Package: ggPMX 1.2.11.9000

Matthew Fidler

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

At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.

Authors:Amine Gassem [aut], Bruno Bieth [aut], Irina Baltcheva [aut], Thomas Dumortier [aut], Christian Bartels [aut], Souvik Bhattacharya [aut], Inga Ludwig [aut], Ines Paule [aut], Didier Renard [aut], Matthew Fidler [aut, cre], Seid Hamzic [aut], Benjamin Guiastrennec [ctb], Kyle T Baron [ctb], Qing Xi Ooi [ctb], Novartis Pharma AG [cph]

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ggPMX.pdf |ggPMX.html✨
ggPMX/json (API)
NEWS

# Install 'ggPMX' in R:
install.packages('ggPMX', repos = c('https://ggpmxdevelopment.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ggpmxdevelopment/ggpmx/issues

On CRAN:

pharmacometricspmxreporting

7.21 score 37 stars 79 scripts 634 downloads 86 exports 83 dependencies

Last updated 12 months agofrom:bd679e25ff. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winERROROct 25 2024
R-4.5-linuxERROROct 25 2024
R-4.4-winERROROct 25 2024
R-4.4-macERROROct 25 2024
R-4.3-winERROROct 25 2024
R-4.3-macERROROct 25 2024

Exports:%>%abbrevcheck_shrinkget_abbrevget_catsget_contsget_covariatesget_dataget_occget_plotget_plot_configget_stratsgetPmxOptionis.pmx_gparload_configload_sourceparam_tableparse_mlxtranpk_occpk_pdplot_namesplot_pmxplotspmxpmx_bloqpmx_comp_shrinkpmx_configpmx_copypmx_covpmx_endpointpmx_filterpmx_get_configspmx_gparpmx_mlxpmx_mlxtranpmx_nlmixrpmx_nmpmx_plotpmx_plot_abs_iwres_ipredpmx_plot_abs_iwres_timepmx_plot_catspmx_plot_cwres_cpredpmx_plot_cwres_predpmx_plot_cwres_qqpmx_plot_cwres_timepmx_plot_dv_ipredpmx_plot_dv_predpmx_plot_eta_boxpmx_plot_eta_catspmx_plot_eta_contspmx_plot_eta_histpmx_plot_eta_matrixpmx_plot_eta_qqpmx_plot_individualpmx_plot_iwres_denspmx_plot_iwres_ipredpmx_plot_iwres_qqpmx_plot_iwres_timepmx_plot_npd_epredpmx_plot_npd_predpmx_plot_npd_qqpmx_plot_npd_timepmx_plot_npde_predpmx_plot_npde_qqpmx_plot_npde_timepmx_plot_vpcpmx_register_plotpmx_reportpmx_report_templatepmx_settingspmx_shrinkpmx_simpmx_themepmx_updatepmx_vpcpmx_vpc_binpmx_vpc_cipmx_vpc_obspmx_vpc_pipmx_vpc_rugpmxOptionsread_extfileset_abbrevset_dataset_plottheophylline

Dependencies:assertthatbackportsbase64encbitbit64bslibcachemcheckmateclicliprcolorspacecpp11crayondata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforcatsfsgenericsGGallyggforceggplot2ggstatsgluegtablehighrhmshtmltoolsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepatchworkpillarpkgconfigplyrpolyclipprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppEigenreadrrlangrmarkdownsassscalesstringistringrsystemfontstibbletidyrtidyselecttinytextweenrtzdbutf8vctrsviridisLitevroomwithrxfunyamlzoo

ggPMX - User Guide

Rendered fromggPMX-guide.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-11-30
Started: 2019-04-25

Readme and manuals

Help Manual

Help pageTopics
Method for subsetting "pmx_gpar" objects[.pmx_gpar
Give the whole abbreviation definitionabbrev
Add draft layer annotationadd_draft
Performs checks of names in shrink listcheck_shrink
creates a graphic distribution objectdistrib
This creates an ETA covariance matrix which can be used to define the co-relation between the parameters and its shrinkage..eta_cov
Eta Covariates plotsdummy eta_cov_plot pmx_plot_eta_cats pmx_plot_eta_conts
Eta distribution plotseta_distribution_plot pmx_plot_eta_box pmx_plot_eta_hist
This creates an eta correlation which defines the relationship between parameterseta_pairs
Try to evaluate a symbol in the parent frame (on errorr eturn the symbol)eval_sym_parent_env
Get abbreviation definition by keyget_abbrev
Get category covariatesget_cats
Get continuous covariatesget_conts
Get covariates variablesget_covariates
Get controller data setget_data
Get controller occasional covariatesget_occ
Get plot objectget_plot
Get the plot config by nameget_plot_config
Get extra stratification variablesget_strats
Get ggPMX OptiongetPmxOption
Remove named elements from gtablegtable_remove_grobs
This function can be used to obtain individual prediction and compare with observed data and population prediction for each individual separatelyindividual
Merge input and fingrid data setsinput_finegrid
Check if an object is a pmx_gpar classis.pmx_gpar
Merge 2 listsl_left_join
Obtain the data source configload_config
Load data setload_data_set
Load all/or some source data setload_source
Determine the number of pages in a paginated facet plotn_pages
Creates parameter kableparam_table
Parse MONOLIX mlxtran fileparse_mlxtran
Creates pmx controller using monlix data having Occasional variablepk_occ
Creates pkpd pmx controller using package internal datapk_pd
Get plot namesplot_names
This is a generic plot method that produces all plots by default described in pmx model evaluation guidance.plot_pmx plot_pmx.pmx_vpc
Plot EBE distributionplot_pmx.distrib
This plots an ETA covariance matrix which can be used to define the co-relation between the parameters and its shrinkageplot_pmx.eta_cov
Plot random effect correlation plotplot_pmx.eta_pairs
This function can be used to plot individual prediction and compare with observed data and population prediction for each individual separatelyplot_pmx.individual
This function plots EBE versus covariates using qq plotsplot_pmx.pmx_dens
The ggPMX base plot functionplot_pmx.pmx_gpar
This function plot EBE versus covariates using qq plotsplot_pmx.pmx_qq
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_pmx.residual
Plot shrink in eta matricplot_shrink
Get plots descriptionplots
Create a pmx objectpmx pmx_mlx pmx_mlxtran
Creates BLOQ object attributespmx_bloq
Compute Shrinkagepmx_comp_shrink
This function can be used to define the pmx configuration used in plots. e.g. Monolix/Nonmempmx_config
Creates a deep copy of the controllerpmx_copy
Select/Map covariates using human labelspmx_cov
Creates a density plot objectpmx_dens
Creates pmx endpoint objectpmx_endpoint
filter data in a pmx controllerpmx_filter
Get List of built-in configurationspmx_get_configs
Handling pmx Graphical parameterspmx_gpar
List NONMEM output tablespmx_list_nm_tables
Manually define nonmem tables to be importedpmx_manual_nm_import
Creates pmx controller from an nlimxr fit objectpmx_nlmixr
Creates pmx controller from NONMEM model outputspmx_nm
Generic pmx plotpmx_plot
Generic pmx stratified plotpmx_plot_cats
Eta matrix plotpmx_plot_eta_matrix
Individual plotpmx_plot_individual
IWRES density plotpmx_plot_iwres_dens
VPC plotpmx_plot_vpc
This function creates a qq plot objectpmx_qq
Quantile-quantile plotspmx_plot_cwres_qq pmx_plot_eta_qq pmx_plot_iwres_qq pmx_plot_npde_qq pmx_plot_npd_qq pmx_qq_plot
NONMEM output file import functionpmx_read_nm_files
NONMEM model file parserpmx_read_nm_model
NONMEM output table import functionpmx_read_nm_tables
Register plotpmx_register_plot
Generates ggpmX report from a pre-defined templatepmx_report
Gets build-in report templatespmx_report_template
Create controller global settingspmx_settings
Create shrinkage parameter objectpmx_shrink
Create simulation objectpmx_sim
Define ggPMX themepmx_theme
Update plot objectpmx_update
Creates vpc objectpmx_vpc
Creates vpc binspmx_vpc_bin
Sets vpc confidence interval layerpmx_vpc_ci
Sets vpc observation layerpmx_vpc_obs
Sets vpc percentile layerpmx_vpc_pi
Sets vpc rug layerpmx_vpc_rug
This function can be used to set ggPMX optionspmxOptions
S3 print abbreviationprint.abbreviation
This function can be used to print configuration of the defined object using S3 method.print.configs
Print pmx_gpar objectprint.pmx_gpar
Print pmxClass objectprint.pmxClass
S3 method print pmxConfig objectprint.pmxConfig
Reads .ext files generated by NONMEMread_extfile
Read Modelling input dataread_input
Read MONOLIX individual parametersread_mlx_ind_est
Read MONOLIX parameter estimation fileread_mlx_par_est
Read MONOLIX model predictionsread_mlx_pred
This function create a residual for each observed value and also generates a residual distributionresidual
Scatter residual plotspmx_plot_abs_iwres_ipred pmx_plot_abs_iwres_time pmx_plot_cwres_cpred pmx_plot_cwres_pred pmx_plot_cwres_time pmx_plot_dv_ipred pmx_plot_dv_pred pmx_plot_iwres_ipred pmx_plot_iwres_time pmx_plot_npde_pred pmx_plot_npde_time pmx_plot_npd_epred pmx_plot_npd_pred pmx_plot_npd_time residual_scatter
update or add a new abbreviationset_abbrev
Set a controller data setset_data
Create a new plot of the desired typeset_plot
Creates pmx controller using theophylline datatheophylline
merge facets formula with new formulawrap_formula