heemod

Changelog

heemod 1.0.0

Breaking changes

• dplyr’s pipe now causes an error when chaining survival operation. The new pipe |> is required in this situation.
• define_survival() has been renamed define_surv_dist() for naming consistency
• It is now necessary to use define_surv_fit() to specify a survival fit created with survfit(), flexsurvreg() or flexsurvspline()

New Features

• It is now possible to run probabilistic sensitivity analysis (PSA) with survival objects - either created from a parametric distribution (with define_surv_dist) or with real data fitted with survfit() or flexsurvreg(). See vignette("j-survival_2_psa")
• plot.surv_object() gains psa argument allowing to plot the distribution to check for its variability.
• Created method c.uneval_parameters() to combine outputs of define_parameters().

Other changes

• All operation functions on survival objects are now of class surv_object

heemod 0.16.0

• Remove lazyeval, plyr and pryr dependency
• For PSM, when OS is lower to PFS, force the transition probability to be 0 (#7 @william-rawlinson)
• get_who_mr() is working again
• Mortality rates gathered with get_who_mr(..., local = TRUE) are only available as
  pooled for high income countries.
• prop, multinom and make_gamma, deprecated since a long time are now unavailable, to be replaced with binomial, multinomial and gamma, respectively.
• markov_cycle is now deprecated in favor of model_time and state_cycle in favor of state_time

heemod 0.15.1

Compliance with r-devel

heemod 0.15.0

• Performance improvements: using state_time is much faster now, as well as probabilistic sensitivity analyses

heemod 0.14.5

• Rebuild vignettes
• fix guides( = FALSE)

heemod 0.14.4

• updates for compatibility with rlang 1.0.0

heemod 0.14.2

• checks cairo_pdf availability

heemod 0.14.0

Breaking changes

• argument “method” for run_model was inverted. Now “beginning” overestimates costs and “end” underestimates costs (#345 @zaddyzad)

heemod 0.13.0

Prepare for dplyr 1.0.0

Bugfixes

• Fix problem with state_time (fix #343 @Reale3)

heemod 0.12.0

Bugfixes

• Ready for tibble 3.0
• look_up() displays a more informative message when searching several values at once

heemod 0.11.0

Backend changes

• States are now length 2 lists:
  • .dots: the state values
  • starting_values: the state values when entering the state
• Compatibility with dplyr 0.8: replaced all underscored (SE) versions of all verbs

Bugfixes

• get_who_mr() is again able to fetch data from GHO server

heemod 0.10.0

New features

• define_state() gains the starting_values argument (same as define_strategy()).

heemod 0.9.4

• Compatibility with dplyr v0.8

heemod 0.9.3

Backend changes

• Remove Hmisc dependency for weighted summaries.

heemod 0.9.2

Breaking changes

• Survival function renamed: pool()=>mix().

New features

• Starting values with define_starting_values().
• Check for comma as a decimal separator in tabular data.
• Auto-re-indent transition matrices with reindent_transition().
• Discounting per year with the period argument.
• BCEA interface with run_bcea().
• use_distribution() to re-sample from empirical data (e.g. MCMC fit posterior distribution).

Bugfixes

• Better error-checking in multinomial parameters definition.
• Cleaner define_psa() back-end code, variables can now be used to define distribution parameters.
• Handle cases when parameters depend on state_time but those parameters are not used by a strategy.
• Empty calls to modify() are supported.
• Fix error in survival vignette.

Backend changes

• The development branch is now called master, the release branch is called cran.
• Survival operation are wrapped in a common class.
• Expansion code moved to own function.
• Faster computation of expanded states.
• Stricter dependency version management (to avoid install failures on an outdated system).
• Removed dependency to tidyr.

heemod 0.9.1

Breaking changes

• Survival function renamed: project()=>join().
• Removed get_code().

New features

• NMB is now reported as relative values.

Bugfixes

• Fixed error with run_dsa() in state expansion situations.

Backend changes

• Multiple changes to prepare for the dplyr update 0.6.0.

heemod 0.9.0

heemod can now be cited with:

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

• Model calibration with calibrate_model().
• init and inflow can refer to values from define_parameters(), and are thus accessible to PSA / DSA.
• inflow can be time-varying.

Breaking changes

• get_probs_from_surv()=>compute_surv().

New features

• Operations on survival functions, see vignette("j-survival"). Thanks to Jordan Amdahl.
• Model calibration with calibrate_model(). Thanks to Matthew Wiener.
• State membership correction works for partitioned survival model.
• Custom state membership correction functions can be passed to the method argument of run_model().
• get_who__mr() can take a region argument, and automatically pool results when sex is not passed.
• Additional DSA plotting options.

Bugfixes

• heemod::discount() now produces results similar to discount().

Backend changes

• Renamed memoised functions.
• NSE aliases (*_) to survival operation functions.

heemod 0.8.0

Breaking changes

• strategy becomes a reserved parameter name.
• Counting method "half-cycle" is deprecated.
• resample argument in run_psa() renamed to psa.
• Probability distributions for PSA were renamed, see ?distributions.
• state_cycle renamed to state_time, added a model_time alias to model_time.
• The inflow argument for budget impact analysis is specified with define_inflow().
• prob_to_prob()=>rescale_prob().

New features

• Transition probabilities from survival models with get_probs_from_surv():
  • Parametrically defined by define_survival().
  • Or fitted on data by the flexsurv package.
• Support for partitioned survival models with define_part_surv().
• Plot EVPI.
• Export PSA files for Sheffield Accelerated Value of Information software.
• Individuals can enter the model after the beginning with the inflow argument in run_model() (mainly for budget impact analysis).
• Strategy name can be used to define values with dispatch_strategy() or using the strategy name (vignettes homogeneous and probabilistic have been updated to use this feature).
• Beta and triangle distributions for PSA.
• Custom distributions can be defined.
• Co-variance analysis on strategy differences, more options for gam() fitting.

Other features

• Convenience function rescale_discount_rate().
• Better error messages at parameter evaluation.
• combine_probs(): given several independent probabilities of an event, return the total probability of the event.
• More informative error messages for incorrect matrices.
• Infinite parameter values generate an error.
• New parameters can be added with modify().

Backend changes

• Cleaner handling of clusters.
• Package diagram, Hmisc and logitnorm moved from Imports to Suggests.

Bugfixes

• Fixed several bugs that would return incorrect efficiency frontiers in some situations, or would return duplicated strategy names in some edge cases (thanks to Vince Daniels).
• Fixed a failure of tabular input when a column could be read as all numeric.
• Character variables from newdata were mistakenly parsed as lazy expressions.
• newdata now handles factor variables.
• state_cycle_limit was not passed to PSA, DSA, or updating.
• PSA and DSA tabular files were not saved.

Acknowledgments

• Thanks to Matthew Wiener, especially for the survival analysis code.

heemod 0.7.1

Bugfixes

• Fixed an error resulting in incorrect co-variance analysis results when relations between values and parameters were negative.

heemod 0.7.0

Breaking changes

• Some plotting arguments changed (e.g. type=>results).

New features

• Added co-variance analysis for PSA with type = "cov" plot.
• All plotting functions can now represent multiple strategies with facets.
• CECA plotted on a log scale by default.
• Black & white plots for publications with the bw plot option.
• Remove variables that are not sensitive in DSA with remove_ns.

Backend changes

• Important object structure change (from attributes to lists).
• More systematic use of getter functions.
• More standardized processing of model objects.
• Unit tests rely less on printed results.
• Using new nomenclature in back-end functions (model=>strategy).
• base_strategy divided in 3 concepts: central_strategy, root_strategy, noncomparable_strategy.
• Non-heemod versions of discount() throw warnings.

heemod 0.6.0

Breaking changes

• Base model cannot be specified anymore: it is always the least costly model.
• Renamed argument transition_matrix => transition in define_strategy().

New features

• Parallel computing with use_cluster().
• Compute average values from PSA.

Bugfixes

• Acceptability curve returns probabilities at 0.
• Correctly identify efficiency frontier.
• ICER are computed on the efficiency frontier.

Acknowledgments

• Thanks to Matthew Wiener, Zdenek Kabat and Vojtech Filipec for their great contributions to this update.

heemod 0.5.1

Bugfixes

• Added formatR to suggest list.

heemod 0.5.0

Breaking changes

• Some functions were renamed for clarification:
  • define_model() => define_strategy()
  • run_models() => run_model()
  • define_matrix() => define_transition()
  • define_sensitivity() => define_dsa()
  • define_distrib() => define_psa()
  • run_sensitivity() => run_dsa()
  • run_probabilistic() => run_psa()

New features

• Values and probabilities can depend on state time with state_cycle, allowing to reproduce the results of micro-simulations.
• define_sensitivity() now accepts any expression as input, and can call references to model parameters.
• Discount rates can now be specified as parameters (allows for rates to be modified in DSA & PSA).
• Any state value can be plotted.
• Additional output: csv files for many of the tabular results.

Bugfixes

• Edges where P=0 are not plotted anymore for transition matrices.
• There used to be a potential error when you wanted to save output but there had been no psa.

heemod 0.4.0

New features

• update() for heterogeneity analysis and to compute population-level values, with vignette.
• run_models_tabular() to import models from tabular input, with vignette.
• look_up() to look up values from external data.
• Added option to pool female and male mortality rates in WHO data.
• Counting method now defaults to life-table.
• plot_sensitivity() now plots by default the widest bar on top.
• Convenience functions for converting rates to probabilities.
• Models can be run without state values, to compute counts only.
• Much more informative error messages.
• Objects can be converted to the R code to generate them (same idea as dput(), but easier to read).
• New options heemod.verbose and heemod.memotime.
• More informative messages, especially in verbose mode.
• Use WHO data cached locally in case of connection problems.
• New functions: get_counts() and get_init() to get state membership counts.
• Smart sex code conversion for get_who_mr().

Bug fixes

• really fixed problem when the argument to discount() was not defined as a parameter.

Backend changes

• eval_model_newdata(), the function behind re-sampling and sensitivity analysis now returns list-variables.

Acknowledgments

• Thanks to Matthew Wiener, Zdenek Kabat and Vojtech Filipec for their great contributions to this update.

heemod 0.3.3

New features

• Added a vignette to exactly reproduce results from Decision Modelling for Health Economic Evaluation.

Bug fixes

• Fixed problem when argument to discount() was not defined as a parameter.
• Corrected several errors in the vignettes (thanks to Michael Schenkenberg from SBU, Stockholm, Sweden).
• Updated mortality rate tests to reflect GHO database update.

heemod 0.3.2

Bug fixes

• Fix mishandling of matrix index with C in eval_matrix() (thanks to Matthew Wiener).
• Fix problem with upcoming version of tidyr.

heemod 0.3.1

Backend changes

• A single set of parameters is now used for a set of models.

Bug fixes

• Correct error in probabilistic analysis vignette.
• Fix incompatibility with upcoming dplyr update.

heemod 0.3.0

New features

• shiny interface.
• Added support for different counting options.
• get_who_mr() to extract mortality rates from WHO data.

heemod 0.2.0

New features

• Added ability to plot matrix.
• Added framework for probabilistic uncertainty analysis.
• Written vignette for probabilistic and sensitivity analysis.
• Added complement alias for matrix definition.
• run_* functions now output a single table instead of a list of tables.
• Variables corresponding to cost and effect must now be specified in run_models().
• Plotting for sensitivity and probabilistic analysis.

Bug fixes

• added *_ functions.

Removed

• run_model_newdata() cannot run uneval_model anymore.
• Removed need to use define_state_list().

heemod 0.1.0

• Initial CRAN submission.