NEWS | R Documentation |
adaptivetau and deSolve are now suggested, not imported, as they are only needed for simulation. Usage of simulated data sets is now everywhere conditional on successful loading of the dependency.
More simulations set tl.params = list(epsilon = .)
to mitigate noise attributable to too big leaps in the adaptive
tau-leaping algorithm.
plot
method for class fastbeta.bootstrap
uses dev.hold
and dev.flush
from grDevices
to avoid “incremental” graphical output on some devices.
Compartmental model is generalized to support multiple
infected compartments: m
latent and n
infectious,
resulting in several backwards incompatible changes to the API;
see below.
Argument constants
of functions sir
,
fastbeta
, fastbeta.bootstrap
, and ptpi
is
replaced by arguments sigma
, gamma
, delta
,
init
, m
, and n
.
sir
is now a wrapper calling new seir
.
Arguments a
and b
of function ptpi
are replaced by arguments start
and end
so that
the interface is more similar to that of window
.
ptpi
returns list(value, diff, iter, x)
,
no longer list(value, delta, iter, X)
.
Simulations sir.e01
and sir.e02
are replaced
by seir.ts01
and seir.ts02
. The replacements have
a latent compartment and a different set of attributes reflecting
the API of seir
.
‘data/*.R’ are no longer copied to ‘inst/scripts’
at install time by a make
rule in ‘src/Makevars’.
There is no need: the scripts are preserved due to the setting of
BuildResaveData: no
. Hence ‘src/Makevars’ is removed.
Compartmental model is generalized to support loss of
immunity at rate delta
, resulting in several backwards
incompatible changes to the API; see below.
sir
expects constants = c(S0, I0, R0, gamma, delta)
,
no longer constants = c(gamma, S0, I0, R0)
.
fastbeta
and fastbeta.bootstrap
expect constants = c(S0, I0, R0, gamma, delta)
,
no longer constants = c(gamma, S0, I0)
.
ptpi
gains argument constants
and loses
argument start
.
It expects constants = c(Sa, Ia, Ra, gamma, delta)
,
no longer start = Sa
.
fastbeta
returns (modulo attributes)
cbind(S, I, R, beta)
, no longer cbind(beta, S, I)
.
ptpi(...)[[1L]]
gives the state at time 0
or at time a
conditional on new argument backcalc
.
The default is a
, no longer (implicitly) 0
.
ptpi(...)[[4L]]
has dimensions
c(b-a+1, 3, iter)
, no longer c(b-a+1, iter)
.
Simulation sir.e01
is generated by the same
parameters but is no longer stochastic.
Simulation sir.e02
gives the stochastic variant.
‘data/*.R’ are copied into ‘inst/scripts’
at install time by a make
rule in ‘src/Makevars’.
Depends: R (>= 4.3.0)
for amsmath
in PDF
output, which was not supported until 4.2.2.
Typo in ‘src/sir.c’ triggering -Wformat is fixed.
Changes are logged in ‘inst/NEWS.Rd’.
‘DESCRIPTION’ sets BuildResaveData: no
,
so that R CMD build
works without
--no-resave-data when fastbeta is not installed.