serofoi 1.0.3

serofoi 1.0.3

New features

• Add options to plot single FOI estimates and r-hats:

We introduced parameters plot_constant and x_axis to the visualisation functions of the package. These enable the option to plot constant FoI estimates and their corresponding r-hat values, avoiding ambiguity in the specification of the x-axis by means of x_axis = "time" or x_axis = "age".

Minor changes

• Documentation corrections
  • Fix incorrect cross referencing in documentation
  • Update table 1 in article foi_models to show the prior specification options available in the package.
  • Add example of a particular model specification using the package in article foi_models
  • Complete missing documentation and tags.
• Shorten long function and internal parameter names (mainly in the simulation module)
  • Change seroprevalence_ and seropositive_ for seroprev_
  • Change probability_ for prob_
  • Remove _model
• Other
  • Make consistent use of Force-of-Infection (FoI) acronym across the package
  • Fix broken link to contributing guidelines in README

Internal changes

• Implement lintr v3.2.0 new suggestions
• Update the stan code to use new syntax.
• Update workflows based on Epiverse template.
• Remove Hmisc dependency.
• Replace Matrix package for expm
• Add donttest to examples taking too long to run