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-reindent transition matrices with
reindent_transition().
- Discounting per year with the
period argument.
- BCEA interface with
run_bcea().
use_distribution() to resample from empirical data (e.g. MCMC fit posterior distribution).
Bugfixes
- Better error-checking in multinomial parameters definition.
- Cleaner
define_psa() backend code, variables can now be used to define distributin parameters.
- Handle cases when parameters depend on
state_time but thoses 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- Stricter dependency version management (to avoid install failures on an outdated system).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:
Filipović-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, <URL: https://pierucci.org/heemod>.
- Model calibration with
calibrate_model().
init and inflow can refer to values from define_parameters(), and are thus accesible 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 restults 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 arguement 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 markov_cycle.- 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 sofware.
- 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.
- Covariance 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 sevral 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.
Acknowledments
heemod 0.7.1
Bugfixes
- Fixed an error resulting in incorrect covariance 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 covariance 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 standarized processing of model objects.
- Unit tests rely less on printed results.
- Using new nomenclature in backend 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 arguement
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.
Acknowledments
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 microsimulations.
define_sensitivity() now accepts any expression as input, and can call references to model parameteres.- 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 localy 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 resampling and sensitivity analysis now returns list-variables.
Acknowledments
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
Removed
run_model_newdata() cannot run uneval_model anymore.- Removed need to use
define_state_list().
heemod 0.1.0