+.dist_spec |
Creates a delay distribution as the sum of two other delay distributions. |
apply_tolerance |
Applies a threshold to all nonparametric distributions in a <dist_spec> |
backcalc_opts |
Back Calculation Options |
bootstrapped_dist_fit |
Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters |
c.dist_spec |
Combines multiple delay distributions for further processing |
calc_CrI |
Calculate Credible Interval |
calc_CrIs |
Calculate Credible Intervals |
calc_summary_measures |
Calculate All Summary Measures |
calc_summary_stats |
Calculate Summary Statistics |
clean_nowcasts |
Clean Nowcasts for a Supplied Date |
clean_regions |
Clean Regions |
collapse |
Collapse nonparametric distributions in a <dist_spec> |
convert_to_logmean |
Convert mean and sd to log mean for a log normal distribution |
convert_to_logsd |
Convert mean and sd to log standard deviation for a log normal distribution |
convolve_and_scale |
Convolve and scale a time series |
delay_opts |
Delay Distribution Options |
discretise |
Discretise a <dist_spec> |
discretize |
Discretise a <dist_spec> |
Distributions |
Probability distributions |
dist_fit |
Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions |
dist_skel |
Distribution Skeleton |
epinow |
Real-time Rt Estimation, Forecasting and Reporting |
estimate_delay |
Estimate a Delay Distribution |
estimate_infections |
Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth |
estimate_secondary |
Estimate a Secondary Observation from a Primary Observation |
estimate_truncation |
Estimate Truncation of Observed Data |
example_confirmed |
Example Confirmed Case Data Set |
example_generation_time |
Example generation time |
example_incubation_period |
Example incubation period |
example_reporting_delay |
Example reporting delay |
example_truncated |
Example Case Data Set with Truncation |
expose_stan_fns |
Expose internal package stan functions in R |
extract_CrIs |
Extract Credible Intervals Present |
extract_inits |
Generate initial conditions from a Stan fit |
extract_samples |
Extract all samples from a stan fit |
extract_stan_param |
Extract a Parameter Summary from a Stan Object |
filter_opts |
Filter Options for a Target Region |
Fixed |
Probability distributions |
fix_dist |
Fix the parameters of a <dist_spec> |
forecast_infections |
Forecast infections from a given fit and trajectory of the time-varying reproduction number |
forecast_secondary |
Forecast Secondary Observations Given a Fit from estimate_secondary |
Gamma |
Probability distributions |
generation_times |
Literature Estimates of Generation Times |
generation_time_opts |
Generation Time Distribution Options |
get_distribution |
Get the distribution of a 'dist_spec()' |
get_parameters |
Get parameters of a parametric distribution |
get_pmf |
Get the probability mass function of a nonparametric distribution |
get_regional_results |
Get Combined Regional Results |
gp_opts |
Approximate Gaussian Process Settings |
growth_to_R |
Convert Growth Rates to Reproduction numbers. |
incubation_periods |
Literature Estimates of Incubation Periods |
LogNormal |
Probability distributions |
make_conf |
Format Credible Intervals |
map_prob_change |
Categorise the Probability of Change for Rt |
max.dist_spec |
Returns the maximum of one or more delay distribution |
mean.dist_spec |
Returns the mean of one or more delay distribution |
new_dist_spec |
Internal function for generating a 'dist_spec' given parameters and a distribution. |
NonParametric |
Probability distributions |
Normal |
Probability distributions |
obs_opts |
Observation Model Options |
opts_list |
Return an _opts List per Region |
plot |
Plot method for estimate_infections |
plot.dist_spec |
Plot PMF and CDF for a dist_spec object |
plot.epinow |
Plot method for epinow |
plot.estimate_infections |
Plot method for estimate_infections |
plot.estimate_secondary |
Plot method for estimate_secondary |
plot.estimate_truncation |
Plot method for estimate_truncation |
plot_CrIs |
Plot EpiNow2 Credible Intervals |
plot_estimates |
Plot Estimates |
plot_summary |
Plot a Summary of the Latest Results |
print.dist_spec |
Prints the parameters of one or more delay distributions |
regional_epinow |
Real-time Rt Estimation, Forecasting and Reporting by Region |
regional_summary |
Regional Summary Output |
report_plots |
Report plots |
report_summary |
Provide Summary Statistics for Estimated Infections and Rt |
rstan_opts |
Rstan Options |
rstan_sampling_opts |
Rstan Sampling Options |
rstan_vb_opts |
Rstan Variational Bayes Options |
rt_opts |
Time-Varying Reproduction Number Options |
run_region |
Run epinow with Regional Processing Code |
R_to_growth |
Convert Reproduction Numbers to Growth Rates |
secondary_opts |
Secondary Reports Options |
setup_default_logging |
Setup Default Logging |
setup_future |
Set up Future Backend |
setup_logging |
Setup Logging |
simulate_infections |
Simulate infections using the renewal equation |
simulate_secondary |
Simulate secondary observations from primary observations |
stan_laplace_opts |
Stan Laplace algorithm Options |
stan_opts |
Stan Options |
stan_pathfinder_opts |
Stan pathfinder algorithm Options |
stan_sampling_opts |
Stan Sampling Options |
stan_vb_opts |
Stan Variational Bayes Options |
summary |
Summary output from epinow |
summary.epinow |
Summary output from epinow |
summary.estimate_infections |
Summary output from estimate_infections |
trunc_opts |
Truncation Distribution Options |
update_secondary_args |
Update estimate_secondary default priors |