Package: heemod 1.1.0

Kevin Zarca

heemod: Markov Models for Health Economic Evaluations

An implementation of the modelling and reporting features described in reference textbook and guidelines (Briggs, Andrew, et al. Decision Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011; Siebert, U. et al. State-Transition Modeling. Medical Decision Making 32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis, heterogeneity analysis, time dependency on state-time and model-time (semi-Markov and non-homogeneous Markov models), etc.

Authors:Kevin Zarca [aut, cre], Antoine Filipovic-Pierucci [aut], Matthew Wiener [ctb], Zdenek Kabat [ctb], Vojtech Filipec [ctb], Jordan Amdahl [ctb], Yonatan Carranza Alarcon [ctb], Vince Daniels [ctb]

heemod_1.1.0.tar.gz
heemod_1.1.0.zip(r-4.7)heemod_1.1.0.zip(r-4.6)heemod_1.1.0.zip(r-4.5)
heemod_1.1.0.tgz(r-4.6-any)heemod_1.1.0.tgz(r-4.5-any)
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heemod_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
heemod/json (API)

# Install 'heemod' in R:
install.packages('heemod', repos = c('https://aphp.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aphp/heemod/issues

Pkgdown/docs site:https://aphp.github.io

On CRAN:

Conda:

9.41 score 18 stars 1 packages 248 scripts 680 downloads 4 mentions 70 exports 30 dependencies

Last updated from:9dddd4c36e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK215
source / vignettesOK243
linux-release-x86_64OK219
macos-release-arm64OK234
macos-oldrel-arm64OK243
windows-develOK173
windows-releaseOK197
windows-oldrelOK173
wasm-releaseOK150

Exports:%>%add_hazardsadd_hazards_apply_afapply_hrapply_orapply_shiftcalibrate_modelclose_clustercombine_probscompute_survcompute_surv_define_calibration_fndefine_correlationdefine_distributiondefine_dsadefine_inflowdefine_inflow_define_initdefine_init_define_parametersdefine_parameters_define_part_survdefine_part_surv_define_psadefine_psa_define_starting_valuesdefine_starting_values_define_statedefine_state_define_strategydefine_strategy_define_surv_distdefine_surv_fitdefine_surv_splinedefine_surv_tabledefine_transitiondefine_transition_discountdispatch_strategyexport_saviget_countsget_valuesjoinjoin_load_surv_modelslook_upmixmix_modifyor_to_probpart_survs_from_surv_inputsprob_to_probrate_to_probreindent_transitionresample_survrescale_discount_raterescale_probrr_to_probrun_bcearun_dsarun_modelrun_model_run_model_tabularrun_psaset_covariatesset_covariates_status_clusteruse_clusteruse_distribution

Dependencies:BHclicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrmvnfastpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadillorlangS7scalestibbletidyselectutf8vctrsviridisLitewithr

An Introduction to heemod
Transition probabilities | Attach values to states | Combine information in a model | Run the model | Analyze results | Convenience functions | External data | Compare strategies | Time-variability | Transition costs | Parallel computing | Going further
Rendered froma_introduction.Rmdusingknitr::rmarkdown

Last update: 2025-06-16
Started: 2017-05-09

Calibrating heemod models
Rendered fromk_calibration.Rmdusingknitr::rmarkdown

Last update: 2025-06-16
Started: 2017-05-09

Heterogeneity & Demographic Analysis
Introduction | Population characteristics | Running the analysis | Interpreting results | Weighted results | Parallel computing
Rendered fromg_heterogeneity.Rmdusingknitr::rmarkdown

Last update: 2025-06-16
Started: 2017-05-09

Time-varying Markov Models (Non-Homogeneous)
Model description | Other-Cause death | THR revision | Parameter definition | Transition matrix definition | State & strategy definition | Model analysis
Rendered fromd_non_homogeneous.Rmdusingknitr::rmarkdown

Last update: 2025-06-16
Started: 2017-05-09

Deterministic Sensitivity Analysis
Introduction | Define the analysis | Interpretation
Rendered fromf_sensitivity.Rmdusingknitr::rmarkdown

Last update: 2024-01-31
Started: 2017-05-09

Simple Markov Models (Homogeneous)
Model description | Transition probabilities | State values | Strategy definitions | Running the model | Result interpretation
Rendered fromc_homogeneous.Rmdusingknitr::rmarkdown

Last update: 2024-01-31
Started: 2017-05-09

Survival models
Distributions | Operations | Applications | Transition matrix | Partitioned survival model
Rendered fromj_survival.Rmdusingknitr::rmarkdown

Last update: 2024-01-31
Started: 2017-05-09

Tabular Input
Introduction | Reference file | States file | Transition probabilities | Parameters | User-defined data | Model options | Run the analysis
Rendered fromh_tabular.Rmdusingknitr::rmarkdown

Last update: 2024-01-31
Started: 2017-05-09

Time-varying values
How to specify time-dependency | Details
Rendered fromb_time_dependency.Rmdusingknitr::rmarkdown

Last update: 2024-01-31
Started: 2017-05-09

Survival Models Part 2 - PSA
From a user-defined parametric distribution | From real data
Rendered fromj_survival_2_psa.Rmdusingknitr::rmarkdown

Last update: 2024-01-30
Started: 2023-08-08

Reproducing Exact Results from DMHEE
HIV model | THR model
Rendered fromi_reproduction.Rmdusingknitr::rmarkdown

Last update: 2023-07-12
Started: 2017-05-09

Probabilistic Uncertainty Analysis
Model definition | Resampling distributions | Run probabilistic model | Result interpretation | Parallel computing | Interface with BCEA and SAVI
Rendered frome_probabilistic.Rmdusingknitr::rmarkdown

Last update: 2023-07-12
Started: 2017-05-09

Readme and manuals

Help Manual

Help pageTopics
Add Hazardsadd_hazards add_hazards_
Apply an Acceleration Factorapply_af
Apply a Hazard Ratioapply_hr
Apply an Odds Ratioapply_or
Apply a time shift to a survival distributionapply_shift
Calibrate Model Parameterscalibrate_model
Run 'heemod' on a Clusterclose_cluster cluster status_cluster use_cluster
Combine Probabilitiescombine_probs
Evaluate Survival Distributionscompute_surv
construct a survival object from tabular specificationconstruct_part_surv_tib
Define Calibration Functiondefine_calibration_fn
Define a Correlation Structure for Probabilistic Uncertainty Analysisdefine_correlation define_correlation_
Define a Sensitivity Analysisdefine_dsa define_dsa_
Define Inflow for a BIAdefine_inflow define_inflow_
Define Initial Countsdefine_init define_init_
Define Markov Model Parametersdefine_parameters define_parameters_ modify.uneval_parameters
Define Partitioned Survivaldefine_part_surv define_part_surv_
Define Parameters Distribution for Probabilistic Analysisdefine_psa define_psa_
Define Starting State Valuesdefine_starting_values define_starting_values_
Define a Markov Model Statedefine_state define_state_ modify.state
Define a Markov Modeldefine_strategy define_strategy_
Define a Survival Distributiondefine_surv_dist
Define a Fitted Survival Modeldefine_surv_fit
Define a Restricted Cubic Spline Survival Distributiondefine_surv_spline
Define a survival distribution based on explicit survival probabilitiesdefine_surv_table define_surv_table.character define_surv_table.data.frame
Define Transition Matrix for Markov Modeldefine_transition define_transition_ modify.uneval_matrix plot.uneval_matrix
Dispatch Values According to Strategydispatch_strategy
Probability Density Functions for Probabilistic Uncertainty Analysisbeta binomial define_distribution distributions gamma logitnormal lognormal multinomial normal poisson triangle use_distribution
Export PSA Results for SAVIexport_savi
Get State Membership Countsget_counts get_counts.combined_model get_counts.eval_strategy get_counts.list get_counts.run_model get_counts.updated_model
Get Strategy Valuesget_values get_values.combined_model get_values.eval_strategy get_values.list get_values.run_model get_values.updated_model
Project Beyond a Survival Distribution with Anotherjoin join_
Load a set of survival fitsload_surv_models
Look Up Values in a Data Framelook_up
Mix Two or More Survival Distributionsmix mix_
Modify Objectmodify
Convert saved fits to partitioned survival objectspart_survs_from_surv_inputs
Plot Sensitivity Analysisplot.dsa
Plot Results of Probabilistic Analysisplot.psa
Plot Results of a Markov Modelplot.run_model
Plot general survival modelsplot.surv_object
Convenience Functions to Compute Probabilitiesor_to_prob probability prob_to_prob rate_to_prob rescale_prob rr_to_prob
Reindent Transition Matrixreindent_transition
Rescale Discount Raterescale_discount_rate
Use the BCEA packagerun_bcea
Run Sensitivity Analysisrun_dsa
Run Markov Modelrun_model run_model_
Run Analyses From Filesrun_model_tabular
Run Probabilistic Uncertainty Analysisrun_psa
Set Covariates of a Survival Distributionset_covariates set_covariates_
Summarise Markov Model Resultssummary.run_model
Summarize surv_shift objectssummary.surv_shift
Run Model on New Dataplot.updated_model update.run_model update_model
Use WHO Mortality Rateget_who_mr who_mortality