Prepare for dplyr 1.0.0
look_up()
displays a more informative message when searching several values at onceStates are now length 2 lists:
Compatibility with dplyr 0.8: replaced all underscored (SE) versions of all verbs
get_who_mr()
is again able to fetch data from GHO serverdefine_state()
gains the starting_values
argument (same as define_strategy()
).Hmisc
dependency for weighted summaries.pool()
=>mix()
.define_starting_values()
.reindent_transition()
.period
argument.run_bcea()
.use_distribution()
to re-sample from empirical data (e.g. MCMC fit posterior distribution).define_psa()
back-end code, variables can now be used to define distribution parameters.state_time
but those parameters are not used by a strategy.modify()
are supported.master
, the release branch is called cran
.tidyr
.project()
=>join()
.get_code()
.run_dsa()
in state expansion situations.dplyr
update 0.6.0.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
calibrate_model()
.init
and inflow
can refer to values from define_parameters()
, and are thus accessible to PSA / DSA.inflow
can be time-varying.get_probs_from_surv()
=>compute_surv()
.vignette("j-survival")
. Thanks to Jordan Amdahl.calibrate_model()
. Thanks to Matthew Wiener.method
argument of run_model()
.get_who__mr()
can take a region
argument, and automatically pool results when sex
is not passed.heemod::discount()
now produces results similar to discount()
.*_
) to survival operation functions.strategy
becomes a reserved parameter name."half-cycle"
is deprecated.resample
argument in run_psa()
renamed to psa
.?distributions
.state_cycle
renamed to state_time
, added a model_time
alias to markov_cycle
.inflow
argument for budget impact analysis is specified with define_inflow()
.prob_to_prob()
=>rescale_prob()
.get_probs_from_surv()
:define_survival()
.flexsurv
package.define_part_surv()
.inflow
argument in run_model()
(mainly for budget impact analysis).dispatch_strategy()
or using the strategy
name (vignettes homogeneous and probabilistic have been updated to use this feature).gam()
fitting.rescale_discount_rate()
.combine_probs()
: given several independent probabilities of an event, return the total probability of the event.modify()
.diagram
, Hmisc
and logitnorm
moved from Imports
to Suggests
.newdata
were mistakenly parsed as lazy expressions.newdata
now handles factor variables.state_cycle_limit
was not passed to PSA, DSA, or updating.type
=>results
).type = "cov"
plot.bw
plot option.remove_ns
.model
=>strategy
).base_strategy
divided in 3 concepts: central_strategy
, root_strategy
, noncomparable_strategy
.discount()
throw warnings.transition_matrix
=> transition
in define_strategy()
.use_cluster()
.formatR
to suggest list.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()
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.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.plot_sensitivity()
now plots by default the widest bar on top.R
code to generate them (same idea as dput()
, but easier to read).heemod.verbose
and heemod.memotime
.get_counts()
and get_init()
to get state membership counts.get_who_mr()
.discount()
was not defined as a parameter.eval_model_newdata()
, the function behind re-sampling and sensitivity analysis now returns list-variables.discount()
was not defined as a parameter.C
in eval_matrix()
(thanks to Matthew Wiener).tidyr
.dplyr
update.shiny
interface.get_who_mr()
to extract mortality rates from WHO data.run_*
functions now output a single table instead of a list of tables.run_models()
.*_
functions.run_model_newdata()
cannot run uneval_model
anymore.define_state_list()
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