R: News for R Package 'fastbeta'

NEWS	R Documentation

News for R Package fastbeta

Entry [2, 2] of the Jacobian matrix constructed by seir(stochastic = FALSE, useCompiled = FALSE) was wrong.
seir handles more comprehensively the situation in which the number of rows of the matrix returned by deSolve function lsoda is less than length.out. It now distinguishes termination due to found roots from termination due to an unsuccessful solver call.
Warnings caught by -Wconversion are squashed.

seir gains logical argument aggregate indicating whether latent and infectious compartments should be aggregated.
seir arguments nu and mu gain default values. In both cases, it is function (t) 0, indicating no vital dynamics.
seir.R0, seir.ee, and seir.jacobian for calculating the basic reproduction number, endemic equilibrium, and Jacobian matrix.
fastbeta.matrix for calculating lower triangular coefficient matrix.

Formal argument init of fastbeta, fastbeta.bootstrap, ptpi, and seir is repositioned.
Formal arguments sigma and m of fastbeta, fastbeta.bootstrap, ptpi, and seir have constant default values (sigma = 1, m = 1L) not depending on the values of other arguments.

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.

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.