Package index • xpose.xtras

xp_xtras objects

Functions for creating, checking and manipulating xp_xtras objects.

as_xpdb_x() as_xp_xtras() check_xpdb_x() check_xp_xtras(): Convert an object to an xpose_data and xp_xtras object

check_xpose_set() check_xpose_set_item(): Check an xpose_set object

is_xp_xtras(): Basic class checker for xp_xtras

set_var_levels(): Set variable levels

set_var_types() experimental: Set variable types

set_var_types(<default>) experimental: Set variable types

set_var_types(<xp_xtras>) experimental: Set variable types

set_var_types_x() experimental: Set variable types

as_leveler() is_leveler() lvl_bin() lvl_sex() lvl_inord(): Level-defining helper functions

val2lvl(): Translate values to levels

backfill_iofv(): Add individual objective function to data

attach_nlmixr2(): Attach nlmixr2 fit object to xpose data object

backfill_nlmixr2_props(): Populate some properties from nlmixr2 fit

get_prm_nlmixr2(): get_prm equivalent for nlmixr2 fits

nlmixr2_as_xtra(): Convenience function for ingesting an nlmixr2 model to xpose and xpose.xtras

nlmixr2_m3: An xp_xtra example based on a nlmixr2 fit with M3 censoring

nlmixr2_prm_associations(): Based on associations baked into nlmixr2, automatically add to xpose data

nlmixr2_warfarin: An xp_xtra example based on a complex nlmixr2 fit

xpdb_nlmixr2 xpdb_nlmixr2_saem: An xp_xtra example based on an nlmixr2 fit

xp_var(): xp_var Method

check_levels(): Verify validity of level list

xpose sets

Work with collections of models using xpose_set.

xpose_set(): Generate a set of xpdb objects

xset_lineage(): Determine lineage within a set

xset_waterfall(): Waterfall plot

add_xpdb(): Add one or more xpdb objects to an xpose_set

focus_xpdb() unfocus_xpdb() focused_xpdbs() focus_function() focus_qapply(): Focus on an xpdb object in an xpose_set

reshape_set() unreshape_set(): Convert xpose_set to a nested list.

diagram_lineage() experimental: Visualize xpose_set

add_prm_association() drop_prm_association(): Describe parameter associations

mutate_prm(): Transform parameter values in place

add_relationship() remove_relationship(): Add relationship(s) to an xpose_set

`%p%`: Binary check if LHS is parent of LHS

Plotting helpers

Additional plotting functions and themes extending xpose.

xplot_boxplot(): Default xpose boxplot function

xplot_pairs(): Wrapper around ggpairs

xplot_rocplot(): Default xpose ROC plot function

iofv_vs_mod(): Objective function changes across models

prm_waterfall() eta_waterfall() iofv_waterfall(): Specific waterfall plots

shark_plot() dofv_vs_id(): Individual contributions to dOFV

eta_vs_catcov(): Eta categorical covariate plots (typical)

eta_vs_contcov(): Eta continuous covariate plots (typical)

eta_grid() cov_grid() eta_vs_cov_grid(): Grid plots

dv_vs_ipred_modavg() dv_vs_pred_modavg() ipred_vs_idv_modavg() pred_vs_idv_modavg() plotfun_modavg() experimental: Model average plots

ipred_vs_ipred() pred_vs_pred(): Compare model predictions

catdv_vs_dvprobs(): Non-simulation based likelihood model diagnostic

roc_by_mod(): ROC curve across models

roc_plot(): ROC Plot for categorical DVs

shark_colors(): Change colors of shark plots

ind_roc(): Individual ROC plots

xset_waterfall(): Waterfall plot

xp_xtra_theme(): Extra theme defaults

xp4_xtra_theme(): Updated version of the xpose4 theme

grab_xpose_plot(): Grab processed xpose_plot

wrap_xp_ggally(): Ensure consistent style with GGally functions

Utilities

Miscellaneous helpers and integrations.

modavg_xpdb() experimental: Create a model-averaged xpose data object

eta_grid() cov_grid() eta_vs_cov_grid(): Grid plots

nlmixr2_as_xtra(): Convenience function for ingesting an nlmixr2 model to xpose and xpose.xtras

nlmixr2_m3: An xp_xtra example based on a nlmixr2 fit with M3 censoring

nlmixr2_prm_associations(): Based on associations baked into nlmixr2, automatically add to xpose data

nlmixr2_warfarin: An xp_xtra example based on a complex nlmixr2 fit

desc_from_comments(): Backfill utility for descriptions

edit_xpose_data(): Master xpdb editing function

expose_param(): Expose a model parameter of xpdb objects in an xpose_set

expose_property(): Expose a property of xpdb objects in an xpose_set

get_prop(): Generic function to extract a property from a model summary

set_prop(): Set a summary property

get_index() set_index(): Get full index for xpose_data data

set_base_model() get_base_model() unset_base_model(): Base model for xpose_set

set_dv_probs(): Set probability columns for categorical endpoints

list_dv_probs(): For a categorical DV variable, show associated probabilities

group_by_x() ungroup_x(): Group/ungroup and summarize variables in an xpdb

mutate_x() rename_x(): Add, remove or rename variables in an xpdb

select_subset(): Convenience wrapper for tidyselect

set_option(): Set an xpose option

reportable_digits(): Reportable digits for model fit

test_xpdb(): Logical instead of exception for xpose data check

irep() deprecated: Add simulation counter

derive_prm() backfill_derived(): Derive full parameter set for mammillary PK model

diagnose_constants(): Check for potential parameterization issues

get_prm(): Access model parameters

get_shk(): Get shrinkage estimates from model summary

list_vars(): Updates to list_vars

Data

Example objects for documentation.

nlmixr2_m3: An xp_xtra example based on a nlmixr2 fit with M3 censoring

nlmixr2_warfarin: An xp_xtra example based on a complex nlmixr2 fit

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 (dataset)

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_nlmixr2 xpdb_nlmixr2_saem: An xp_xtra example based on an nlmixr2 fit

xpdb_set: An example xpose_set object

xpdb_x: An example xp_xtras object