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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
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
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
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.