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

## Documentation for package ‘ggPMX’ version 1.3.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E G I L N P R S T W misc

## -- 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