A minor version release of simulist containing various minor improvements to the functions and documentation, as well as removing some triggers for warning users. There are also a few bug fixes and internal enhancements.
sim_*() arguments that
previously did not have one. Allowing functions to be run without
specifying any arguments
(e.g. linelist <- sim_linelist()) (#149).sim_*() function arguments that
accept either a function or an
<epiparameter> object has been improved (#149).sim_*() functions no longer warn if the user has not
specified *_risk arguments and have set
onset_to_* arguments to NULL (#149).rmarkdown::html_vignette for to
correctly render the website and for maximum compatibility with
{pkgdown} >= 2.1.0. This removes figure numbering and code folding
(#153)..add_hospitalisation() has been vectorised following
.add_outcome() in PR #101 (#150).infect_period and
prob_infect have been renamed
infectious_period and prob_infection
(#143).sim_*() functions now use NULL instead of
NA to turn off processes
(e.g. onset_to_death = NULL for no deaths) (#148)..sample_infect_period() is added that
errors if the infectious period function generates a negative number
(#142).sim_linelist() no longer errors when
hosp_death_risk is NULL and
onset_to_death is parameterised as a delay distribution
(#144)..add_ct() generates the correct number of values and
does not duplicate Ct values due to vector recycling (#158).The third release of the simulist R package contains a range of new features, enhancements, documentation and unit tests.
The headline changes to the package are:
date_outcome and
outcome columns which can be parameterised with
onset_to_death and onset_to_recovery.onset_to_hosp and onset_to_death
arguments can now take NA as input and will return a column
of NAs in the line list columns date_admission
and date_outcome (#98).
An onset_to_recovery argument has been added to the
simulation functions, sim_linelist() and
sim_outbreak(), and so the recovery date can be explicitly
given in the line list data (#99).
The line list simulation can now use a time-varying case fatality
risk. The create_config() function now returns a
$time_varying_death_risk list element, which is
NULL by default but can take an R function to enable the
fatality risk of cases to change over the epidemic (#101).
A new vignette, time-varying-cfr.Rmd, has been added
to the package to describe how to use the time-varying case fatality
risk functionality and describe a few different time-varying functions
that can be used (#101).
A new vignette, wrangling-linelist.Rmd, has been
added to go over some of the common post-processing steps that might be
required after simulating line list or contact tracing data. This
vignette is short and currently only contains a single post-processing
example, more examples will be added over time (#104).
The README now has a section on related projects to
provide an overview of packages that simulate line list data, or are
related to simulist. This section contains a disclosure widget
containing a feature table providing a high-level description of the
features and development status of each related package (#110).
A Key features section and Complimentary R packages section has
been added to the README (#134).
Updated package architecture diagram in the
design-principles.Rmd vignette (#113).
The .add_deaths() function has been replaced by the
.add_outcome() function which can simulate death and
recovery times (#99).
.cross_check_sim_input() function has been added to
the package to ensure user input is coherent across arguments
(#98).
.anonymise() function has been added to convert
individual’s names into alphanumeric codes to anonymise individuals in
line list and contact tracing data (#106).
The simulation functions are now parameterised with an infectious
period (infect_period argument) instead of a contact
interval (contact_interval argument). This moves away from
parameterising the simulation with the time delay between a person
becoming infected and having contact with a susceptible individual, and
instead uses an infectious period distribution within which contacts are
uniformly distributed in time (#96).
The simulation functions can now set a maximum as well as a
minimum outbreak size. The min_outbreak_size argument in
the exported sim_*() functions has been renamed
outbreak_size and takes a numeric vector of
two elements, the minimum and maximum outbreak size. The maximum
outbreak size is a soft limit due to the stochastic nature of the
branching process model, so epidemiological data returned can contain
more cases and/or contacts that the maximum in
outbreak_size but in these case a warning is returned
explaining to the user how many cases/contacts are being returned
(#93).
The add_ct argument in sim_linelist()
and sim_outbreak() has been removed. The functionality is
now equivalent to add_ct = TRUE in the previous
simulist version. The add_ct argument was removed
to move the package to always returning <data.frame>s
with the same number of columns, for consistency and predictability
(#104).
The add_names argument in the simulation functions
has been renamed to anonymise. The new argument controls
whether names are given to each case (anonymise = FALSE,
default behaviour) or whether fixed length hexadecimal codes are given
to each case (anonymise = TRUE), this ensures the returned
<data.frame> has the same number of columns
(#106).
.sim_network_bp() now indexes the time vector
correctly. Previously a vector indexing bug meant the epidemic would not
progress through time (#95).Second release of simulist, updates the core simulation
model and, as a result, the arguments for sim_*() functions
for simulating line list data and/or contact table data exported from
simulist are updated. The internal package architecture is also
refactored.
create_config() now returns a new element in the list:
$network. By default create_config() returns
network = "adjusted", which assumes the simulation is a
random network and samples contacts with an excess degree distribution
(see Details in ?create_config()). The network effect can
be changed to "unadjusted" to switch off the
network effect. $network is checked internally (in
.sim_network_bp()) and will error if not valid (#60).design-principles.Rmd (#66).lint-changed-files.yaml)
is added to the suite of continuous integration workflows (#68).vis-linelist.Rmd (#70)..sim_network_bp() is added as an internal function and
replaces bpmodels::chain_sim() as the core simulation model
producing contacted and infected individuals. {bpmodels} is
removed as a dependency as a result (#60)..sample_names() is added as an internal function to
utilise randomNames::randomNames() to produce more unique
names than
randomNames(..., sample.with.replacement = FALSE)..sim_bp_linelist(), .sim_clinical_linelist()
and .sim_contacts_tbl() with .sim_internal()
(#66).sim_utils.R file was renamed to
utils.R (#66) and the empty create_linelist.R
file was removed (#72)..add_date_contact() argument
outbreak_start_date is now NULL by default
instead of missing (#82).sim_*() functions now use snapshot
testing for more detailed data checking (#65).testdata) files have been
updated, as has the testdata/README.md with instructions
(#64).R and serial_interval arguments have been
removed from sim_linelist(), sim_contacts()
and sim_outbreak() functions and instead
contact_distribution, contact_interval and
prob_infect are used to parameterise the simulation.
Documentation, both functions and vignettes, have been updated with
these changes (#60).contact_distribution argument in
sim_*() functions requires a density function if supplied
as an anonymous function. Information is added to
simulist.Rmd to explain this.sim_linelist() now uses
column header sex instead of gender. The
contacts table output from sim_contacts() and
sim_outbreak() now uses column headers age and
sex instead of cnt_age and
cnt_gender (#60, #79).contact_distribution is redefined and redocumented as
the distribution of contacts per individual, rather than the number of
contacts that do not get infected as it was in v0.1.0.row.names for <data.frame>s output
by sim_linelist(), sim_contacts() and
sim_outbreak() are now sequential from 1:nrows
(#63).sim_contacts() now correctly runs with an
age-structured population. In the previous version (v0.1.0),
sim_contacts() did not call .check_age_df()
and as a result the function errored, this is fixed as of PR #81.Initial release of simulist, an R package containing tools to simulate epidemiological data such as line lists and contact tables.
sim_linelist(): simulate line list datasim_contacts(): simulate contacts datasim_outbreak(): simulate both line list and contacts
datasimulist.Rmd)age-strat-risks.Rmd)age-struct-pop.Rmd)vis-linelist.Rmd)design-principles.Rmd)