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heemod - Health Economic Evaluation MODelling

heemod is an R toolset for health economic evaluation modelling. It aims to provide a simple and consistent interface for Markov models specification and comparison (for decision trees or cohort simulation). Non-homogeneous Markov models (with time varying properties) are supported.

Most of the analyses presented in Decision Modelling for Health Economic Evaluation can be performed with heemod. See vignette("i-reproduction", "heemod") for an exact reproduction of the analyses from the book.

You can install:

  • the latest released version from CRAN with:
install.packages("heemod")
  • the latest development version from github with:
devtools::install_github("pierucci/heemod@devel")

Main features

  • Graphical user interface with shiny.
  • Time-varying transition probabilities.
  • Time-varying values attached to states.
  • Microsimulation-like models.
  • Probabilistic uncertainty analysis.
  • Deterministic sensitivity analysis.
  • Multiple state membership correction methods (life-table, half-cycle, etc.).
  • Demographic analysis to compute population-level results.
  • Heterogeneity analysis.

Learning heemod

To get started read the introduction in vignette("a-introduction", "heemod"). Time-varying probabilities and values are explained in vignette("b-time-dependency", "heemod").

Specific analysis examples (mostly inspired from Decision Modelling for Health Economic Evaluation) can be found in the following vignettes:

  • Homogeneous Markov model in vignette("c-homogeneous", "heemod").
  • Non-homogeneous Markov model in vignette("d-non-homogeneous", "heemod").
  • Probabilistic uncertainty analysis in vignette("e-probabilistic", "heemod").
  • Deterministic sensitivity analysis in vignette("f-sensitivity", "heemod").
  • Heterogeneity & Demographic analysis in vignette("g-heterogeneity", "heemod").
  • Running the models from tabular inputs in vignette("h-tabular", "heemod").

Devs

Kevin Zarca and Antoine Filipović-Pierucci.

Contributors

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Install

install.packages('heemod')

Monthly Downloads

1,092

Version

0.5.1

License

GPL (>= 3)

Issues

Pull Requests

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Maintainer

Antoine FilipovicPierucci

Last Published

October 29th, 2016

Functions in heemod (0.5.1)

as_expr_list

Convert Lazy Dots to Expression List
check_matrix

Check Markov Model Transition Matrix
check_names

Check Names
clean_factors

Convert Data Frame Factor Variables to Character
check_model_index

Check Model Index
combine_models

Combine Multiple Models
acceptability_curve

Acceptability Curve from Probabilistic Analysis
compute_counts

Compute Count of Individual in Each State per Cycle
compute_values

Compute State Values per Cycle
create_demographic_table

Read a Demographic Table
create_df_from_tabular

Load Data From a Folder Into an Environment
define_correlation

Define a Correlation Structure for Probabilistic Uncertainty Analysis
create_matrix_from_tabular

Create a Transition Matrix From Tabular Input
define_state_list

Define Markov Model State List
create_states_from_tabular

Create State Definitions From Tabular Input
define_state

Define a Markov Model State
create_model_from_tabular

Create a heemod Model From Tabular Files Info
create_model_list_from_tabular

Read Models Specified by Files
define_parameters

Define Markov Model Parameters
define_sensitivity

Define a Sensitivity Analysis
create_options_from_tabular

Create Model Options From a Tabular Input
define_multinom

Define That Parameters Belong to the Same Multinomial Distribution
define_model

Define a Markov Model
density

Probability Density Functions for Probabilistic Uncertainty Analysis
create_parameters_from_tabular

Create a Parameter Definition From Tabular Input
define_matrix

Define Transition Matrix for Markov Model
define_distrib

Define Parameters Distribution for Probabilistic Analysis
discount

Discount a Quantity Over Time
eval_matrix

Evaluate Markov Model Transition Matrix
eval_resample

Evaluate Resampling Definition
eval_state_list

Evaluate Markov Model States
discount_hack

Hack to Work Around a Discounting Issue
eval_models_from_tabular

Evaluate Models From a Tabular Source
eval_model_newdata

Iteratively Evaluate a Markov Model With New Parameter Values
eval_parameters

Evaluate Markov model parameters
eval_model

Evaluate Markov Model
filter_blanks

Remove Blank Rows From Table
gather_model_info

Gather Information for Running a Model From Tabular Data
expand_state

Expand Time-Dependant States into Tunnel States
is_csv

Check File Type
get_code

Display the Code to Generate an Object
get_init

Get Initial State Values
get_counts

Get State Membership Counts
get_frontier

Return Efficiency Frontier
look_up

Look Up Values in a Data Frame
make_names

Make Syntactically Valid Names
save_outputs

Save Model Outputs
summary.run_model

Summarise Markov Model Results
get_parameter_names

Return parameters names
get_state_names

Get State Names
get_state_number

Return Number of State
normalize_ce

Normalize Cost and Effect
get_state_value_names

Return Names of State Values
modify

Modify Object
wtd_summary

Weighted Summary
check_states

Check Model States for Consistency
get_matrix_order

Return Markov Model Transition Matrix Order
get_matrix

Get Markov Model Transition Matrix
parse_multi_spec

Specify Inputs for Multiple Models From a Single File
plot.eval_sensitivity

Plot Sensitivity Analysis
run_probabilistic

Run Probabilistic Uncertainty Analysis
list_all_same

Check if All the Elements of a List Are the Same
is.wholenumber

Check Wholenumbers
safe-conversion

Safely Convert From Characters to Numbers
plur

Returns "s" if x > 1
probability

Convenience Functions to Compute Probabilities
update-model

Run Model on New Data
who-mortality

Use WHO Mortality Rate
get_values

Get Model Values
heemod

heemod: Health Economic Evaluation MODelling
plot.probabilistic

Plot Results of Probabilistic Analysis
run_model_tabular

Run Analyses From Files
run_models

Run one or more Markov Model
plot.run_model

Plot Results of a Markov Model
compute_icer

Compute ICER
insert

Insert Elements in Vector
run_sensitivity

Run Sensitivity Analysis
read_file

Read the accepted file formats for tabular input
interp_heemod

Interpolate Lazy Dots