Pure-R Core Engine for Optimal Data Analysis (ODA / MultiODA)

Documentation for package ‘oda’ version 0.1.2

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-- A --

as_confusion_matrix	Convert a tidy confusion data frame to a 2x2 integer matrix
as_cta_candidates	Subset a data frame to the SDA-selected candidate columns
as_sda_anchor	Convert an object to an 'sda_anchor'
as_sda_anchor.data.frame	Convert an object to an 'sda_anchor'
as_sda_anchor.sda_fit	Convert an object to an 'sda_anchor'
auto_sda_plan	Dry-run planning and validation layer for SDA

-- C --

cta_assign_endpoints	Assign observations to CTA terminal endpoints
cta_balance_effect_summary	CTA covariate balance evidence-interval summary
cta_balance_plot_data	Renderer-ready plot data for CTA covariate balance
cta_balance_table	Multivariate CTA covariate balance diagnostics
cta_confusion_matrix	Extract training confusion matrix from a fitted CTA tree
cta_confusion_table	Final selected tree training confusion table
cta_demo	CTA demonstration dataset
cta_descendant_family	MDSA descendant family for CTA
cta_d_stat	D statistic for a fitted CTA tree
cta_endpoint_counts	Per-endpoint class count table for a fitted CTA tree
cta_endpoint_denominators	Terminal endpoint denominators of a CTA tree
cta_endpoint_summary	Endpoint reporting summary for a fitted CTA tree
cta_endpoint_table	Canonical terminal endpoint map for a fitted CTA tree
cta_family_table	Tidy table of a CTA descendant family
cta_fit	Fit a Classification Tree Analysis (CTA) model (public wrapper)
cta_min_terminal_denom	Minimum terminal endpoint denominator of a CTA tree
cta_node_table	Canonical CTA node report table
cta_observation_weights	Assign per-observation CTA propensity weights
cta_ort_node_table	Node-level summary table for a fitted LORT (legacy name: cta_ort)
cta_plot_data	Extract layout data for plotting a CTA tree
cta_propensity_weights	Endpoint-level propensity-score weights for a fitted CTA tree
cta_staging_table	Staging table for a fitted CTA tree
cta_strata	Number of terminal leaf endpoints in a CTA tree

-- L --

lort_fit	Fit a Locally Optimal Recursive Tree (LORT)
lort_index_path	LORT path from root to a given node index
lort_local_tree	Extract the local CTA model embedded at a LORT node
lort_path_table	Formatted path table for a LORT recursion path
lort_propensity_weights	LORT terminal strata propensity weights

-- M --

myeloma

Myeloma gene-expression dataset (CTA benchmark)

-- N --

novo_boot_ci	Novometric bootstrap CI from a fixed 2x2 confusion matrix
novo_boot_ci.cta_ort	Novometric bootstrap CI from a fixed 2x2 confusion matrix
novo_boot_ci.cta_tree	Novometric bootstrap CI from a fixed 2x2 confusion matrix
novo_boot_ci.default	Novometric bootstrap CI from a fixed 2x2 confusion matrix
novo_boot_ci.oda_fit	Novometric bootstrap CI from a fixed 2x2 confusion matrix

-- O --

oda_balance_effect_table	ODA covariate balance evidence-interval table
oda_balance_plot_data	Renderer-ready plot data for univariate ODA covariate balance
oda_balance_table	Univariate ODA covariate balance diagnostics
oda_best_ordered_multiclass_partition	Select the best K-segment ordered partition by MegaODA spec: PRIMARY -> SECONDARY -> FIRST IDENTIFIED (enum order via tick()).
oda_clean_missing_codes	Replace missing-code values with NA
oda_confusion	Retrieve a confusion matrix from a fitted ODA model
oda_confusion_binary	Binary confusion table
oda_confusion_multiclass	Multiclass confusion matrix
oda_cta_fit	Fit a Classification Tree Analysis (CTA) model (internal engine)
oda_d_stat	Compute the D statistic for a fitted ODA model
oda_ess_from_mean	ESS from mean metric for a C-class problem
oda_ess_from_meanpac	Effect Strength for Sensitivity from mean PAC
oda_fit	Fit an ODA model
oda_infer_attr_types	Infer attribute types from a predictor data frame
oda_loo_multiclass_ordered	Leave-one-out cross-validation for ordered multiclass ODA.
oda_mc_p_value	Monte Carlo Fisher-randomization p-value with Clopper-Pearson early stopping.
oda_mean_pac	Mean PAC from sensitivity and specificity
oda_metrics	Retrieve scalar performance metrics from a fitted ODA model
oda_multiclass_unioda_core	Fit a univariate multiclass ODA model
oda_power	ODA power analysis via simulation
oda_predictions	Retrieve predictions from a fitted ODA model
oda_propensity_weights	ODA rule strata propensity weights
oda_readiness_check	Preflight readiness check for ODA / CTA analysis
oda_rule_predict	Apply a binary ODA rule to new data
oda_rule_predict_multiclass	Apply a multiclass ODA rule to new data
oda_sample_size	ODA minimum sample size via bisection
oda_univariate_core	Fit a univariate binary-class ODA model
oda_validate_group	Validate a class / group variable
oda_validate_weights	Validate a case weight vector
ort_plot_data	Renderer-independent layout data for a LORT composite tree

-- P --

plot.cta_ort	Plot method for Locally Optimal Recursive Tree (LORT)
plot.cta_tree	Plot a fitted CTA tree
plot_balance_love	Love plot for covariate balance (SMD)
plot_cta_balance	Plot CTA multivariate covariate balance
plot_cta_balance_effects	Evidence card for CTA multivariate covariate balance
plot_cta_family	Plot a CTA descendant family member using ggplot2
plot_cta_tree	Plot a CTA tree using ggplot2
plot_lort_path	Plot the full local CTA models along a LORT recursion path
plot_lort_tree	Plot a LORT (Locally Optimal Recursive Tree) using ggplot2
plot_oda_balance	Plot ODA covariate balance
plot_oda_balance_effects	Forest plot of ODA covariate balance evidence intervals
plot_smd_balance	Plot SMD covariate balance
predict.cta_ort	Predict method for Locally Optimal Recursive Tree (LORT)
predict.cta_tree	Classify new observations using a CTA tree
predict.oda_fit	Predict class labels from a fitted ODA model
predict.sda_fit	Predict from an SDA procedure result
print.auto_sda_plan	Print an auto_sda_plan object
print.cta_family	Print a CTA descendant family
print.cta_family_summary	Print a CTA family summary
print.cta_ort	Print method for Locally Optimal Recursive Tree (LORT)
print.cta_ort_summary	Print method for cta_ort_summary
print.cta_tree	Print a CTA tree in MegaODA node table format
print.cta_tree_summary	Print a CTA tree summary
print.novo_boot_ci	Novometric bootstrap CI from a fixed 2x2 confusion matrix
print.oda_fit	Print a fitted ODA model
print.oda_fit_summary	Print an ODA fit summary
print.sda_anchor	Print an 'sda_anchor'
print.sda_fit	Print an sda_fit object
print.sda_fit_summary	Print an sda_fit_summary object
propensity_ess_balance	Propensity-weighted ESS balance diagnostic

-- S --

sda_anchor	Construct an 'sda_anchor' object
sda_candidate_table	Return the candidate table from one or all SDA steps
sda_fit	Run a Structural Decomposition Analysis (SDA) procedure
sda_selected_attributes	Return the selected attribute names from an SDA procedure result
sda_step_table	Return a summary table of SDA steps
sda_to_cta_data	Prepare X and y for CTA using SDA-selected attributes
smd_balance_table	Conventional SMD companion table for covariate balance
summary.cta_family	Summarise a CTA descendant family
summary.cta_ort	Summary method for Locally Optimal Recursive Tree (LORT)
summary.cta_tree	Summarize a fitted CTA tree
summary.oda_fit	Summarize a fitted ODA model
summary.sda_anchor	Summarise an 'sda_anchor'
summary.sda_fit	Summarise an sda_fit object

-- V --

validate_sda_anchor

Validate an 'sda_anchor' object

-- misc --

.lort_parent_maps

Build parent map and endpoint-index map for LORT nodes (internal helper used by lort_index_path and lort_path_table)