Package: xpose.xtras 0.0.2

John Prybylski

xpose.xtras: Extra Functionality for the 'xpose' Package

Adding some at-present missing functionality, or functions unlikely to be added to the base 'xpose' package. This includes some diagnostic plots that have been missing in translation from 'xpose4', but also some useful features that truly extend the capabilities of what can be done with 'xpose'. These extensions include the concept of a set of 'xpose' objects, and diagnostics for likelihood-based models.

Authors:John Prybylski [aut, cre]

xpose.xtras_0.0.2.tar.gz
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xpose.xtras.pdf |xpose.xtras.html✨
xpose.xtras/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/jprybylski/xpose.xtras/issues

Datasets:
  • pheno_base - An 'xp_xtras' example of a base model
  • pheno_final - An 'xp_xtras' example of a final model
  • pheno_saem - An 'xp_xtras' example of a final model
  • pheno_set - A more complex example of 'xpose_set' object
  • pkpd_m3 - An 'xp_xtras' example of an M3 model
  • pkpd_m3_df - An 'xp_xtras' example of an M3 model
  • vismo_dtmm - An 'xp_xtras' example of the discrete-time Markov model of categorical vismodegib data
  • vismo_pomod - An 'xp_xtras' example of the proportional odds categorical vismodegib model
  • vismodegib - A tibble of mock data used for fitting vismodegib models
  • xpdb_set - An example 'xpose_set' object
  • xpdb_x - An example 'xp_xtras' object

On CRAN:

6.01 score 5 scripts 4 mentions 97 exports 71 dependencies

Last updated 2 days agofrom:318e745bd2. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winOKNov 22 2024
R-4.5-linuxOKNov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winNOTENov 22 2024
R-4.3-macNOTENov 22 2024

Exports:%>%%p%add_prm_associationadd_relationshipadd_xpdball_ofany_ofas_leveleras_xp_xtrasas_xpdb_xbackfill_iofvcatdv_vs_dvprobscheck_xp_xtrascheck_xpdb_xcheck_xpose_setcheck_xpose_set_itemcov_griddesc_from_commentsdiagram_lineagedofv_vs_iddrop_prm_associationdv_vs_ipred_modavgdv_vs_pred_modavgedit_xpose_dataeta_grideta_vs_catcoveta_vs_contcoveta_vs_cov_grideta_waterfallexpose_paramexpose_propertyfilterfocus_functionfocus_qapplyfocus_xpdbfocused_xpdbsfranken_propfranken_xpdbget_base_modelget_indexget_prmget_propget_shkgrab_xpose_plotgroup_by_xiofv_vs_modiofv_waterfallipred_vs_idv_modavgipred_vs_ipredirepis_formula_listis_leveleris_xp_xtraslist_dv_probslist_varslvl_binlvl_inordlvl_sexmodavg_xpdbmutatemutate_prmmutate_xplotfun_modavgpred_vs_idv_modavgpred_vs_predprm_waterfallpullremove_relationshiprenamerename_xreportable_digitsreshape_setselectselect_subsetset_base_modelset_dv_probsset_indexset_optionset_propset_var_levelsset_var_typesset_var_types_xshark_colorsshark_plotunfocus_xpdbungroup_xunreshape_setunset_base_modelval2lvlwrap_xp_ggallyxp_xtra_themexp4_xtra_themexplot_boxplotxplot_pairsxpose_setxset_lineagexset_waterfall

Dependencies:assertthatbitbit64cachemclassclassIntclicliprcolorspaceconflictedcpp11crayondplyre1071fansifarverfastmapforcatsgenericsGGallyggforceggplot2ggstatsgluegtablehmsisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepatchworkpillarpkgconfigplyrpmxcvpolyclipprettyunitsprogressproxypurrrR6RColorBrewerRcppRcppEigenreadrrlangscalesstringistringrsurvivalsystemfontstibbletidyrtidyselecttweenrtzdbutf8vctrsviridisLitevpcvroomwithrxpose

The extended xpose data object

Rendered froma01-the-xp_xtra-object.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-11
Started: 2024-10-29

Useful uncommon plots

Rendered froma03-useful_plots.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-11
Started: 2024-10-29

Using xpose sets

Rendered froma02-xpose-sets.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-11
Started: 2024-10-29

Readme and manuals

Help Manual

Help pageTopics
Binary check if LHS is parent of LHS%p%
Describe parameter associationsadd_prm_association drop_prm_association
Add relationship(s) to an xpose_setadd_relationship remove_relationship
Add one or more 'xpdb' objects to an 'xpose_set'add_xpdb
Level-defining helper functionsas_leveler is_leveler lvl_bin lvl_inord lvl_sex
Convert an object to an 'xpose_data' and 'xp_xtras' objectas_xpdb_x as_xp_xtras check_xpdb_x check_xp_xtras
Add individual objective function to databackfill_iofv
Non-simulation based likelihood model diagnosticcatdv_vs_dvprobs
Verify validity of level listcheck_levels
Check an 'xpose_set' objectcheck_xpose_set check_xpose_set_item
Backfill utility for descriptionsdesc_from_comments
Visualize 'xpose_set'diagram_lineage
Display deltaOFV values across 'xpose_set'diff.xpose_set
Check if any xpose_data objects are repeated in xpose_setduplicated.xpose_set
Model average plotsdv_vs_ipred_modavg dv_vs_pred_modavg ipred_vs_idv_modavg plotfun_modavg pred_vs_idv_modavg
Grid plotscov_grid eta_grid eta_vs_cov_grid
Eta categorical covariate plots (typical)eta_vs_catcov
Eta continuous covariate plots (typical)eta_vs_contcov
Expose a model parameter of xpdb objects in an xpose_setexpose_param
Expose a property of xpdb objects in an xpose_setexpose_property
Place .problem, .subprob and .method into environment consistentlyfill_prob_subprob_method
Filtration method for xpose_setfilter.xpose_set
Focus on an xpdb object in an xpose_setfocused_xpdbs focus_function focus_qapply focus_xpdb unfocus_xpdb
Get full index for xpose_data dataget_index set_index
Access model parametersget_prm
Generic function to extract a property from a model summaryget_prop
Get shrinkage estimates from model summaryget_shk
Grab processed 'xpose_plot'grab_xpose_plot
Objective function changes across modelsiofv_vs_mod
Compare model predictionsipred_vs_ipred pred_vs_pred
Add simulation counterirep
Convenience functions used in packageis_formula_list
Basic class checker for 'xp_xtras'is_xp_xtras
For a categorical DV variable, show associated probabilitieslist_dv_probs
Updates to 'list_vars'list_vars list_vars.default list_vars.xp_xtras
Create a model-averaged xpose data objectmodavg_xpdb
Add, remove or rename variables in an xpdbmodify_xpdb mutate_x rename_x
Transform parameter values in placemutate_prm
Mutation method for xpose_setmutate.xpose_set
An 'xp_xtras' example of a base modelpheno_base
An 'xp_xtras' example of a final modelpheno_final
An 'xp_xtras' example of a final modelpheno_saem
A more complex example of 'xpose_set' objectpheno_set
An 'xp_xtras' example of an M3 modelpkpd_m3
An 'xp_xtras' example of an M3 model (dataset)pkpd_m3_df
Specific waterfall plotseta_waterfall iofv_waterfall prm_waterfall
Convert levels list into tibbleproc_levels
Pulling method for xpose_setpull.xpose_set
Renaming method for xpose_setrename.xpose_set
Reportable digits for model fitreportable_digits
Convert xpose_set to a nested list.reshape_set unreshape_set
Selection method for xpose_setselect.xpose_set
Base model for 'xpose_set'get_base_model set_base_model unset_base_model
Set probability columns for categorical endpointsset_dv_probs
Set an 'xpose' optionset_option
Set a summary propertyset_prop
Set variable levelsset_var_levels
Set variable typesset_var_types
Set variable typesset_var_types_x
Set variable typesset_var_types.default
Set variable typesset_var_types.xp_xtras
Change colors of shark plotsshark_colors
Individual contributions to dOFVdofv_vs_id shark_plot
Group/ungroup and summarize variables in an xpdbgroup_by_x summarise_xpdb ungroup_x
Translate values to levelsval2lvl
An 'xp_xtras' example of the discrete-time Markov model of categorical vismodegib datavismo_dtmm
An 'xp_xtras' example of the proportional odds categorical vismodegib modelvismo_pomod
A tibble of mock data used for fitting vismodegib modelsvismodegib
Ensure consistent style with 'GGally' functionswrap_xp_ggally
'xp_var' Methodxp_var xp_var.default xp_var.xp_xtras
Extra theme defaultsxp_xtra_theme
Updated version of the xpose4 themexp4_xtra_theme
An example 'xpose_set' objectxpdb_set
An example 'xp_xtras' objectxpdb_x
Default xpose boxplot functionxplot_boxplot
Wrapper around ggpairsxplot_pairs
Generate a set of 'xpdb' objectsxpose_set
Determine lineage within a setxset_lineage
Waterfall plotxset_waterfall