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heemod - Health Economic Evaluation MODelling

Markov Models for Health Economic Evaluations. An implementation of the modelling and reporting features described in reference textbooks and guidelines: deterministic and probabilistic sensitivity analysis, heterogeneity analysis, time dependency on state-time and model-time (semi-Markov and non-homogeneous Markov models), etc.

You can install:

the latest released version from CRAN with:

install.packages("heemod")

the latest development version from github with:

devtools::install_github("aphp/heemod")

heemod can be cited with:

Filipović-Pierucci A, Zarca K and Durand-Zaleski I (2017). “Markov Models for Health Economic Evaluation: The R Package heemod.” ArXiv e-prints. R package version 0.8.0, 1702.03252

Features

Main features:

Accounting for time-dependency:
- For both model time and state time.
- Time-varying transition probabilities.
- Time-varying values attached to states.
Probabilistic uncertainty analysis (PSA).
- With correlated resampling.
- Covariance analysis for PSA.
- Expected value of perfect information (EVPI).
Deterministic sensitivity analysis (DSA).

Other features:

Multiple state membership correction methods (life-table, custom method, etc.).
Demographic analysis to compute population-level results.
Heterogeneity analysis.
Parallel computing support.
Features for budget impact analysis.
Interface with SAVI and BCEA.

Most of the analyses presented in Decision Modelling for Health Economic Evaluation can be performed with heemod. See the Reproducing Exact Results from DMHEE vignette for an exact reproduction of the analyses from the book.

Learning heemod

To get started read the An Introduction to heemod vignette. Specific analysis examples (mostly inspired from Decision Modelling for Health Economic Evaluation) can be found in the package vignettes.

Devs

Kevin Zarca and Antoine Filipović-Pierucci.

Contributors

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Version

Install

install.packages('heemod')

Monthly Downloads

880

Version

1.0.2

License

GPL (>= 3)

Maintainer

Kevin Zarca

Last Published

September 11th, 2024

Functions in heemod (1.0.2)

Compute State Values per Cycle

check_strategy_index

Check Strategy Index

define_part_surv

Define Partitioned Survival

Define Parameters Distribution for Probabilistic Analysis

Define Inflow for a BIA

define_starting_values

Define Starting State Values

Evaluate Survival Distributions

Check Model States for Consistency

Combine Probabilities

Define a Sensitivity Analysis

define_strategy

Define a Markov Model

create_states_from_tabular

Create State Definitions From Tabular Input

create_model_from_tabular

Create a heemod Model From Tabular Files Info

create_parameters_from_tabular

Create a Parameter Definition From Tabular Input

create_matrix_from_tabular

Create a Transition Matrix From Tabular Input

define_state_list

Define Markov Model State List

compute_counts.eval_part_surv

Compute Count of Individual in Each State per Cycle

construct_part_surv_tib

construct a survival object from tabular specification

Define a Markov Model State

define_surv_table

Define a survival distribution based on explicit survival probabilities

define_surv_spline

Define a Restricted Cubic Spline Survival Distribution

Convert Data Frame Factor Variables to Character

Check File Type

dispatch_strategy_hack

Hack to Automate Use of Strategy Name

Evaluate Strategy

Evaluate Resampling Definition

define_surv_dist

Define a Survival Distribution

define_surv_fit

Define a Fitted Survival Model

create_demographic_table

Read a Demographic Table

eval_state_list

Evaluate Markov Model States

Probability Density Functions for Probabilistic Uncertainty Analysis

define_calibration_fn

Define Calibration Function

get_parameter_names

Return parameters names

Remove Blank Rows From Table

get_state_names

Get State Names

Export PSA Results for SAVI

extract_stratum

Extract Product-Limit Table for a Stratum

Get count number

eval_strategy_newdata

Iteratively Evaluate a Markov Model With New Parameter Values

get_state_value_names

Return Names of State Values

Extract Product-Limit Tables

Extract Evaluated Parameters

create_df_from_tabular

Load Data From a Folder Into an Environment

scale.combined_model

Normalize Cost and Effect

eval_parameters

Evaluate Markov model parameters

eval_models_from_tabular

Evaluate Models From a Tabular Source

get_state_number

Return Number of State

Use the BCEA package

rescale_discount_rate

Rescale Discount Rate

define_correlation

Define a Correlation Structure for Probabilistic Uncertainty Analysis

Project Beyond a Survival Distribution with Another

Markov Models for Health Economic Evaluations

get_matrix_order

Return Markov Model Transition Matrix Order

Check whole Numbers

get_counts_diff

Get count matrix and difference between two cycles

define_transition

Define Transition Matrix for Markov Model

Define Initial Counts

Look Up Values in a Data Frame

Hack to Work Around a Discounting Issue

define_parameters

Define Markov Model Parameters

expand_if_necessary

Expand States and Transition

dispatch_strategy

Dispatch Values According to Strategy

Run Markov Model

run_model_tabular

Run Analyses From Files

Return Efficiency Frontier

Expand Time-Dependent States into Tunnel States

part_survs_from_surv_inputs

Convert saved fits to partitioned survival objects

Run Model on New Data

Use WHO Mortality Rate

Set Covariates of a Survival Distribution

Insert Elements in Vector

Save Model Outputs

parse_multi_spec

Specify Inputs for Multiple Models From a Single File

Evaluate Survival Distributions

Resample survival distribution

Make Syntactically Valid Names

Run Sensitivity Analysis

get_counts.updated_model

Get State Membership Counts

Mix Two or More Survival Distributions

Discount a Quantity Over Time. Should be a scalar if time is specified, a vector otherwise

Check if All the Elements of a List Are the Same

gather_model_info

Gather Information for Running a Model From Tabular Data

eval_transition

Evaluate Markov Model Transition Matrix

Returns "s" if x > 1

Convenience Functions to Compute Probabilities

load_surv_models

Load a set of survival fits

Run Probabilistic Uncertainty Analysis

Plot Sensitivity Analysis

safe_conversion

Safely Convert From Characters to Numbers

summary.run_model

Summarise Markov Model Results

Plot Results of Probabilistic Analysis

reindent_transition

Reindent Transition Matrix

Interpolate Quosures

Objects exported from other packages

plot.surv_object

Plot general survival models

Plot Results of a Markov Model

get_values.updated_model

Get Strategy Values

Get Markov Model Transition Matrix

Project Beyond a Survival Distribution with Another (pairwise)

Read the accepted file formats for tabular input

Weighted Summary

summary.surv_shift

Summarize surv_shift objects

acceptability_curve

Acceptability Curve from Probabilistic Analysis

Apply an Acceleration Factor

calibrate_model

Calibrate Model Parameters

Apply a Hazard Ratio

Convert Lazy Dots to Expression List

Run heemod on a Cluster

Apply an Odds Ratio

Combine Multiple Models

calc_prob_from_surv

Calculate Probability of Event

calc_surv_from_prob

Calculate Probability of Survival

Apply a time shift to a survival distribution

create_model_list_from_tabular

Read Models Specified by Files

create_options_from_tabular

Create Model Options From a Tabular Input

Check Markov Model Transition Matrix

check_cycle_inputs

Check Cycle and Time Inputs