Provides functions for estimating plant pathogen parameters from
    access period (AP) experiments. Separate functions are implemented for
    semi-persistently transmitted (SPT) and persistently transmitted (PT)
    pathogens. The common AP experiment exposes insect cohorts to infected source
    plants, healthy test plants, and intermediate plants (for PT pathogens). The
    package allows estimation of acquisition and inoculation rates during feeding,
    recovery rates, and latent progression rates (for PT pathogens). Additional
    functions support inference of epidemic risk from pathogen and local
    parameters, and also simulate AP experiment data. The functions implement
    probability models for epidemiological analysis, as derived in Donnelly et
    al. (2025), <doi:10.32942/X29K9P>. These models were originally
    implemented in the 'EpiPv' 'GitHub' package.

Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.

Drafting an epidemiological report in 'Microsoft Word' format for a given disease,
  similar to the Annual Epidemiological Reports published by the European Centre 
  for Disease Prevention and Control. Through standalone functions, it is specifically 
  designed to generate each disease specific output presented in these reports and includes:
  - Table with the distribution of cases by Member State over the last five years;
  - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, 
  by month, over the past five years;
  - Trend plot with the trend and number of cases at the European Union / European Economic Area level, 
  by month, over the past five years;
  - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level.
  Two types of datasets can be used:
  - The default dataset of dengue 2015-2019 data;
  - Any dataset specified as described in the vignette.