx.pmx_vpc	This is a generic plot method that produces all plots by default described in pmx model evaluation guidance.
plot_pmx.residual	This function plots residual for each observed value by finding the difference between observed and predicted points. It also fits a distribution to the residual value.
plot_shrink	Plot shrink in eta matric
pmx	Create a pmx object
pmxOptions	This function can be used to set ggPMX options
pmx_bloq	Creates BLOQ object attributes
pmx_comp_shrink	Compute Shrinkage
pmx_config	This function can be used to define the pmx configuration used in plots. e.g. Monolix/Nonmem
pmx_copy	Creates a deep copy of the controller
pmx_cov	Select/Map covariates using human labels
pmx_dens	Creates a density plot object
pmx_endpoint	Creates pmx endpoint object
pmx_filter	filter data in a pmx controller
pmx_get_configs	Get List of built-in configurations
pmx_gpar	Handling pmx Graphical parameters
pmx_list_nm_tables	List NONMEM output tables
pmx_manual_nm_import	Manually define nonmem tables to be imported
pmx_mlx	Create a pmx object
pmx_mlxtran	Create a pmx object
pmx_nlmixr	Creates pmx controller from an nlimxr fit object
pmx_nm	Creates pmx controller from NONMEM model outputs
pmx_plot	Generic pmx plot
pmx_plot_abs_iwres_ipred	Scatter residual plots
pmx_plot_abs_iwres_time	Scatter residual plots
pmx_plot_cats	Generic pmx stratified plot
pmx_plot_cwres_cpred	Scatter residual plots
pmx_plot_cwres_pred	Scatter residual plots
pmx_plot_cwres_qq	Quantile-quantile plots
pmx_plot_cwres_time	Scatter residual plots
pmx_plot_dv_ipred	Scatter residual plots
pmx_plot_dv_pred	Scatter residual plots
pmx_plot_eta_box	Eta distribution plots
pmx_plot_eta_cats	Eta Covariates plots
pmx_plot_eta_conts	Eta Covariates plots
pmx_plot_eta_hist	Eta distribution plots
pmx_plot_eta_matrix	Eta matrix plot
pmx_plot_eta_qq	Quantile-quantile plots
pmx_plot_individual	Individual plot
pmx_plot_iwres_dens	IWRES density plot
pmx_plot_iwres_ipred	Scatter residual plots
pmx_plot_iwres_qq	Quantile-quantile plots
pmx_plot_iwres_time	Scatter residual plots
pmx_plot_npde_pred	Scatter residual plots
pmx_plot_npde_qq	Quantile-quantile plots
pmx_plot_npde_time	Scatter residual plots
pmx_plot_npd_epred	Scatter residual plots
pmx_plot_npd_pred	Scatter residual plots
pmx_plot_npd_qq	Quantile-quantile plots
pmx_plot_npd_time	Scatter residual plots
pmx_plot_saem_convergence	SAEM Convergence Plot
pmx_plot_vpc	VPC plot
pmx_qq	This function creates a qq plot object
pmx_qq_plot	Quantile-quantile plots
pmx_read_nm_files	NONMEM output file import function
pmx_read_nm_model	NONMEM model file parser
pmx_read_nm_tables	NONMEM output table import function
pmx_register_plot	Register plot (Jun2025, Alex: I believe it doesn't work at all)
pmx_report	Generates ggpmX report from a pre-defined template
pmx_report_template	Gets build-in report templates
pmx_settings	Create controller global settings
pmx_shrink	Create shrinkage parameter object
pmx_sim	Create simulation object
pmx_theme	Define ggPMX theme
pmx_update	Update plot object
pmx_vpc	Creates vpc object
pmx_vpc_bin	Creates vpc bins
pmx_vpc_ci	Sets vpc confidence interval layer
pmx_vpc_obs	Sets vpc observation layer
pmx_vpc_pi	Sets vpc percentile layer
pmx_vpc_rug	Sets vpc rug layer
print.abbreviation	S3 print abbreviation
print.configs	This function can be used to print configuration of the defined object using S3 method.
print.pmxClass	Print pmxClass object
print.pmxConfig	S3 method print pmxConfig object
print.pmx_gpar	Print pmx_gpar object

-- R --

read_extfile	Reads .ext files generated by NONMEM
read_input	Read Modelling input data
read_mlx_ind_est	Read MONOLIX individual parameters
read_mlx_par_est	Read MONOLIX parameter estimation file
read_mlx_pred	Read MONOLIX model predictions
read_mlx_saem_conv	Read MONOLIX SAEM convergence file
residual	This function create a residual for each observed value and also generates a residual distribution
residual_scatter	Scatter residual plots

-- S --

set_abbrev	update or add a new abbreviation
set_data	Set a controller data set
set_plot	Create a new plot of the desired type

-- T --

theophylline

Creates pmx controller using theophylline data

-- W --

wrap_formula

merge facets formula with new formula

-- misc --

[.pmx_gpar

Method for subsetting "pmx_gpar" objects