# Generated by roxygen2: do not edit by hand

S3method("!=",dist_spec)
S3method("$",epinow)
S3method("$",estimate_infections)
S3method("$",estimate_secondary)
S3method("$",estimate_truncation)
S3method("+",dist_spec)
S3method("==",dist_spec)
S3method("[[",epinow)
S3method("[[",estimate_infections)
S3method("[[",estimate_secondary)
S3method("[[",estimate_truncation)
S3method(c,dist_spec)
S3method(collapse,dist_spec)
S3method(collapse,multi_dist_spec)
S3method(discretise,dist_spec)
S3method(discretise,multi_dist_spec)
S3method(fix_parameters,dist_spec)
S3method(fix_parameters,multi_dist_spec)
S3method(get_parameters,dist_spec)
S3method(get_parameters,epinowfit)
S3method(get_parameters,estimate_dist)
S3method(get_predictions,estimate_infections)
S3method(get_predictions,estimate_secondary)
S3method(get_predictions,estimate_truncation)
S3method(get_predictions,forecast_infections)
S3method(get_predictions,forecast_secondary)
S3method(get_samples,epinow)
S3method(get_samples,estimate_infections)
S3method(get_samples,estimate_secondary)
S3method(get_samples,estimate_truncation)
S3method(get_samples,forecast_infections)
S3method(get_samples,forecast_secondary)
S3method(is_constrained,dist_spec)
S3method(is_constrained,multi_dist_spec)
S3method(max,dist_spec)
S3method(max,multi_dist_spec)
S3method(mean,dist_spec)
S3method(mean,multi_dist_spec)
S3method(plot,dist_spec)
S3method(plot,estimate_infections)
S3method(plot,estimate_secondary)
S3method(plot,estimate_truncation)
S3method(plot,forecast_infections)
S3method(plot,forecast_secondary)
S3method(print,dist_spec)
S3method(print,epinowfit)
S3method(print,summary.estimate_dist)
S3method(print,summary.estimate_truncation)
S3method(scoringutils::as_forecast_sample,epinow)
S3method(scoringutils::as_forecast_sample,estimate_infections)
S3method(scoringutils::as_forecast_sample,estimate_truncation)
S3method(scoringutils::as_forecast_sample,forecast_secondary)
S3method(sd,default)
S3method(sd,dist_spec)
S3method(sd,multi_dist_spec)
S3method(summary,epinow)
S3method(summary,estimate_dist)
S3method(summary,estimate_infections)
S3method(summary,estimate_secondary)
S3method(summary,estimate_truncation)
S3method(summary,forecast_infections)
export(Dirichlet)
export(Exp)
export(Fixed)
export(Gamma)
export(LogNormal)
export(NonParametric)
export(Normal)
export(R_to_growth)
export(Weibull)
export(add_breakpoints)
export(backcalc_opts)
export(bootstrapped_dist_fit)
export(bound_dist)
export(calc_CrI)
export(calc_CrIs)
export(calc_summary_measures)
export(calc_summary_stats)
export(clean_nowcasts)
export(collapse)
export(convert_to_logmean)
export(convert_to_logsd)
export(convolve_and_scale)
export(delay_opts)
export(discretise)
export(discretize)
export(dist_fit)
export(epinow)
export(epinow2_cmdstan_model)
export(estimate_delay)
export(estimate_dist)
export(estimate_infections)
export(estimate_secondary)
export(estimate_truncation)
export(expose_stan_fns)
export(extract_CrIs)
export(extract_inits)
export(extract_samples)
export(extract_stan_param)
export(fill_missing)
export(filter_leading_zeros)
export(fix_parameters)
export(forecast_infections)
export(forecast_opts)
export(forecast_secondary)
export(generation_time_opts)
export(get_distribution)
export(get_parameters)
export(get_pmf)
export(get_predictions)
export(get_regional_results)
export(get_samples)
export(gp_opts)
export(growth_to_R)
export(gt_opts)
export(is_constrained)
export(make_conf)
export(map_prob_change)
export(new_dist_spec)
export(obs_opts)
export(opts_list)
export(plot_estimates)
export(plot_summary)
export(regional_epinow)
export(regional_runtimes)
export(regional_summary)
export(report_plots)
export(report_summary)
export(rt_opts)
export(secondary_opts)
export(set_dt_single_thread)
export(setup_default_logging)
export(setup_future)
export(setup_logging)
export(simulate_infections)
export(simulate_secondary)
export(stan_laplace_opts)
export(stan_opts)
export(stan_pathfinder_opts)
export(stan_sampling_opts)
export(stan_vb_opts)
export(trunc_opts)
export(update_secondary_args)
import(Rcpp)
import(methods)
import(rstantools)
importFrom(R.utils,isDirectory)
importFrom(R.utils,withTimeout)
importFrom(checkmate,assert_character)
importFrom(checkmate,assert_class)
importFrom(checkmate,assert_data_frame)
importFrom(checkmate,assert_date)
importFrom(checkmate,assert_integer)
importFrom(checkmate,assert_integerish)
importFrom(checkmate,assert_list)
importFrom(checkmate,assert_logical)
importFrom(checkmate,assert_names)
importFrom(checkmate,assert_number)
importFrom(checkmate,assert_numeric)
importFrom(checkmate,assert_path_for_output)
importFrom(checkmate,assert_string)
importFrom(checkmate,assert_subset)
importFrom(checkmate,test_data_frame)
importFrom(checkmate,test_numeric)
importFrom(cli,cli_abort)
importFrom(cli,cli_inform)
importFrom(cli,cli_warn)
importFrom(cli,col_blue)
importFrom(cli,col_red)
importFrom(data.table,":=")
importFrom(data.table,.N)
importFrom(data.table,CJ)
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fcase)
importFrom(data.table,fifelse)
importFrom(data.table,frollmean)
importFrom(data.table,frollsum)
importFrom(data.table,fwrite)
importFrom(data.table,getDTthreads)
importFrom(data.table,melt)
importFrom(data.table,merge.data.table)
importFrom(data.table,nafill)
importFrom(data.table,rbindlist)
importFrom(data.table,setDT)
importFrom(data.table,setDTthreads)
importFrom(data.table,setcolorder)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(data.table,setorderv)
importFrom(data.table,shift)
importFrom(futile.logger,appender.file)
importFrom(futile.logger,appender.tee)
importFrom(futile.logger,flog.appender)
importFrom(futile.logger,flog.debug)
importFrom(futile.logger,flog.error)
importFrom(futile.logger,flog.fatal)
importFrom(futile.logger,flog.info)
importFrom(futile.logger,flog.threshold)
importFrom(futile.logger,flog.trace)
importFrom(futile.logger,flog.warn)
importFrom(futile.logger,ftry)
importFrom(ggplot2,.data)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_linerange)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_step)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_x_date)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,vars)
importFrom(lifecycle,deprecate_soft)
importFrom(lifecycle,deprecate_stop)
importFrom(lifecycle,deprecate_warn)
importFrom(lubridate,days)
importFrom(lubridate,wday)
importFrom(patchwork,plot_layout)
importFrom(posterior,mcse_mean)
importFrom(primarycensored,dprimarycensored)
importFrom(primarycensored,qprimarycensored)
importFrom(purrr,compact)
importFrom(purrr,flatten)
importFrom(purrr,keep)
importFrom(purrr,list_assign)
importFrom(purrr,list_transpose)
importFrom(purrr,map)
importFrom(purrr,map2_dbl)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,map_vec)
importFrom(purrr,pmap_dbl)
importFrom(purrr,quietly)
importFrom(purrr,reduce)
importFrom(purrr,safely)
importFrom(purrr,transpose)
importFrom(purrr,walk)
importFrom(rlang,"%||%")
importFrom(rlang,abort)
importFrom(rlang,arg_match)
importFrom(rlang,cnd_muffle)
importFrom(rstan,expose_stan_functions)
importFrom(rstan,extract)
importFrom(rstan,sampling)
importFrom(rstan,sflist2stanfit)
importFrom(rstan,stanc)
importFrom(rstan,summary)
importFrom(rstan,vb)
importFrom(runner,mean_run)
importFrom(scales,comma)
importFrom(stats,aggregate)
importFrom(stats,glm)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,pexp)
importFrom(stats,pgamma)
importFrom(stats,plnorm)
importFrom(stats,pnorm)
importFrom(stats,pweibull)
importFrom(stats,quantile)
importFrom(stats,quasipoisson)
importFrom(stats,rexp)
importFrom(stats,rgamma)
importFrom(stats,rlnorm)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,uniroot)
importFrom(stats,var)
importFrom(stats,weighted.mean)
importFrom(truncnorm,rtruncnorm)
importFrom(utils,capture.output)
importFrom(utils,head)
importFrom(utils,modifyList)
importFrom(utils,tail)
useDynLib(EpiNow2, .registration=TRUE)
