Package: WARDEN 0.99.2

WARDEN: Workflows for Health Technology Assessments in R using Discrete EveNts

Toolkit to support and perform discrete event simulations without resource constraints in the context of health technology assessments (HTA). The package focuses on cost-effectiveness modelling and aims to be submission-ready to relevant HTA bodies in alignment with 'NICE TSD 15' <https://www.sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>. More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.

Authors:Javier Sanchez Alvarez [aut, cre], Gabriel Lemyre [ctb], Valerie Aponte Ribero [ctb]

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WARDEN.pdf |WARDEN.html✨
WARDEN/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/jsanchezalv/warden/issues

Pkgdown site:https://jsanchezalv.github.io

Datasets:

On CRAN:

6.62 score 5 stars 9 scripts 53 downloads 49 exports 66 dependencies

Last updated 11 days agofrom:0e33168852. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winOKDec 18 2024
R-4.5-linuxOKDec 18 2024
R-4.4-winOKDec 18 2024
R-4.4-macOKDec 18 2024
R-4.3-winOKDec 18 2024
R-4.3-macOKDec 18 2024

Exports:add_itemadd_reactevtadd_tteast_as_listceac_descond_dirichletcond_mvncreate_indicatorsdisc_cycledisc_cycle_vdisc_instantdisc_instant_vdisc_ongoingdisc_ongoing_vdraw_tteevpi_desextract_elements_from_listextract_from_reactionsextract_psa_resultluck_adjmodify_eventmodify_itemmodify_item_seqnew_eventpcond_gompertzpick_psapick_val_vqbeta_mseqcond_expqcond_gammaqcond_gompertzqcond_llogisqcond_lnormqcond_normqcond_weibullqgamma_mserbeta_msercond_gompertzrcond_gompertz_lurdirichletrdirichlet_probreplicate_profilesrgamma_mserpoisgammarun_simrun_sim_parallelsummary_results_detsummary_results_senssummary_results_sim

Dependencies:assertthatbbmlebdsmatrixBHclicodetoolscolorspacecpp11data.tabledeSolvedigestdoFuturedplyrfansifarverfastGHQuadflexsurvforeachfuturefuture.applygenericsggplot2globalsgluegtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmstatemuhazmunsellmvtnormnlmenumDerivparallellypillarpkgconfigprogressrpurrrquadprogR6RColorBrewerRcppRcppArmadillorlangrstpm2scalesstatmodstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithrzoo

Example for a Sick-Sicker-Dead model

Javier Sanchez Alvarez and Valerie Aponte Ribero

Rendered fromexample_ssd.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-12-18
Started: 2021-10-22

Readme and manuals

Help Manual

Help pageTopics
Defining parameters that may be used in model calculationsadd_item
Define the modifications to other events, costs, utilities, or other items affected by the occurrence of the eventadd_reactevt
Define events and the initial event timeadd_tte
Transform a substituted expression to its Abstract Syntax Tree (AST) as a listast_as_list
Calculate the cost-effectiveness acceptability curve (CEAC) for a DES model with a PSA resultceac_des
Calculate conditional dirichlet valuescond_dirichlet
Calculate conditional multivariate normal valuescond_mvn
Creates a vector of indicators (0 and 1) for sensitivity/DSA analysiscreate_indicators
Cycle discountingdisc_cycle
Cycle discounting for vectorsdisc_cycle_v
Calculate instantaneous discounted costs or qalysdisc_instant
Calculate instantaneous discounted costs or qalys for vectorsdisc_instant_v
Calculate discounted costs and qalys between eventsdisc_ongoing
Calculate discounted costs and qalys between events for vectorsdisc_ongoing_v
Draw a time to event from a list of parametric survival functionsdraw_tte
Calculate the Expected Value of Perfect Information (EVPI) for a DES model with a PSA resultevpi_des
Extracts items and events by looking into modify_item, modify_item_seq, modify_event and new_eventextract_elements_from_list
Extract all items and events and their interactions from the event reactions listextract_from_reactions
Extract PSA results from a treatmentextract_psa_result
Perform luck adjustmentluck_adj
Modify the time of existing eventsmodify_event
Modify the value of existing itemsmodify_item
Modify the value of existing itemsmodify_item_seq
Generate new events to be added to existing vector of eventsnew_event
Survival Probaility function for conditional Gompertz distribution (lower bound only)pcond_gompertz
Helper function to create a list with random draws or whenever a series of functions needs to be called. Can be implemented within 'pick_val_v'.pick_psa
Select which values should be applied in the corresponding loop for several values (vector or list).pick_val_v
Draw from a beta distribution based on mean and se (quantile)qbeta_mse
Conditional quantile function for exponential distributionqcond_exp
Conditional quantile function for gamma distributionqcond_gamma
Quantile function for conditional Gompertz distribution (lower bound only)qcond_gompertz
Conditional quantile function for loglogistic distributionqcond_llogis
Conditional quantile function for lognormal distributionqcond_lnorm
Conditional quantile function for normal distributionqcond_norm
Conditional quantile function for weibull distributionqcond_weibull
Use quantiles from a gamma distribution based on mean and seqgamma_mse
Draw from a beta distribution based on mean and serbeta_mse
Draw from a conditional Gompertz distribution (lower bound only)rcond_gompertz
Draw from a Conditional Gompertz distribution (lower and upper bound)rcond_gompertz_lu
Draw from a dirichlet distribution based on number of counts in transition. Adapted from brms::rdirichletrdirichlet
Draw from a dirichlet distribution based on mean transition probabilities and standard errorsrdirichlet_prob
Replicate profiles data.framereplicate_profiles
Draw from a gamma distribution based on mean and sergamma_mse
Draw time to event (tte) from a Poisson or Poisson-Gamma (PG) Mixture/Negative Binomial (NB) Processrpoisgamma
Run the simulationrun_sim
Run simulations in parallel mode (at the simulation level)run_sim_parallel
Deterministic results for a specific treatmentsummary_results_det
Summary of sensitivity outputs for a treatmentsummary_results_sens
Summary of PSA outputs for a treatmentsummary_results_sim
Example TTE IPD datatte.df