# Extra Functionality for the 'xpose' Package

## Documentation for package ‘xpose.xtras’ version 0.2.0

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

## Help Pages

A B C D E F G I L M N P R S U V W X misc

## -- A --

add_cov_association | Describe parameter/covariate associations
add_prm_association | Describe parameter associations
add_process_preset | Add, apply, list, amend or remove 'xpdb' processing presets
add_relationship | Add relationship(s) to an xpose_set
add_watermark | Add a watermark to a plot
add_xpdb | Add one or more 'xpdb' objects to an 'xpose_set'
AIC.xpose_set | Log-likelihood, AIC and BIC across an 'xpose_set'
amend_process_preset | Add, apply, list, amend or remove 'xpdb' processing presets
apply_default_labs | Apply default label overrides to a plot
as_leveler | Level-defining helper functions
as_xpdb_x | Convert an object to an 'xpose_data' and 'xp_xtras' object
as_xp_xtras | Convert an object to an 'xpose_data' and 'xp_xtras' object
attach_nlmixr2 | Attach nlmixr2 fit object to xpose data object

## -- B --

backfill_derived | Derive full parameter set for mammillary PK model
backfill_iofv | Add individual objective function to data
backfill_nlmixr2_props | Populate some properties from nlmixr2 fit
BIC.xpose_set | Log-likelihood, AIC and BIC across an 'xpose_set'

## -- C --

catdv_vs_dvprobs | Non-simulation based likelihood model diagnostic
catdv_vs_ipred | Binned calibration plot for categorical DVs
catdv_vs_occ | Longitudinal binned observed vs. predicted plot for categorical DVs
check_levels | Verify validity of level list
check_xpdb_x | Convert an object to an 'xpose_data' and 'xp_xtras' object
check_xpose_set | Check an 'xpose_set' object
check_xpose_set_item | Check an 'xpose_set' object
check_xp_xtras | Convert an object to an 'xpose_data' and 'xp_xtras' object
cormat | Parameter correlation/covariance matrix heatmap
cov_forest | Covariate effect forest plot
cov_grid | Grid plots

## -- D --

derive_prm | Derive full parameter set for mammillary PK model
desc_from_comments | Backfill utility for descriptions
diagnose_constants | Check for potential parameterization issues
diagram_lineage | Visualize 'xpose_set'
dofv_vs_id | Individual contributions to dOFV
drop_cov_association | Describe parameter/covariate associations
drop_prm_association | Describe parameter associations
dv_vs_ipred_modavg | Model average plots
dv_vs_pred_modavg | Model average plots

## -- E --

eta_grid | Grid plots
eta_vs_catcov | Eta categorical covariate plots (typical)
eta_vs_contcov | Eta continuous covariate plots (typical)
eta_vs_cov_grid | Grid plots
eta_waterfall | Specific waterfall plots
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

## -- F --

focused_xpdbs | Focus on an xpdb object in an xpose_set
focus_function | Focus on an xpdb object in an xpose_set
focus_qapply | Focus on an xpdb object in an xpose_set
focus_xpdb | Focus on an xpdb object in an xpose_set

## -- G --

get_base_model | Base model for 'xpose_set'
get_cov_matrix | Extract a parameter covariance or correlation matrix
get_index | Get full index for xpose_data data
get_prm | Access model parameters
get_prm_nlmixr2 | get_prm equivalent for nlmixr2 fits
get_prop | Generic function to extract a property from a model summary
get_shk | Get shrinkage estimates from model summary
get_xtras_option | Inspect which 'xpose.xtras' option value is dominant
ggsave_xp | Save a plot with 'xpose.xtras' default output resolution
grab_xpose_plot | Grab processed 'xpose_plot'
group_by_x | Group/ungroup and summarize variables in an xpdb

## -- I --

ind_plots_sample | Individual plots for a (stratified) sample of individuals
ind_roc | Individual ROC plots
iofv_vs_mod | Objective function changes across models
iofv_waterfall | Specific waterfall plots
ipred_vs_idv_modavg | Model average plots
ipred_vs_ipred | Compare model predictions
irep | Add simulation counter
is_leveler | Level-defining helper functions
is_xp_xtras | Basic class checker for 'xp_xtras'

## -- L --

left_join.xpose_data | Backfill missing variables via a left join
left_join_x | Backfill missing variables via a left join
list_dv_probs | For a categorical DV variable, show associated probabilities
list_vars | Updates to 'list_vars'
list_vars.default | Updates to 'list_vars'
list_vars.xp_xtras | Updates to 'list_vars'
logLik.xpose_data | Log-likelihood, AIC and BIC for 'xpose_data' objects
logLik.xpose_set | Log-likelihood, AIC and BIC across an 'xpose_set'
lvl_bin | Level-defining helper functions
lvl_inord | Level-defining helper functions
lvl_sex | Level-defining helper functions

## -- M --

modavg_xpdb | Create a model-averaged xpose data object
modify_xpdb | Add, remove or rename variables in an xpdb
mutate_prm | Transform parameter values in place
mutate_x | Add, remove or rename variables in an xpdb

## -- N --

nlmixr2_as_xtra | Convenience function for ingesting an nlmixr2 model to xpose and xpose.xtras
nlmixr2_example | Generate example 'xp_xtras' objects from nlmixr2 fits
nlmixr2_prm_associations | Based on associations baked into nlmixr2, automatically add to xpose data
nlmixr_example | Generate example 'xp_xtras' objects from nlmixr2 fits

## -- P --

patch_condn | Patch condition number extraction
persist_process_presets | Write current process presets out to a '.Rprofile'
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)
plot.xpose_data | Generate a batch of diagnostic plots from an 'xpdb'
plotfun_modavg | Model average plots
pred_vs_idv_modavg | Model average plots
pred_vs_pred | Compare model predictions
print_process_preset | Add, apply, list, amend or remove 'xpdb' processing presets
prm_catcov | Continuous/categorical covariate effect tables
prm_contcov | Continuous/categorical covariate effect tables
prm_cov | Continuous/categorical covariate effect tables
prm_waterfall | Specific waterfall plots
process_preset | Add, apply, list, amend or remove 'xpdb' processing presets

## -- R --

remove_process_preset | Add, apply, list, amend or remove 'xpdb' processing presets
remove_relationship | Add relationship(s) to an xpose_set
rename_x | Add, remove or rename variables in an xpdb
reportable_digits | Reportable digits for model fit
reshape_set | Convert xpose_set to a nested list.
roc_by_mod | ROC curve across models
roc_plot | ROC Plot for categorical DVs

## -- S --

set_base_model | Base model for 'xpose_set'
set_default_labs | Set default plot label overrides on an 'xp_xtras' object
set_default_plots | Set a default plot spec on an 'xp_xtras' object
set_default_watermark | Set default watermark options on an 'xp_xtras' object
set_dv_probs | Set probability columns for categorical endpoints
set_index | Get full index for xpose_data data
set_option | Set an 'xpose' option
set_prop | Set a summary property
set_var_levels | Set variable levels
set_var_types | Set variable types
set_var_types.default | Set variable types
set_var_types.xp_xtras | Set variable types
set_var_types_x | Set variable types
set_xtras_options | Set 'xpose.xtras' session options
shark_colors | Change colors of shark plots
shark_plot | Individual contributions to dOFV
summarise_xpdb | Group/ungroup and summarize variables in an xpdb

## -- U --

unfocus_xpdb | Focus on an xpdb object in an xpose_set
ungroup_x | Group/ungroup and summarize variables in an xpdb
unreshape_set | Convert xpose_set to a nested list.
unset_base_model | Base model for 'xpose_set'

## -- V --

val2lvl | Translate values to levels
vismodegib | A tibble of mock data used for fitting vismodegib models
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

## -- W --

wrap_xp_ggally | Ensure consistent style with 'GGally' functions

## -- X --

xp4_xtra_theme | Updated version of the xpose4 theme
xpdb_set | An example 'xpose_set' object
xpdb_x | An example 'xp_xtras' object
xplot_binned | Generic binned trend plotting function
xplot_boxplot | Default xpose boxplot function
xplot_forest | Default xpose forest plot function
xplot_heatmap | Generic heatmap plotting function
xplot_pairs | Wrapper around ggpairs
xplot_rocplot | Default xpose ROC plot function
xpose_set | Generate a set of 'xpdb' objects
xp_from_bbr | Convenience function for ingesting a bbr model into xpose and xpose.xtras
xp_var | 'xp_var' Method
xp_var.default | 'xp_var' Method
xp_var.xp_xtras | 'xp_var' Method
xp_xtra_theme | Extra theme defaults
xset_lineage | Determine lineage within a set
xset_waterfall | Waterfall plot

## -- misc --

%p% | Binary check if LHS is parent of RHS