News for R Package fastbeta

Changes in version 0.5.1 (2025-10-25)

Description

• David Earn is a contributor.

Changes in version 0.5.0 (2025-10-15)

Significant User-Visible Changes

• sir.aoi(..., root = function) is a multiple time series object storing the solution until the last root or time point. Attribute root.info stores details about the system at the roots in the format list(tau, state). Previously, sir.aoi discarded the solution and returned only details about the system at the first root.

• sir.aoi(..., root = function) no longer has an attribute curvature storing the curvature of Y at the root.

New Features

• sir.aoi(..., aggregate = TRUE) has additional columns storing the force of infection, incidence, and the curvature of Y.

• sir.aoi accepts new argument eps in order to support equations with equal, nonzero rates of birth and death.

• sir.aoi accepts new arguments F and Fargs, enabling the user to set a forcing function.

• sir.aoi accepts new arguments H and Hargs, enabling the user to set a susceptible hetereogeneity function.

• sir.aoi accepts new arguments root.max and root.break, enabling the user to set the number of roots sought and indicate whether the solver should stop once that number of roots is reached. The default behaviour is to stop once one root is found and agrees with the previous behaviour.

• sir.aoi accepts new argument skip.Y indicating if solution of the equation for Y should not be attempted.

• The method for generic function summary and class sir.aoi accepts new argument name, enabling approximation of tail exponents of different variables.

• Function cbind.ts for working around PR#18583.

• deconvolve accepts new argument x.pad, enabling the user to decide the value of the elements with which x is padded when start is unset.

• New data set pneumonia, used in an example of deconvolve usage.

Bug Fixes

• The expression for \text{d}Y/\text{d}\tau used by sir.aoi was wrong.

Changes in version 0.4.0 (2025-04-28)

Deprecated and Defunct

• seir.canonical is removed in favour of more general sir.aoi. The method for generic function summary and class seir.canonical is removed in favour of a method for class sir.aoi.

New Features

• Function sir.aoi generalizing seir.canonical in order to support rates of transmission and recovery structured by age of infection.

Changes in version 0.3.2 (2025-03-23)

New Features

• Function seir.canonical providing a nondimensional interface to a special case (constant transmission, without vital dynamics, without loss of immunity) of seir usage. The nondimensional parameters are the basic reproduction number and the ratio of the mean latent period and mean generation interval.

• A method for generic function summary and class seir.canonical approximating the tail exponents of prevalence.

Changes in version 0.3.1 (2024-11-22)

Installation

• Compilation uses -DSTRICT_R_HEADERS and -DR_NO_REMAP.

Significant User-Visible Changes

• 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.

New Features

• 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.

Bug Fixes

• 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.

Changes in version 0.3.0 (2024-05-17)

Installation

• Suggests: adaptivetau, deSolve rather than Imports: adaptivetau, deSolve as those packages are needed only for simulation. Usage of simulated data sets is now everywhere conditional on successful loading of the dependency.

Significant User-Visible Changes

• 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.

New Features

• Compartmental model is generalized to support multiple infected compartments, m latent and n infectious, resulting in several backwards incompatible changes to the API; see above.

Bug Fixes

• 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.

Changes in version 0.2.0 (2023-12-11)

Installation

• ‘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.

Significant User-Visible Changes

• 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.

New Features

• Compartmental model is generalized to support loss of immunity at rate delta, resulting in several backwards incompatible changes to the API; see below.

Changes in version 0.1.1 (2023-11-28)

Description

• Depends: R (>= 4.3.0) for ⁠amsmath⁠ in PDF output, which was not supported until 4.2.2.

• BuildResaveData: no so that R CMD build works without --no-resave-data when fastbeta is not installed.

Installation

• ‘data/*.R’ are copied into ‘inst/scripts’ at install time by a make rule in ‘src/Makevars’.

Documentation

• Changes are logged in ‘inst/NEWS.Rd’.

Bug Fixes

• Typo in ‘src/sir.c’ triggering -Wformat is fixed.