# Tidy Intensive Longitudinal Data Analysis

## Documentation for package ‘tidyILD’ version 0.4.0

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

## Help Pages

A B E G I N P T V

tidyILD-package | tidyILD: Tidy Intensive Longitudinal Data Analysis

## -- A --

as_ild | Coerce to ILD object
augment.ild_lme | Tidy and augment ild_lme fits with broom.mixed
augment_ild_model | Augment an ILD model fit with fitted values and residuals

## -- B --

broom_ild_lme | Tidy and augment ild_lme fits with broom.mixed

## -- E --

ema_example | Example EMA-style intensive longitudinal dataset

## -- G --

guardrail_registry | Guardrail rule registry (analysis safety layer)

## -- I --

ild_acf | Autocorrelation function for ILD variables or model residuals
ild_align | Align a secondary stream to primary ILD within a time window
ild_as_tsibble | Convert an ILD object to a tsibble
ild_augment | Augment observations with fitted values and residuals (S3 generic)
ild_augment.brmsfit | Augment observations with fitted values and residuals (S3 generic)
ild_augment.default | Augment observations with fitted values and residuals (S3 generic)
ild_augment.ild_fit_ctsem | Augment observations with fitted values and residuals (S3 generic)
ild_augment.ild_fit_kfas | Augment observations with fitted values and residuals (S3 generic)
ild_augment.lme | Augment observations with fitted values and residuals (S3 generic)
ild_augment.lmerMod | Augment observations with fitted values and residuals (S3 generic)
ild_augment_schema | Column dictionary for 'ild_augment()' outputs
ild_augment_states | Per-row latent states (long format) for complex multi-state models
ild_autoplot | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.brmsfit | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.default | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.ild_diagnostics | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.ild_diagnostics_bundle | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.ild_fit_ctsem | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.ild_fit_kfas | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.ild_heterogeneity | Heterogeneity and person-specific effects from mixed models
ild_autoplot.lme | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_autoplot.lmerMod | Autoplot for ILD model fits or diagnostics (S3 generic)
ild_brms | Fit a Bayesian mixed model to ILD data with 'brms'
ild_brms_dynamics_formula | Template brms formula for person-varying lag slope
ild_build_msm_history | Build MSM lagged history columns from a spec
ild_bundle | Bundle a result with a reproducibility manifest
ild_center | Within-person and between-person decomposition (centering)
ild_center_plot | Standalone WP/BP centering plot
ild_check_lags | Check lag variable validity (gap-aware)
ild_circadian | Time-of-day pattern plot for ILD (circadian-style)
ild_compare_fits | Compare fitted models (AIC, BIC, nobs)
ild_compare_pipelines | Compare provenance of two objects and report differences
ild_crosslag | Cross-lag model: lag predictor then fit outcome ~ lag
ild_ctsem | Fit a continuous-time state-space model via ctsem
ild_decomposition | Within-person and between-person variance decomposition
ild_design_check | ILD design diagnostics: spacing, WP/BP, missingness, and recommendations
ild_diagnose | Engine-agnostic diagnostics façade
ild_diagnose.brmsfit | Engine-agnostic diagnostics façade
ild_diagnose.default | Engine-agnostic diagnostics façade
ild_diagnose.ild_fit_ctsem | Engine-agnostic diagnostics façade
ild_diagnose.ild_fit_kfas | Engine-agnostic diagnostics façade
ild_diagnose.lme | Engine-agnostic diagnostics façade
ild_diagnose.lmerMod | Engine-agnostic diagnostics façade
ild_diagnostics | Residual diagnostics for an ILD model
ild_diagnostics_bundle | Canonical ILD diagnostics bundle
ild_diagnostics_utilities | Standalone diagnostics utilities and bundle section providers
ild_export_provenance | Export provenance to a JSON or YAML file
ild_fit | Fit a mixed model to ILD data (unified entry point)
ild_heatmap | ILD heatmap (alias for ild_plot with type = "heatmap")
ild_heterogeneity | Heterogeneity and person-specific effects from mixed models
ild_heterogeneity.brmsfit | Heterogeneity and person-specific effects from mixed models
ild_heterogeneity.lme | Heterogeneity and person-specific effects from mixed models
ild_heterogeneity.lmerMod | Heterogeneity and person-specific effects from mixed models
ild_heterogeneity_stratified | Heterogeneity and person-specific effects from mixed models
ild_history | Print a human-readable log of preprocessing or analysis steps
ild_ipcw_weights | Inverse probability of censoring weights (IPCW) for monotone dropout
ild_iptw_msm_weights | Sequential MSM inverse probability of treatment weights (IPTW for A_t)
ild_iptw_weights | Inverse probability of treatment weights (IPTW)
ild_ipw_ess | Effective sample size from weights
ild_ipw_refit | Refit an ILD model with inverse-probability weights (sensitivity analysis)
ild_ipw_weights | Compute inverse-probability-of-observation weights from a missingness model
ild_joint_msm_weights | Joint MSM weights from IPTW and IPCW components
ild_kfas | Fit a Gaussian state-space model via KFAS (single-subject ILD)
ild_lag | Spacing-aware lag within person
ild_lme | Fit a linear mixed-effects model to ILD
ild_manifest | Create a reproducibility manifest
ild_meta | Get ILD metadata attributes
ild_methods | Generate methods-style narrative from provenance
ild_missingness_report | Missingness workflow report (orchestration)
ild_missing_bias | Test whether missingness is associated with a predictor (informative missingness)
ild_missing_cohort | Cohort-level fraction observed by occasion index
ild_missing_compliance | Person-level missingness compliance for one outcome
ild_missing_hazard_first | Discrete hazard of first missing outcome on an ordinal schedule
ild_missing_model | Fit a model for missingness (diagnostic / sensitivity)
ild_missing_pattern | Summarize missingness pattern in ILD
ild_msm_balance | Covariate balance (weighted SMD) for MSM / IPW
ild_msm_bootstrap | Cluster bootstrap inference for weighted 'lmer' (MSM / IPW sensitivity)
ild_msm_contrast_over_time | Compute MSM contrasts over time from a fitted weighted model
ild_msm_diagnose | Diagnose an 'ild_msm_fit' result in one call
ild_msm_estimand | Define an MSM estimand specification
ild_msm_fit | Fit an MSM-style weighted mixed model from an estimand spec
ild_msm_history_spec | Build a declarative MSM history specification
ild_msm_overlap_plot | Propensity overlap plot (pooled or sequential MSM IPTW)
ild_msm_recovery | MSM recovery simulation harness
ild_msm_simulate_scenario | Simulate a simple longitudinal MSM scenario
ild_panel_lag_prepare | Prepare several lag columns and audit them
ild_person_distribution | Plot distribution of person-level estimates from ild_person_model
ild_person_model | Fit a model separately per person (N-of-1 / idiographic)
ild_plot | ILD-specific plots
ild_plot_filtered_vs_smoothed | Plot filtered vs smoothed state (first state)
ild_plot_forecast | Plot forecast or future simulation (stub when no horizon)
ild_plot_predicted_trajectory | Observed and fitted values vs time (trajectory overlay)
ild_plot_states | Plot smoothed latent states (first state by default)
ild_power | Simulation-based power analysis for a fixed effect in ILD models
ild_prepare | Prepare a data frame as an ILD (intensive longitudinal data) object
ild_prior_ild | Prior specifications for common ILD mixed models
ild_provenance | Return the raw provenance object
ild_recovery_metrics | Recovery metrics from simulation replications
ild_report | Assemble a light report from a model fit
ild_robust_se | Cluster-robust variance-covariance matrix for ILD model fits
ild_simulate | Simulate simple ILD for examples, tests, and power analysis
ild_spacing | Spacing diagnostics and correlation-structure recommendation
ild_spacing_class | Classify spacing as regular-ish vs irregular-ish
ild_spaghetti | ILD spaghetti / person trajectories (alias for ild_plot with type = "trajectory")
ild_summary | One-shot summary of an ILD object
ild_tidy | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy.brmsfit | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy.default | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy.ild_fit_ctsem | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy.ild_fit_kfas | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy.ild_heterogeneity | Heterogeneity and person-specific effects from mixed models
ild_tidy.lme | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy.lmerMod | Tidy fixed effects from an ILD model fit (S3 generic)
ild_tidy_schema | Column dictionary for ild_tidy() outputs
ild_tidy_states | Tidy per-time state summaries for ild_kfas
ild_tsibble_meta | Tsibble provenance from an ILD object
ild_tvem | Fit a time-varying effects model (TVEM) for ILD
ild_tvem_plot | Plot the time-varying coefficient from a TVEM fit
is_ild | Check if an object is a valid ILD tibble
is_ild_diagnostics_bundle | Canonical ILD diagnostics bundle

## -- N --

new_ild_diagnostics_bundle | Canonical ILD diagnostics bundle

## -- P --

plot_ild_diagnostics | Plot diagnostics from an ild_diagnostics object

## -- T --

tidy.ild_lme | Tidy and augment ild_lme fits with broom.mixed
tidyILD | tidyILD: Tidy Intensive Longitudinal Data Analysis
tidy_ild_model | Tidy fixed effects from an ILD model fit
tidy_ild_msm_bootstrap | Tidy fixed effects from 'ild_msm_bootstrap'

## -- V --

validate_ild | Validate an ILD object and error if invalid