Package: xpose 0.4.18.9000

Benjamin Guiastrennec

xpose: Diagnostics for Pharmacometric Models

Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.

Authors:Benjamin Guiastrennec [aut, cre, cph], Andrew C. Hooker [aut, cph], Sebastian Ueckert [aut, cph], Mike K. Smith [ctb], Mats O. Karlsson [aut, cph]

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

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

Peer review:

Bug tracker:https://github.com/uupharmacometrics/xpose/issues

Datasets:

On CRAN:

diagnosticsggplot2nonmempharmacometricsxpose

10.43 score 56 stars 2 packages 186 scripts 874 downloads 4 mentions 130 exports 59 dependencies

Last updated 6 months agofrom:39f80b949b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-winOKNov 11 2024
R-4.5-linuxOKNov 11 2024
R-4.4-winOKNov 11 2024
R-4.4-macOKNov 11 2024
R-4.3-winOKNov 11 2024
R-4.3-macOKNov 11 2024

Exports:%>%absval_res_vs_idvabsval_res_vs_predadd_facet_varaes_caes_filteraes_renameall_data_problemall_file_problemamt_vs_idvappend_suffixas.ctimeas.nm.table.listas.xpdbas.xpose.plotas.xpose.themecheck_plot_typecheck_problemcheck_quo_varscheck_scalescheck_xpdbcombine_tablescov_distribcov_qqdata_optdefault_plot_problemdistinctdrop_fixed_colsdv_preds_vs_idvdv_vs_idvdv_vs_ipreddv_vs_prededit_xpose_dataeta_distribeta_qqfacet_grid_paginatefacet_wrap_paginatefetch_datafile_pathfilterfilter_xp_themeget_codeget_dataget_extensionget_fileget_prmget_prm_transformation_formulasget_specialget_summarygrab_itergrd_vs_iterationgroup_byind_plotsindex_tableipred_vs_idvirepis.formulais.nm.modelis.nm.table.listis.xpdbis.xpose.plotis.xpose.themelast_data_problemlast_file_methodlast_file_problemlast_file_subproblist_datalist_fileslist_nm_tableslist_nm_tables_manuallist_speciallist_varsmake_extensionmanual_nm_importmerge_firstonlymsgmutateonly_distinctonly_obsparse_argparse_nm_filesparse_titlepred_vs_idvprm_distribprm_qqprm_tableprm_vs_iterationraw_to_tibbleread_argsread_funsread_nm_filesread_nm_modelread_nm_tablesrenamereorder_factorsres_distribres_qqres_vs_idvres_vs_predselectset_var_labelsset_var_typesset_var_unitsslicesoftwaresummarisesummarizetheme_bw2theme_readabletheme_xp_defaulttheme_xp_xpose4tidyr_new_interfacetransform_prmungroupupdate_argsupdate_extensionupdate_themesvpcvpc_datavpc_optxp_geomsxp_mapxp_varxpdb_index_updatexplot_distribxplot_qqxplot_scatterxpose_dataxpose_panelsxpose_save

Dependencies:bitbit64classclassIntclicliprcolorspacecpp11crayondplyre1071fansifarvergenericsggforceggplot2gluegtablehmsisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpolyclipprettyunitsprogressproxypurrrR6RColorBrewerRcppRcppEigenreadrrlangscalesstringistringrsurvivalsystemfontstibbletidyrtidyselecttweenrtzdbutf8vctrsviridisLitevpcvroomwithr

Access the xpdb data

Benjamin Guiastrennec

Rendered fromaccess_xpdb_data.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2019-03-18
Started: 2017-06-08

Customize plots

Benjamin Guiastrennec

Rendered fromcustomize_plots.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2023-02-25
Started: 2017-06-08

Import model outputs

Benjamin Guiastrennec

Rendered fromimport_model_outputs.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2019-03-18
Started: 2017-06-08

Introduction

Benjamin Guiastrennec

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2019-03-18
Started: 2017-06-03

Plots with multiple pages

Benjamin Guiastrennec

Rendered frommultiple_pages.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2019-03-18
Started: 2017-09-26

Visual Predictive Checks (VPC)

Benjamin Guiastrennec

Rendered fromvpc.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2023-02-25
Started: 2017-10-15

Readme and manuals

Help Manual

Help pageTopics
Compartment kineticsamt_vs_idv
Create options for data importdata_opt
Distribution plots of ETA and parameterscov_distrib distrib_plot eta_distrib prm_distrib res_distrib
Observations plotted against model predictionsdv_vs_ipred dv_vs_pred
Access model codeget_code
Access model output table dataget_data
Access model output file dataget_file
Access model parametersget_prm
Access special model dataget_special
Access model summary dataget_summary
An additional set of themes for ggplot2gg_themes theme_bw2 theme_readable
Observations, individual predictions and population predictions plotted against the independent variable for every individualind_plots
Add simulation counterirep
List NONMEM output tableslist_nm_tables
List available variableslist_vars
List available datasetslist_data list_files list_special list_xpdb
Manually define nonmem tables to be importedmanual_nm_import
Parameter value or gradient vs. iterationsgrd_vs_iteration minimization_plots prm_vs_iteration
Add, remove or rename variables in an xpdbmodify_xpdb mutate.xpose_data rename.xpose_data select.xpose_data
Observations and model predictions plotted against the independent variabledv_preds_vs_idv dv_vs_idv ipred_vs_idv pred_vs_idv
Print an xpose_data objectprint.xpose_data
Draw an xpose_plot objectprint.xpose_plot
Display a parameter estimates to the consoleprm_table
QQ plots of ETA and residualscov_qq eta_qq prm_qq qq_plot res_qq
NONMEM output file import functionread_nm_files
NONMEM model file parserread_nm_model
NONMEM output table import functionread_nm_tables
Residuals plotted against the independent variableabsval_res_vs_idv res_vs_idv
Residuals plotted against population predictionsabsval_res_vs_pred res_vs_pred
Set variable type, label or unitsset_vars set_var_labels set_var_types set_var_units
Subset datasets in an xpdbdistinct.xpose_data filter.xpose_data slice.xpose_data subset_xpdb
Group/ungroup and summarize variables in an xpdbgroup_by.xpose_data summarise.xpose_data summarise_xpdb summarize.xpose_data ungroup.xpose_data
Summarizing xpose_datasummary.xpose_data
Template titlestemplate_titles
Create xpose themeupdate_themes
Visual predictive checksvpc
Visual predictive checks datavpc_data
Generate a list of options for VPC data generationvpc_opt
A set of xpose themestheme_xp_default theme_xp_xpose4 xp_themes
'xpose_data' examplesxpdb_ex_pk
Default xpose distribution plot functionxplot_distrib
Default xpose QQ plot functionxplot_qq
Default xpose scatter plot functionxplot_scatter
Import NONMEM output into Rxpose_data
Save xpose plotxpose_save