From 37ccab540573399c572e9447693a4971a476c6ff Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Tue, 20 Feb 2024 20:54:39 +0000 Subject: [PATCH] remove author tags [ci skip] --- R/adjust.R | 1 - R/checks.R | 1 - R/create.R | 15 --------------- R/dist.R | 17 ----------------- R/epinow-internal.R | 6 ------ R/epinow.R | 2 -- R/estimate_infections.R | 5 ----- R/estimate_secondary.R | 6 ------ R/estimate_truncation.R | 3 --- R/extract.R | 5 ----- R/get.R | 8 -------- R/opts.R | 22 ---------------------- R/simulate_infections.R | 1 - R/stan.R | 1 - inst/stan/functions/pmfs.stan | 3 +-- man/adjust_infection_to_report.Rd | 3 --- man/backcalc_opts.Rd | 3 --- man/bootstrapped_dist_fit.Rd | 3 --- man/c.dist_spec.Rd | 3 --- man/check_reports_valid.Rd | 3 --- man/construct_output.Rd | 3 --- man/copy_results_to_latest.Rd | 3 --- man/create_backcalc_data.Rd | 3 --- man/create_clean_reported_cases.Rd | 5 ----- man/create_complete_cases.Rd | 3 --- man/create_future_rt.Rd | 3 --- man/create_gp_data.Rd | 3 --- man/create_obs_model.Rd | 3 --- man/create_rt_data.Rd | 3 --- man/create_shifted_cases.Rd | 3 --- man/create_stan_args.Rd | 3 --- man/create_stan_data.Rd | 5 ----- man/create_stan_delays.Rd | 3 --- man/delay_opts.Rd | 5 ----- man/dist_fit.Rd | 3 --- man/dist_skel.Rd | 5 ----- man/dist_spec.Rd | 5 ----- man/dist_spec_plus.Rd | 5 ----- man/epinow.Rd | 3 --- man/estimate_delay.Rd | 3 --- man/estimate_infections.Rd | 3 --- man/estimate_secondary.Rd | 3 --- man/estimate_truncation.Rd | 5 ----- man/estimates_by_report_date.Rd | 3 --- man/extract_inits.Rd | 3 --- man/extract_parameter.Rd | 3 --- man/extract_parameter_samples.Rd | 3 --- man/extract_stan_param.Rd | 3 --- man/extract_static_parameter.Rd | 3 --- man/filter_opts.Rd | 3 --- man/fit_model_with_nuts.Rd | 3 --- man/fit_model_with_vb.Rd | 3 --- man/fix_dist.Rd | 3 --- man/forecast_secondary.Rd | 3 --- man/format_fit.Rd | 3 --- man/gamma_dist_def.Rd | 3 --- man/generation_time_opts.Rd | 5 ----- man/get_dist.Rd | 3 --- man/get_generation_time.Rd | 3 --- man/get_incubation_period.Rd | 3 --- man/get_raw_result.Rd | 3 --- man/get_regional_results.Rd | 3 --- man/get_regions.Rd | 3 --- man/get_regions_with_most_reports.Rd | 3 --- man/get_seeding_time.Rd | 3 --- man/gp_opts.Rd | 3 --- man/init_cumulative_fit.Rd | 3 --- man/lognorm_dist_def.Rd | 3 --- man/mean.dist_spec.Rd | 3 --- man/obs_opts.Rd | 3 --- man/opts_list.Rd | 3 --- man/plot.dist_spec.Rd | 3 --- man/plot.estimate_secondary.Rd | 3 --- man/plot.estimate_truncation.Rd | 3 --- man/plus-.dist_spec.Rd | 3 --- man/print.dist_spec.Rd | 3 --- man/rstan_opts.Rd | 3 --- man/rstan_sampling_opts.Rd | 3 --- man/rstan_vb_opts.Rd | 3 --- man/rt_opts.Rd | 3 --- man/save_estimate_infections.Rd | 3 --- man/save_input.Rd | 3 --- man/secondary_opts.Rd | 3 --- man/simulate_infections.Rd | 3 --- man/simulate_secondary.Rd | 5 ----- man/stan_model.Rd | 3 --- man/stan_opts.Rd | 5 ----- man/stan_sampling_opts.Rd | 5 ----- man/stan_vb_opts.Rd | 5 ----- man/trunc_opts.Rd | 5 ----- man/update_horizon.Rd | 3 --- man/update_secondary_args.Rd | 3 --- 92 files changed, 1 insertion(+), 352 deletions(-) diff --git a/R/adjust.R b/R/adjust.R index 4858eafc1..d1352689c 100644 --- a/R/adjust.R +++ b/R/adjust.R @@ -25,7 +25,6 @@ #' @inheritParams sample_approx_dist #' @importFrom data.table setorder data.table data.table #' @importFrom lubridate wday -#' @author Sam Abbott #' @examples #' \donttest{ #' # define example cases diff --git a/R/checks.R b/R/checks.R index ab08fe691..b25a372bd 100644 --- a/R/checks.R +++ b/R/checks.R @@ -18,7 +18,6 @@ #' assert_numeric #' @importFrom rlang arg_match #' @return Called for its side effects. -#' @author James M. Azam #' @keywords internal check_reports_valid <- function(reports, model) { # Check that the case time series (reports) is a data frame diff --git a/R/create.R b/R/create.R index 835a1f873..b5ead963f 100644 --- a/R/create.R +++ b/R/create.R @@ -21,8 +21,6 @@ #' @inheritParams estimate_infections #' @importFrom data.table copy merge.data.table setorder setDT frollsum #' @return A cleaned data frame of reported cases -#' @author Sam Abbott -#' @author Lloyd Chapman #' @export #' @examples #' create_clean_reported_cases(example_confirmed, 7) @@ -84,7 +82,6 @@ create_clean_reported_cases <- function(reported_cases, horizon = 0, #' start of the time series be filtered out. #' #' @return A data frame without NA values, with two columns: confirm (number) -#' @author Sebastian Funk #' @importFrom data.table setDT #' @keywords internal create_complete_cases <- function(cases) { @@ -116,7 +113,6 @@ create_complete_cases <- function(cases) { #' @importFrom runner mean_run #' @return A `` for shifted reported cases #' @export -#' @author Sam Abbott #' @examples #' create_shifted_cases(example_confirmed, 7, 14, 7) create_shifted_cases <- function(reported_cases, shift, @@ -185,7 +181,6 @@ create_shifted_cases <- function(reported_cases, shift, #' @param delay Numeric mean delay #' @importFrom rlang arg_match #' @return A list containing a logical called fixed and an integer called from -#' @author Sam Abbott create_future_rt <- function(future = "latest", delay = 0) { out <- list(fixed = FALSE, from = 0) if (is.character(future)) { @@ -226,7 +221,6 @@ create_future_rt <- function(future = "latest", delay = 0) { #' @return A list of settings defining the time-varying reproduction number #' @inheritParams create_future_rt #' @export -#' @author Sam Abbott #' @examples #' # default Rt data #' create_rt_data() @@ -293,7 +287,6 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL, #' @importFrom data.table fcase #' @return A list of settings defining the Gaussian process #' @export -#' @author Sam Abbott #' @examples #' create_backcalc_data(backcalc = backcalc_opts()) create_backcalc_data <- function(backcalc = backcalc_opts()) { @@ -322,7 +315,6 @@ create_backcalc_data <- function(backcalc = backcalc_opts()) { #' @seealso [gp_opts()] #' @return A list of settings defining the Gaussian process #' @export -#' @author Sam Abbott #' @examples #' # define input data required #' data <- list( @@ -392,7 +384,6 @@ create_gp_data <- function(gp = gp_opts(), data) { #' @return A list of settings ready to be passed to stan defining #' the Observation Model #' @export -#' @author Sam Abbott #' @examples #' dates <- seq(as.Date("2020-03-15"), by = "days", length.out = 15) #' # default observation model data @@ -448,8 +439,6 @@ create_obs_model <- function(obs = obs_opts(), dates) { #' @importFrom stats lm #' @importFrom purrr safely #' @return A list of stan data -#' @author Sam Abbott -#' @author Sebastian Funk #' @export #' @examples #' create_stan_data( @@ -539,8 +528,6 @@ create_stan_data <- function(reported_cases, seeding_time, #' @importFrom truncnorm rtruncnorm #' @importFrom data.table fcase #' @export -# @author Sam Abbott -# @author Sebastian Funk create_initial_conditions <- function(data) { init_fun <- function() { out <- list() @@ -656,7 +643,6 @@ create_initial_conditions <- function(data) { #' @importFrom utils modifyList #' #' @return A list of stan arguments -#' @author Sam Abbott #' @export #' @examples #' # default settings @@ -707,7 +693,6 @@ create_stan_args <- function(stan = stan_opts(), ##' @param weight Numeric, weight associated with delay priors; default: 1 ##' @return A list of variables as expected by the stan model ##' @importFrom purrr list_transpose map -##' @author Sebastian Funk create_stan_delays <- function(..., weight = 1) { dot_args <- list(...) ## combine delays diff --git a/R/dist.R b/R/dist.R index 201dcf198..1f33bc0db 100644 --- a/R/dist.R +++ b/R/dist.R @@ -34,8 +34,6 @@ #' #' @return A vector of samples or a probability distribution. #' @export -#' @author Sam Abbott -#' @author Sebastian Funk #' @examples #' #' ## Exponential model @@ -197,7 +195,6 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model, #' be printed. #' #' @return A stan fit of an interval censored distribution -#' @author Sam Abbott #' @export #' @inheritParams stan_opts #' @examples @@ -311,7 +308,6 @@ dist_fit <- function(values = NULL, samples = 1000, cores = 1, #' @export #' @inheritParams dist_skel #' @inheritParams lognorm_dist_def -#' @author Sam Abbott #' @examples #' # using estimated shape and scale #' def <- gamma_dist_def( @@ -394,7 +390,6 @@ gamma_dist_def <- function(shape, shape_sd, #' @param to_log Logical, should parameters be logged before use. #' #' @return A `` defining the distribution as used by [dist_skel()] -#' @author Sam Abbott #' @importFrom truncnorm rtruncnorm #' @export #' @inheritParams dist_skel @@ -498,7 +493,6 @@ lognorm_dist_def <- function(mean, mean_sd, #' data. Maximum delay to allow (added to output but does impact fitting). #' #' @return A `` object summarising the bootstrapped distribution -#' @author Sam Abbott #' @importFrom purrr list_transpose #' @importFrom future.apply future_lapply #' @importFrom rstan extract @@ -603,7 +597,6 @@ bootstrapped_dist_fit <- function(values, dist = "lognormal", #' @param ... Arguments to pass to internal methods. #' #' @return A `` summarising the bootstrapped distribution -#' @author Sam Abbott #' @export #' @seealso [bootstrapped_dist_fit()] #' @examples @@ -898,8 +891,6 @@ tune_inv_gamma <- function(lower = 2, upper = 21) { #' reduces compute requirement but may produce spuriously precise estimates. #' @return A list of distribution options. #' -#' @author Sebastian Funk -#' @author Sam Abbott #' @importFrom rlang warn arg_match #' @export #' @examples @@ -1084,8 +1075,6 @@ dist_spec <- function(mean, sd = 0, mean_sd = 0, sd_sd = 0, #' @return A delay distribution representing the sum of the two delays #' (with class [dist_spec()]) #' -#' @author Sebastian Funk -#' @author Sam Abbott #' @importFrom stats convolve dist_spec_plus <- function(e1, e2, tolerance = 0.001) { ## process delay distributions @@ -1125,7 +1114,6 @@ dist_spec_plus <- function(e1, e2, tolerance = 0.001) { #' @return A delay distribution representing the sum of the two delays #' (with class [dist_spec()]) #' @inheritParams dist_spec_plus -#' @author Sebastian Funk #' @method + dist_spec #' @export #' @examples @@ -1155,7 +1143,6 @@ dist_spec_plus <- function(e1, e2, tolerance = 0.001) { #' #' @param ... The delay distributions (from calls to [dist_spec()]) to combine #' @return Combined delay distributions (with class ``) -#' @author Sebastian Funk #' @method c dist_spec #' @importFrom purrr list_transpose map c.dist_spec <- function(...) { @@ -1185,7 +1172,6 @@ c.dist_spec <- function(...) { ##' @param x The `` to use ##' @param ... Not used ##' @return A vector of means. -##' @author Sebastian Funk ##' @method mean dist_spec ##' @importFrom utils head ##' @export @@ -1237,7 +1223,6 @@ mean.dist_spec <- function(x, ...) { #' @param x The `` to use #' @param ... Not used #' @return invisible -#' @author Sebastian Funk #' @method print dist_spec #' @export #' @examples @@ -1309,7 +1294,6 @@ print.dist_spec <- function(x, ...) { #' @param ... Additional arguments to pass to `{ggplot}`. #' @importFrom ggplot2 aes geom_col geom_step facet_wrap vars theme_bw #' @export -#' @author Sam Abbott #' @examples #' #' # A fixed lognormal distribution with mean 5 and sd 1. #' lognormal <- dist_spec( @@ -1393,7 +1377,6 @@ plot.dist_spec <- function(x, ...) { ##' If the given `` has any uncertainty, it is removed and the ##' corresponding distribution converted into a fixed one. ##' @return A `` object without uncertainty -##' @author Sebastian Funk ##' @export ##' @param x A `` object ##' @param strategy Character; either "mean" (use the mean estimates of the diff --git a/R/epinow-internal.R b/R/epinow-internal.R index 539e1ed41..648a6f923 100644 --- a/R/epinow-internal.R +++ b/R/epinow-internal.R @@ -6,7 +6,6 @@ #' @inheritParams setup_target_folder #' @inheritParams estimate_infections #' @return Numeric forecast horizon adjusted for the users intention -#' @author Sam Abbott #' @export update_horizon <- function(horizon, target_date, reported_cases) { if (horizon != 0) { @@ -25,7 +24,6 @@ update_horizon <- function(horizon, target_date, reported_cases) { #' @inheritParams setup_target_folder #' @inheritParams epinow #' @return No return value, called for side effects -#' @author Sam Abbott #' @export save_input <- function(reported_cases, target_folder) { if (!is.null(target_folder)) { @@ -51,7 +49,6 @@ save_input <- function(reported_cases, target_folder) { #' be returned. #' #' @seealso estimate_infections -#' @author Sam Abbott #' @inheritParams setup_target_folder #' @inheritParams estimate_infections #' @return No return value, called for side effects @@ -88,7 +85,6 @@ save_estimate_infections <- function(estimates, target_folder = NULL, #' #' @return A list of samples and summarised estimates of estimated cases by #' date of report. -#' @author Sam Abbott #' @export #' @importFrom data.table := rbindlist estimates_by_report_date <- function(estimates, CrIs = c(0.2, 0.5, 0.9), @@ -134,7 +130,6 @@ estimates_by_report_date <- function(estimates, CrIs = c(0.2, 0.5, 0.9), #' @inheritParams setup_target_folder #' #' @return No return value, called for side effects -#' @author Sam Abbott #' @export copy_results_to_latest <- function(target_folder = NULL, latest_folder = NULL) { if (!is.null(target_folder)) { @@ -175,7 +170,6 @@ copy_results_to_latest <- function(target_folder = NULL, latest_folder = NULL) { #' @inheritParams save_estimate_infections #' #' @return A list of output as returned by `epinow` -#' @author Sam Abbott #' @export construct_output <- function(estimates, estimated_reported_cases, diff --git a/R/epinow.R b/R/epinow.R index 7a7d1bf1b..827fb86dd 100644 --- a/R/epinow.R +++ b/R/epinow.R @@ -22,7 +22,6 @@ #' #' @return A list of output from estimate_infections with additional elements #' summarising results and reporting errors if they have occurred. -#' @author Sam Abbott #' @export #' @seealso [estimate_infections()] [forecast_infections()] [regional_epinow()] #' @inheritParams setup_target_folder @@ -35,7 +34,6 @@ #' @importFrom checkmate assert_string assert_path_for_output #' assert_date assert_logical #' @importFrom R.utils isDirectory -#' @author Sam Abbott #' @examples #' \donttest{ #' # set number of cores to use diff --git a/R/estimate_infections.R b/R/estimate_infections.R index dc065be35..26a5c7189 100644 --- a/R/estimate_infections.R +++ b/R/estimate_infections.R @@ -50,7 +50,6 @@ #' @return A list of output including: posterior samples, summarised posterior #' samples, data used to fit the model, and the fit object itself. #' -#' @author Sam Abbott #' @seealso [epinow()] [regional_epinow()] [forecast_infections()] #' [estimate_truncation()] #' @inheritParams create_stan_args @@ -312,7 +311,6 @@ estimate_infections <- function(reported_cases, #' @inheritParams fit_model_with_nuts #' @inheritParams stan_opts #' @return A stanfit object -#' @author Sam Abbott init_cumulative_fit <- function(args, samples = 50, warmup = 50, id = "init", verbose = FALSE, backend = "rstan") { @@ -389,7 +387,6 @@ init_cumulative_fit <- function(args, samples = 50, warmup = 50, #' @importFrom rstan sflist2stanfit sampling #' @importFrom rlang abort cnd_muffle #' @return A stan model object -#' @author Sam Abbott fit_model_with_nuts <- function(args, future = FALSE, max_execution_time = Inf, id = "stan") { args$method <- NULL @@ -528,7 +525,6 @@ fit_model_with_nuts <- function(args, future = FALSE, max_execution_time = Inf, #' @importFrom rstan vb #' @importFrom rlang abort #' @return A stan model object -#' @author Sam Abbott fit_model_with_vb <- function(args, future = FALSE, id = "stan") { args$method <- NULL futile.logger::flog.debug( @@ -612,7 +608,6 @@ fit_model_with_vb <- function(args, future = FALSE, id = "stan") { #' @importFrom lubridate days #' @importFrom futile.logger flog.info #' @return A list of samples and summarised posterior parameter estimates. -#' @author Sam Abbott format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date, CrIs) { format_out <- list() diff --git a/R/estimate_secondary.R b/R/estimate_secondary.R index 285ceb2a8..c47ba4c1a 100644 --- a/R/estimate_secondary.R +++ b/R/estimate_secondary.R @@ -57,7 +57,6 @@ #' estimated secondary observations), `posterior` which contains a summary of #' the entire model posterior, `data` (a list of data used to fit the #' model), and `fit` (the `stanfit` object). -#' @author Sam Abbott #' @export #' @inheritParams estimate_infections #' @inheritParams update_secondary_args @@ -252,7 +251,6 @@ estimate_secondary <- function(reports, #' variables: `variable`, `mean`, and `sd`. #' #' @return A list as produced by `create_stan_data()`. -#' @author Sam Abbott #' @export #' @inheritParams create_stan_args #' @importFrom data.table as.data.table @@ -319,7 +317,6 @@ update_secondary_args <- function(data, priors, verbose = TRUE) { #' #' @return A `ggplot` object. #' -#' @author Sam Abbott #' @seealso plot estimate_secondary #' @method plot estimate_secondary #' @importFrom ggplot2 ggplot aes geom_col geom_point labs scale_x_date @@ -395,8 +392,6 @@ plot.estimate_secondary <- function(x, primary = FALSE, #' @return A `` containing simulated data in the format required by #' [estimate_secondary()]. #' -#' @author Sam Abbott -#' @author Sebastian Funk #' @seealso estimate_secondary #' @inheritParams secondary_opts #' @importFrom data.table as.data.table copy shift @@ -530,7 +525,6 @@ simulate_secondary <- function(data, type = "incidence", family = "poisson", #' of forecast secondary observation posterior samples, and `forecast` a summary #' of the forecast secondary observation posterior. #' -#' @author Sam Abbott #' @importFrom rstan extract sampling #' @importFrom data.table rbindlist merge.data.table as.data.table setorderv #' @importFrom data.table setcolorder copy diff --git a/R/estimate_truncation.R b/R/estimate_truncation.R index d228e438f..d6b50db94 100644 --- a/R/estimate_truncation.R +++ b/R/estimate_truncation.R @@ -66,8 +66,6 @@ #' observed data (`last_obs`, useful for plotting and validation), the data #' used for fitting (`data`) and the fit object (`fit`). #' -#' @author Sam Abbott -#' @author Sebastian Funk #' @export #' @inheritParams calc_CrIs #' @inheritParams estimate_infections @@ -320,7 +318,6 @@ estimate_truncation <- function(obs, max_truncation, trunc_max = 10, #' @param ... Pass additional arguments to plot function. Not currently in use. #' #' @return `ggplot2` object -#' @author Sam Abbott #' @seealso plot estimate_truncation #' @method plot estimate_truncation #' @importFrom ggplot2 ggplot aes geom_col geom_point labs scale_x_date diff --git a/R/extract.R b/R/extract.R index ae2e18e0f..c0e9abce5 100644 --- a/R/extract.R +++ b/R/extract.R @@ -13,7 +13,6 @@ #' #' @return A `` containing the parameter name, date, sample id and #' sample value. -#' @author Sam Abbott #' @importFrom data.table melt as.data.table extract_parameter <- function(param, samples, dates) { param_df <- data.table::as.data.table( @@ -44,7 +43,6 @@ extract_parameter <- function(param, samples, dates) { #' @inheritParams extract_parameter #' @return A `` containing the parameter name, sample id and sample #' value -#' @author Sam Abbott extract_static_parameter <- function(param, samples) { data.table::data.table( parameter = param, @@ -144,7 +142,6 @@ extract_samples <- function(stan_fit, pars = NULL, include = TRUE) { #' @inheritParams extract_samples #' @return A list of ``'s each containing the posterior of a #' parameter -#' @author Sam Abbott #' @importFrom rstan extract #' @importFrom data.table data.table extract_parameter_samples <- function(stan_fit, data, reported_dates, @@ -275,7 +272,6 @@ extract_parameter_samples <- function(stan_fit, data, reported_dates, #' `lower_`, `upper_` followed by credible interval labels indicating the #' credible intervals present. #' -#' @author Sam Abbott #' @inheritParams calc_summary_measures #' @export #' @importFrom posterior mcse_mean @@ -350,7 +346,6 @@ extract_stan_param <- function(fit, params = NULL, #' @return A function that when called returns a set of initial conditions as a #' named list. #' -#' @author Sam Abbott #' @importFrom purrr map #' @importFrom rstan extract #' @importFrom utils modifyList diff --git a/R/get.R b/R/get.R index 6eab29738..583878a6b 100644 --- a/R/get.R +++ b/R/get.R @@ -6,7 +6,6 @@ #' are stored (as produced by [regional_epinow()]). #' #' @return A named character vector containing the results to plot. -#' @author Sam Abbott #' @export get_regions <- function(results_dir) { # regions to include - based on folder names @@ -35,7 +34,6 @@ get_regions <- function(results_dir) { #' directory. #' #' @return An R object read in from the targeted `.rds` file -#' @author Sam Abbott #' @export get_raw_result <- function(file, region, date, result_dir) { @@ -65,7 +63,6 @@ get_raw_result <- function(file, region, date, #' returned. #' #' @return A list of estimates, forecasts and estimated cases by date of report. -#' @author Sam Abbott #' @export #' @importFrom purrr map safely #' @importFrom data.table rbindlist @@ -176,7 +173,6 @@ get_regional_results <- function(regional_output, #' #' @return A list defining a distribution #' -#' @author Sam Abbott #' @seealso [dist_spec()] #' @export get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) { @@ -207,7 +203,6 @@ get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) { #' @inherit get_dist #' @export #' @seealso [dist_spec()] -#' @author Sam Abbott get_generation_time <- function(disease, source, max_value = 14, fixed = FALSE) { lifecycle::deprecate_warn( @@ -234,7 +229,6 @@ get_generation_time <- function(disease, source, max_value = 14, #' #' @inheritParams get_dist #' @inherit get_dist -#' @author Sam Abbott #' @export #' @seealso [dist_spec()] get_incubation_period <- function(disease, source, max_value = 14, @@ -268,7 +262,6 @@ get_incubation_period <- function(disease, source, max_value = 14, #' #' @return A character vector of regions with the highest reported cases #' -#' @author Sam Abbott #' @importFrom data.table copy setorderv #' @importFrom lubridate days #' @export @@ -299,7 +292,6 @@ get_regions_with_most_reports <- function(reported_cases, ##' @param delays Delays as specified using [dist_spec()] ##' @param generation_time Generation time as specified using [dist_spec()] ##' @return An integer seeding time -##' @author Sebastian Funk get_seeding_time <- function(delays, generation_time) { # Estimate the mean delay ----------------------------------------------- seeding_time <- sum(mean(delays)) diff --git a/R/opts.R b/R/opts.R index bfa3c3556..624827372 100644 --- a/R/opts.R +++ b/R/opts.R @@ -17,8 +17,6 @@ #' [estimate_infections()] instead. #' @return A `` object summarising the input delay #' distributions. -#' @author Sebastian Funk -#' @author Sam Abbott #' @seealso [convert_to_logmean()] [convert_to_logsd()] #' [bootstrapped_dist_fit()] [dist_spec()] #' @export @@ -137,7 +135,6 @@ generation_time_opts <- function(dist = dist_spec(mean = 1), ..., #' additive or subtractive). #' #' @export -#' @author Sam Abbott #' @examples #' # incidence model #' secondary_opts("incidence") @@ -181,8 +178,6 @@ secondary_opts <- function(type = "incidence", ...) { #' @param ... deprecated; use `dist` instead #' @param fixed deprecated; use `dist` instead #' @return A `` object summarising the input delay distributions. -#' @author Sam Abbott -#' @author Sebastian Funk #' @seealso [convert_to_logmean()] [convert_to_logsd()] #' [bootstrapped_dist_fit()] [dist_spec()] #' @export @@ -248,8 +243,6 @@ delay_opts <- function(dist = dist_spec(), ..., fixed = FALSE) { #' @return A `` object summarising the input truncation #' distribution. #' -#' @author Sam Abbott -#' @author Sebastian Funk #' @seealso [convert_to_logmean()] [convert_to_logsd()] #' [bootstrapped_dist_fit()] [dist_spec()] #' @export @@ -319,7 +312,6 @@ trunc_opts <- function(dist = dist_spec()) { #' #' @return An `` object with settings defining the time-varying #' reproduction number. -#' @author Sam Abbott #' @inheritParams create_future_rt #' @importFrom rlang arg_match #' @export @@ -391,7 +383,6 @@ rt_opts <- function(prior = list(mean = 1, sd = 1), #' @importFrom rlang arg_match #' #' @return A `` object of back calculation settings. -#' @author Sam Abbott #' @export #' @examples #' # default settings @@ -457,7 +448,6 @@ backcalc_opts <- function(prior = "reports", prior_window = 14, rt_window = 1) { #' #' @importFrom rlang arg_match #' @return A `` object of settings defining the Gaussian process -#' @author Sam Abbott #' @export #' @examples #' # default settings @@ -532,7 +522,6 @@ gp_opts <- function(basis_prop = 0.2, #' be returned by the model. #' @importFrom rlang arg_match #' @return An `` object of observation model settings. -#' @author Sam Abbott #' @export #' @examples #' # default settings @@ -602,7 +591,6 @@ obs_opts <- function(family = "negbin", #' Deprecated; use [stan_sampling_opts()] instead. #' @inheritParams stan_sampling_opts #' @return A list of arguments to pass to [rstan::sampling()]. -#' @author Sam Abbott #' @export rstan_sampling_opts <- function(cores = getOption("mc.cores", 1L), warmup = 250, @@ -669,8 +657,6 @@ rstan_sampling_opts <- function(cores = getOption("mc.cores", 1L), #' @param ... Additional parameters to pass to [rstan::sampling()]. #' @importFrom utils modifyList #' @return A list of arguments to pass to [rstan::sampling()]. -#' @author Sam Abbott -#' @author Sebastian Funk #' @export #' @examples #' stan_sampling_opts(samples = 2000) @@ -728,7 +714,6 @@ stan_sampling_opts <- function(cores = getOption("mc.cores", 1L), #' Deprecated; use [stan_vb_opts()] instead. #' @inheritParams stan_vb_opts #' @return A list of arguments to pass to [rstan::vb()]. -#' @author Sam Abbott #' @export rstan_vb_opts <- function(samples = 2000, trials = 10, @@ -761,8 +746,6 @@ rstan_vb_opts <- function(samples = 2000, #' #' @return A list of arguments to pass to [rstan::vb()] or #' [cmdstanr::variational()], depending on the chosen backend. -#' @author Sam Abbott -#' @author Sebastian Funk #' @export #' @examples #' stan_vb_opts(samples = 1000) @@ -792,7 +775,6 @@ stan_vb_opts <- function(samples = 2000, #' @param ... Additional parameters to pass underlying option functions. #' @importFrom rlang arg_match #' @return A list of arguments to pass to the appropriate rstan functions. -#' @author Sam Abbott #' @export #' @inheritParams rstan_sampling_opts #' @seealso [rstan_sampling_opts()] [rstan_vb_opts()] @@ -869,8 +851,6 @@ rstan_opts <- function(object = NULL, #' @importFrom rlang arg_match #' @return A `` object of arguments to pass to the appropriate #' rstan functions. -#' @author Sam Abbott -#' @author Sebastian Funk #' @export #' @inheritParams rstan_opts #' @seealso [stan_sampling_opts()] [stan_vb_opts()] @@ -952,7 +932,6 @@ stan_opts <- function(object = NULL, #' #' @return A named list of options per region which can be passed to the `_opt` #' accepting arguments of `regional_epinow`. -#' @author Sam Abbott #' @seealso [regional_epinow()] [rt_opts()] #' @export #' @examples @@ -993,7 +972,6 @@ opts_list <- function(opts, reported_cases, ...) { #' @param region A character string indicating a region of interest. #' #' @return A list of options -#' @author Sam Abbott filter_opts <- function(opts, region) { if (region %in% names(opts)) { out <- opts[[region]] diff --git a/R/simulate_infections.R b/R/simulate_infections.R index b627b4c74..f8bcfcde6 100644 --- a/R/simulate_infections.R +++ b/R/simulate_infections.R @@ -33,7 +33,6 @@ #' @importFrom data.table data.table merge.data.table nafill rbindlist #' @return A data.table of simulated infections (variable `infections`) and #' reported cases (variable `reported_cases`) by date. -#' @author Sebastian Funk #' @export #' @examples #' \donttest{ diff --git a/R/stan.R b/R/stan.R index 86847ac69..9aecb9d3e 100644 --- a/R/stan.R +++ b/R/stan.R @@ -58,7 +58,6 @@ package_model <- function(model = "estimate_infections", ##' @inheritParams package_model ##' @return A stan model object (either \code{rstan::stanmodel} or ##' \code{cmdstanr::CmdStanModel}, depending on the backend) -##' @author Sebastian Funk ##' @importFrom rlang arg_match ##' @keywords internal stan_model <- function(backend = c("rstan", "cmdstanr"), diff --git a/inst/stan/functions/pmfs.stan b/inst/stan/functions/pmfs.stan index 03fbec1f5..103ef7b49 100644 --- a/inst/stan/functions/pmfs.stan +++ b/inst/stan/functions/pmfs.stan @@ -2,8 +2,7 @@ // distributions up to the maximum observed delay. // If sigma is 0 all the probability mass is put on n. // Adapted from https://github.com/epiforecasts/epinowcast -// @author Sam Abbott -// @author Adrian Lison +// (MIT License, copyright: epinowcast authors) vector discretised_pmf(real mu, real sigma, int n, int dist) { vector[n] lpmf; if (sigma > 0) { diff --git a/man/adjust_infection_to_report.Rd b/man/adjust_infection_to_report.Rd index cbfb34b19..6501c1dfb 100644 --- a/man/adjust_infection_to_report.Rd +++ b/man/adjust_infection_to_report.Rd @@ -100,6 +100,3 @@ report_stochastic <- adjust_infection_to_report( print(report_stochastic) } } -\author{ -Sam Abbott -} diff --git a/man/backcalc_opts.Rd b/man/backcalc_opts.Rd index 030e94580..81dc71c6b 100644 --- a/man/backcalc_opts.Rd +++ b/man/backcalc_opts.Rd @@ -41,6 +41,3 @@ of cases. Only used if \code{rt = NULL}. # default settings backcalc_opts() } -\author{ -Sam Abbott -} diff --git a/man/bootstrapped_dist_fit.Rd b/man/bootstrapped_dist_fit.Rd index 00a19ff9c..ed0f28e54 100644 --- a/man/bootstrapped_dist_fit.Rd +++ b/man/bootstrapped_dist_fit.Rd @@ -60,6 +60,3 @@ out <- bootstrapped_dist_fit(delays, out } } -\author{ -Sam Abbott -} diff --git a/man/c.dist_spec.Rd b/man/c.dist_spec.Rd index 728fecc9d..15bf25be1 100644 --- a/man/c.dist_spec.Rd +++ b/man/c.dist_spec.Rd @@ -16,6 +16,3 @@ Combined delay distributions (with class \verb{}) This combines the parameters so that they can be fed as multiple delay distributions to \code{\link[=epinow]{epinow()}} or \code{\link[=estimate_infections]{estimate_infections()}}. } -\author{ -Sebastian Funk -} diff --git a/man/check_reports_valid.Rd b/man/check_reports_valid.Rd index e87f74f24..271a4f722 100644 --- a/man/check_reports_valid.Rd +++ b/man/check_reports_valid.Rd @@ -28,7 +28,4 @@ and that it has the right column names and types. In particular, it checks that the date column is in date format and does not contain NA's, and that the other columns are numeric. } -\author{ -James M. Azam -} \keyword{internal} diff --git a/man/construct_output.Rd b/man/construct_output.Rd index 30ab3cc69..2700aa77d 100644 --- a/man/construct_output.Rd +++ b/man/construct_output.Rd @@ -31,6 +31,3 @@ A list of output as returned by \code{epinow} \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} Combines the output produced internally by \code{epinow} into a single list. } -\author{ -Sam Abbott -} diff --git a/man/copy_results_to_latest.Rd b/man/copy_results_to_latest.Rd index 08276f220..e9fb5d46b 100644 --- a/man/copy_results_to_latest.Rd +++ b/man/copy_results_to_latest.Rd @@ -21,6 +21,3 @@ No return value, called for side effects Copies output from the dated folder to a latest folder. May be undergo changes in later releases. } -\author{ -Sam Abbott -} diff --git a/man/create_backcalc_data.Rd b/man/create_backcalc_data.Rd index 7f5af3b4c..87190e25d 100644 --- a/man/create_backcalc_data.Rd +++ b/man/create_backcalc_data.Rd @@ -24,6 +24,3 @@ create_backcalc_data(backcalc = backcalc_opts()) \seealso{ backcalc_opts } -\author{ -Sam Abbott -} diff --git a/man/create_clean_reported_cases.Rd b/man/create_clean_reported_cases.Rd index 5daf45877..8188d2c4f 100644 --- a/man/create_clean_reported_cases.Rd +++ b/man/create_clean_reported_cases.Rd @@ -45,8 +45,3 @@ which point 0 cases are replaced with a user supplied value (defaults to \examples{ create_clean_reported_cases(example_confirmed, 7) } -\author{ -Sam Abbott - -Lloyd Chapman -} diff --git a/man/create_complete_cases.Rd b/man/create_complete_cases.Rd index 79eb108c6..9d98bfd11 100644 --- a/man/create_complete_cases.Rd +++ b/man/create_complete_cases.Rd @@ -19,7 +19,4 @@ A data frame without NA values, with two columns: confirm (number) \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} Creates a complete data set without NA values and appropriate indices } -\author{ -Sebastian Funk -} \keyword{internal} diff --git a/man/create_future_rt.Rd b/man/create_future_rt.Rd index 133df3d8e..17ebed01d 100644 --- a/man/create_future_rt.Rd +++ b/man/create_future_rt.Rd @@ -25,6 +25,3 @@ A list containing a logical called fixed and an integer called from Converts the \code{future} argument from \code{\link[=rt_opts]{rt_opts()}} into arguments that can be passed to stan. } -\author{ -Sam Abbott -} diff --git a/man/create_gp_data.Rd b/man/create_gp_data.Rd index 9d8807576..427fe693e 100644 --- a/man/create_gp_data.Rd +++ b/man/create_gp_data.Rd @@ -42,6 +42,3 @@ create_gp_data(gp_opts(ls_mean = 14), data) \seealso{ \code{\link[=gp_opts]{gp_opts()}} } -\author{ -Sam Abbott -} diff --git a/man/create_obs_model.Rd b/man/create_obs_model.Rd index 18190aa8a..6295cbcf4 100644 --- a/man/create_obs_model.Rd +++ b/man/create_obs_model.Rd @@ -40,6 +40,3 @@ create_obs_model(obs_opts(week_length = 3), dates = dates) \seealso{ \code{\link[=obs_opts]{obs_opts()}} } -\author{ -Sam Abbott -} diff --git a/man/create_rt_data.Rd b/man/create_rt_data.Rd index 35fce8dea..573b0aba6 100644 --- a/man/create_rt_data.Rd +++ b/man/create_rt_data.Rd @@ -39,6 +39,3 @@ create_rt_data(rt_opts(use_breakpoints = TRUE), breakpoints = rep(1, 10)) \seealso{ rt_settings } -\author{ -Sam Abbott -} diff --git a/man/create_shifted_cases.Rd b/man/create_shifted_cases.Rd index ffbfb3830..3b5ad54d7 100644 --- a/man/create_shifted_cases.Rd +++ b/man/create_shifted_cases.Rd @@ -33,6 +33,3 @@ calculation method (see \code{\link[=backcalc_opts]{backcalc_opts()}}) is based. \examples{ create_shifted_cases(example_confirmed, 7, 14, 7) } -\author{ -Sam Abbott -} diff --git a/man/create_stan_args.Rd b/man/create_stan_args.Rd index aff1b64a0..76c06a7f8 100644 --- a/man/create_stan_args.Rd +++ b/man/create_stan_args.Rd @@ -50,6 +50,3 @@ create_stan_args() # increasing warmup create_stan_args(stan = stan_opts(warmup = 1000)) } -\author{ -Sam Abbott -} diff --git a/man/create_stan_data.Rd b/man/create_stan_data.Rd index 9ec1a8e3d..b1a1e95e1 100644 --- a/man/create_stan_data.Rd +++ b/man/create_stan_data.Rd @@ -56,8 +56,3 @@ create_stan_data( backcalc_opts(), create_shifted_cases(example_confirmed, 7, 14, 7) ) } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/create_stan_delays.Rd b/man/create_stan_delays.Rd index 60defa3d6..79fc44e8f 100644 --- a/man/create_stan_delays.Rd +++ b/man/create_stan_delays.Rd @@ -18,6 +18,3 @@ A list of variables as expected by the stan model \description{ Create delay variables for stan } -\author{ -Sebastian Funk -} diff --git a/man/delay_opts.Rd b/man/delay_opts.Rd index 6f6973f58..02699c09c 100644 --- a/man/delay_opts.Rd +++ b/man/delay_opts.Rd @@ -41,8 +41,3 @@ delay_opts(delay + delay) \code{\link[=convert_to_logmean]{convert_to_logmean()}} \code{\link[=convert_to_logsd]{convert_to_logsd()}} \code{\link[=bootstrapped_dist_fit]{bootstrapped_dist_fit()}} \code{\link[=dist_spec]{dist_spec()}} } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/dist_fit.Rd b/man/dist_fit.Rd index a61b95e75..df32dfb4c 100644 --- a/man/dist_fit.Rd +++ b/man/dist_fit.Rd @@ -66,6 +66,3 @@ dist_fit(rlnorm(1:100, log(5), 0.2), ) } } -\author{ -Sam Abbott -} diff --git a/man/dist_skel.Rd b/man/dist_skel.Rd index 37d1aff83..7df4625cd 100644 --- a/man/dist_skel.Rd +++ b/man/dist_skel.Rd @@ -98,8 +98,3 @@ dist_skel(0:10, params = list(mean = log(5), sd = log(2)) ) } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/dist_spec.Rd b/man/dist_spec.Rd index 09ff18824..a853ba54b 100644 --- a/man/dist_spec.Rd +++ b/man/dist_spec.Rd @@ -91,8 +91,3 @@ dist_spec( distribution = "gamma" ) } -\author{ -Sebastian Funk - -Sam Abbott -} diff --git a/man/dist_spec_plus.Rd b/man/dist_spec_plus.Rd index d04f85078..0886a791c 100644 --- a/man/dist_spec_plus.Rd +++ b/man/dist_spec_plus.Rd @@ -31,8 +31,3 @@ that can be combined are processed together, and their cumulative distribution function is truncated at a specified tolerance level, ensuring numeric stability. } -\author{ -Sebastian Funk - -Sam Abbott -} diff --git a/man/epinow.Rd b/man/epinow.Rd index b19481e3a..fe7331332 100644 --- a/man/epinow.Rd +++ b/man/epinow.Rd @@ -178,6 +178,3 @@ options(old_opts) \seealso{ \code{\link[=estimate_infections]{estimate_infections()}} \code{\link[=forecast_infections]{forecast_infections()}} \code{\link[=regional_epinow]{regional_epinow()}} } -\author{ -Sam Abbott -} diff --git a/man/estimate_delay.Rd b/man/estimate_delay.Rd index cea324b92..2e29d2ddc 100644 --- a/man/estimate_delay.Rd +++ b/man/estimate_delay.Rd @@ -28,6 +28,3 @@ estimate_delay(delays, samples = 1000, bootstraps = 10) \seealso{ \code{\link[=bootstrapped_dist_fit]{bootstrapped_dist_fit()}} } -\author{ -Sam Abbott -} diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd index 156a733d2..ccf64fe71 100644 --- a/man/estimate_infections.Rd +++ b/man/estimate_infections.Rd @@ -162,6 +162,3 @@ options(old_opts) \code{\link[=epinow]{epinow()}} \code{\link[=regional_epinow]{regional_epinow()}} \code{\link[=forecast_infections]{forecast_infections()}} \code{\link[=estimate_truncation]{estimate_truncation()}} } -\author{ -Sam Abbott -} diff --git a/man/estimate_secondary.Rd b/man/estimate_secondary.Rd index 6bdc44b1a..43ee38215 100644 --- a/man/estimate_secondary.Rd +++ b/man/estimate_secondary.Rd @@ -162,6 +162,3 @@ plot(prev_preds, new_obs = cases, from = "2020-06-01") options(old_opts) } } -\author{ -Sam Abbott -} diff --git a/man/estimate_truncation.Rd b/man/estimate_truncation.Rd index 399d15f52..bc5f333f6 100644 --- a/man/estimate_truncation.Rd +++ b/man/estimate_truncation.Rd @@ -121,8 +121,3 @@ plot(est) options(old_opts) } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/estimates_by_report_date.Rd b/man/estimates_by_report_date.Rd index 2b230ba95..288c73b91 100644 --- a/man/estimates_by_report_date.Rd +++ b/man/estimates_by_report_date.Rd @@ -30,6 +30,3 @@ date of report. Either extracts or converts reported cases from an input data table. For output from \code{estimate_infections} this is a simple filtering step. } -\author{ -Sam Abbott -} diff --git a/man/extract_inits.Rd b/man/extract_inits.Rd index f03f7dc1e..fd5e22d09 100644 --- a/man/extract_inits.Rd +++ b/man/extract_inits.Rd @@ -34,6 +34,3 @@ This implementation is based on the approach taken in \href{https://github.com/ImperialCollegeLondon/epidemia/}{epidemia} authored by James Scott. } -\author{ -Sam Abbott -} diff --git a/man/extract_parameter.Rd b/man/extract_parameter.Rd index ddfd9ddbf..e17227f9d 100644 --- a/man/extract_parameter.Rd +++ b/man/extract_parameter.Rd @@ -23,6 +23,3 @@ sample value. Extracts a single from a list of stan output and returns it as a \verb{}. } -\author{ -Sam Abbott -} diff --git a/man/extract_parameter_samples.Rd b/man/extract_parameter_samples.Rd index 808da3670..e657732c4 100644 --- a/man/extract_parameter_samples.Rd +++ b/man/extract_parameter_samples.Rd @@ -39,6 +39,3 @@ parameter Extracts a custom set of parameters from a stan object and adds stratification and dates where appropriate. } -\author{ -Sam Abbott -} diff --git a/man/extract_stan_param.Rd b/man/extract_stan_param.Rd index a5beed183..9cf9c7b9c 100644 --- a/man/extract_stan_param.Rd +++ b/man/extract_stan_param.Rd @@ -34,6 +34,3 @@ Extracts summarised parameter posteriors from a \code{stanfit} object using \code{rstan::summary()} in a format consistent with other summary functions in \code{{EpiNow2}}. } -\author{ -Sam Abbott -} diff --git a/man/extract_static_parameter.Rd b/man/extract_static_parameter.Rd index f0a4c0a5c..b99b6a934 100644 --- a/man/extract_static_parameter.Rd +++ b/man/extract_static_parameter.Rd @@ -18,6 +18,3 @@ value \description{ Extract Samples from a Parameter with a Single Dimension } -\author{ -Sam Abbott -} diff --git a/man/filter_opts.Rd b/man/filter_opts.Rd index a663296f5..d91b96dfb 100644 --- a/man/filter_opts.Rd +++ b/man/filter_opts.Rd @@ -20,6 +20,3 @@ A list of options A helper function that allows the selection of region specific settings if present and otherwise applies the overarching settings. } -\author{ -Sam Abbott -} diff --git a/man/fit_model_with_nuts.Rd b/man/fit_model_with_nuts.Rd index 93b50bd09..e57b492f9 100644 --- a/man/fit_model_with_nuts.Rd +++ b/man/fit_model_with_nuts.Rd @@ -34,6 +34,3 @@ Fits a stan model using \code{\link[rstan:stanmodel-method-sampling]{rstan::samp run chains using \code{future} with error catching, timeouts and merging of completed chains. } -\author{ -Sam Abbott -} diff --git a/man/fit_model_with_vb.Rd b/man/fit_model_with_vb.Rd index 2c3897d3b..262b2b435 100644 --- a/man/fit_model_with_vb.Rd +++ b/man/fit_model_with_vb.Rd @@ -23,6 +23,3 @@ A stan model object \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#maturing}{\figure{lifecycle-maturing.svg}{options: alt='[Maturing]'}}}{\strong{[Maturing]}} Fits a stan model using variational inference. } -\author{ -Sam Abbott -} diff --git a/man/fix_dist.Rd b/man/fix_dist.Rd index 565d59d8e..52846c51c 100644 --- a/man/fix_dist.Rd +++ b/man/fix_dist.Rd @@ -20,6 +20,3 @@ A \verb{} object without uncertainty If the given \verb{} has any uncertainty, it is removed and the corresponding distribution converted into a fixed one. } -\author{ -Sebastian Funk -} diff --git a/man/forecast_secondary.Rd b/man/forecast_secondary.Rd index affbd86f0..14e199892 100644 --- a/man/forecast_secondary.Rd +++ b/man/forecast_secondary.Rd @@ -68,6 +68,3 @@ for an example of forecasting Covid-19 deaths from Covid-19 cases. \seealso{ \code{\link[=estimate_secondary]{estimate_secondary()}} } -\author{ -Sam Abbott -} diff --git a/man/format_fit.Rd b/man/format_fit.Rd index cd4263ae5..cb222e6c6 100644 --- a/man/format_fit.Rd +++ b/man/format_fit.Rd @@ -27,6 +27,3 @@ A list of samples and summarised posterior parameter estimates. \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} Summaries posterior samples and adds additional custom variables. } -\author{ -Sam Abbott -} diff --git a/man/gamma_dist_def.Rd b/man/gamma_dist_def.Rd index 7fa2af023..7ef135149 100644 --- a/man/gamma_dist_def.Rd +++ b/man/gamma_dist_def.Rd @@ -67,6 +67,3 @@ def <- gamma_dist_def( print(def) def$params[[1]] } -\author{ -Sam Abbott -} diff --git a/man/generation_time_opts.Rd b/man/generation_time_opts.Rd index 1b14e2885..7f3bdf647 100644 --- a/man/generation_time_opts.Rd +++ b/man/generation_time_opts.Rd @@ -60,8 +60,3 @@ generation_time_opts(example_generation_time) \code{\link[=convert_to_logmean]{convert_to_logmean()}} \code{\link[=convert_to_logsd]{convert_to_logsd()}} \code{\link[=bootstrapped_dist_fit]{bootstrapped_dist_fit()}} \code{\link[=dist_spec]{dist_spec()}} } -\author{ -Sebastian Funk - -Sam Abbott -} diff --git a/man/get_dist.Rd b/man/get_dist.Rd index fb00282f9..029ec46ea 100644 --- a/man/get_dist.Rd +++ b/man/get_dist.Rd @@ -30,6 +30,3 @@ using \code{\link[=dist_spec]{dist_spec()}} instead. \seealso{ \code{\link[=dist_spec]{dist_spec()}} } -\author{ -Sam Abbott -} diff --git a/man/get_generation_time.Rd b/man/get_generation_time.Rd index cff27d564..b1fa3293f 100644 --- a/man/get_generation_time.Rd +++ b/man/get_generation_time.Rd @@ -29,6 +29,3 @@ using \code{\link[=dist_spec]{dist_spec()}} instead. \seealso{ \code{\link[=dist_spec]{dist_spec()}} } -\author{ -Sam Abbott -} diff --git a/man/get_incubation_period.Rd b/man/get_incubation_period.Rd index 56897967f..b514a02c1 100644 --- a/man/get_incubation_period.Rd +++ b/man/get_incubation_period.Rd @@ -29,6 +29,3 @@ using \code{\link[=dist_spec]{dist_spec()}} instead \seealso{ \code{\link[=dist_spec]{dist_spec()}} } -\author{ -Sam Abbott -} diff --git a/man/get_raw_result.Rd b/man/get_raw_result.Rd index ce925261d..e14fdf660 100644 --- a/man/get_raw_result.Rd +++ b/man/get_raw_result.Rd @@ -22,6 +22,3 @@ An R object read in from the targeted \code{.rds} file \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} } -\author{ -Sam Abbott -} diff --git a/man/get_regional_results.Rd b/man/get_regional_results.Rd index d3b4a4d0b..40b71489b 100644 --- a/man/get_regional_results.Rd +++ b/man/get_regional_results.Rd @@ -45,6 +45,3 @@ regional_out <- readRDS(system.file( # from output results <- get_regional_results(regional_out$regional, samples = FALSE) } -\author{ -Sam Abbott -} diff --git a/man/get_regions.Rd b/man/get_regions.Rd index 56f6d55b6..abb8d811f 100644 --- a/man/get_regions.Rd +++ b/man/get_regions.Rd @@ -16,6 +16,3 @@ A named character vector containing the results to plot. \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} } -\author{ -Sam Abbott -} diff --git a/man/get_regions_with_most_reports.Rd b/man/get_regions_with_most_reports.Rd index 85a791fde..5b7fa827f 100644 --- a/man/get_regions_with_most_reports.Rd +++ b/man/get_regions_with_most_reports.Rd @@ -23,6 +23,3 @@ A character vector of regions with the highest reported cases Extract a vector of regions with the most reported cases in a set time window. } -\author{ -Sam Abbott -} diff --git a/man/get_seeding_time.Rd b/man/get_seeding_time.Rd index 16cdc814b..4a0058995 100644 --- a/man/get_seeding_time.Rd +++ b/man/get_seeding_time.Rd @@ -18,6 +18,3 @@ An integer seeding time The seeding time is set to the mean of the specified delays, constrained to be at least the maximum generation time } -\author{ -Sebastian Funk -} diff --git a/man/gp_opts.Rd b/man/gp_opts.Rd index cec05a340..ded91e9f3 100644 --- a/man/gp_opts.Rd +++ b/man/gp_opts.Rd @@ -69,6 +69,3 @@ gp_opts() # add a custom length scale gp_opts(ls_mean = 4) } -\author{ -Sam Abbott -} diff --git a/man/init_cumulative_fit.Rd b/man/init_cumulative_fit.Rd index e57623c46..b9ececde4 100644 --- a/man/init_cumulative_fit.Rd +++ b/man/init_cumulative_fit.Rd @@ -47,6 +47,3 @@ This implementation is based on the approach taken in \href{https://github.com/ImperialCollegeLondon/epidemia/}{epidemia} authored by James Scott. } -\author{ -Sam Abbott -} diff --git a/man/lognorm_dist_def.Rd b/man/lognorm_dist_def.Rd index 56e3aa4a2..766b40834 100644 --- a/man/lognorm_dist_def.Rd +++ b/man/lognorm_dist_def.Rd @@ -49,6 +49,3 @@ def <- lognorm_dist_def( print(def) def$params[[1]] } -\author{ -Sam Abbott -} diff --git a/man/mean.dist_spec.Rd b/man/mean.dist_spec.Rd index af1a9ce4e..0cf374ce8 100644 --- a/man/mean.dist_spec.Rd +++ b/man/mean.dist_spec.Rd @@ -35,6 +35,3 @@ mean(gamma) # The mean of the sum of two distributions mean(lognormal + gamma) } -\author{ -Sebastian Funk -} diff --git a/man/obs_opts.Rd b/man/obs_opts.Rd index c49c8bb2e..2910d2cdd 100644 --- a/man/obs_opts.Rd +++ b/man/obs_opts.Rd @@ -76,6 +76,3 @@ obs_opts(week_effect = TRUE) # Scale reported data obs_opts(scale = list(mean = 0.2, sd = 0.02)) } -\author{ -Sam Abbott -} diff --git a/man/opts_list.Rd b/man/opts_list.Rd index 2c6884e8a..05b4c2177 100644 --- a/man/opts_list.Rd +++ b/man/opts_list.Rd @@ -49,6 +49,3 @@ rt \seealso{ \code{\link[=regional_epinow]{regional_epinow()}} \code{\link[=rt_opts]{rt_opts()}} } -\author{ -Sam Abbott -} diff --git a/man/plot.dist_spec.Rd b/man/plot.dist_spec.Rd index c7eeef97e..cda878a99 100644 --- a/man/plot.dist_spec.Rd +++ b/man/plot.dist_spec.Rd @@ -36,6 +36,3 @@ plot(lognormal + gamma + lognormal) # A combination of the two fixed distributions plot(lognormal + lognormal) } -\author{ -Sam Abbott -} diff --git a/man/plot.estimate_secondary.Rd b/man/plot.estimate_secondary.Rd index 4cc93e6c5..946203bc9 100644 --- a/man/plot.estimate_secondary.Rd +++ b/man/plot.estimate_secondary.Rd @@ -32,6 +32,3 @@ A \code{ggplot} object. \seealso{ plot estimate_secondary } -\author{ -Sam Abbott -} diff --git a/man/plot.estimate_truncation.Rd b/man/plot.estimate_truncation.Rd index 1b7bdf404..e16d37256 100644 --- a/man/plot.estimate_truncation.Rd +++ b/man/plot.estimate_truncation.Rd @@ -24,6 +24,3 @@ as dots and the truncation adjusted estimates as a ribbon. \seealso{ plot estimate_truncation } -\author{ -Sam Abbott -} diff --git a/man/plus-.dist_spec.Rd b/man/plus-.dist_spec.Rd index c917d175e..962da9708 100644 --- a/man/plus-.dist_spec.Rd +++ b/man/plus-.dist_spec.Rd @@ -40,6 +40,3 @@ lognormal + gamma # Using tolerance parameter EpiNow2:::dist_spec_plus(lognormal, lognormal, tolerance = 0.5) } -\author{ -Sebastian Funk -} diff --git a/man/print.dist_spec.Rd b/man/print.dist_spec.Rd index ef8c10487..c2e6a294e 100644 --- a/man/print.dist_spec.Rd +++ b/man/print.dist_spec.Rd @@ -32,6 +32,3 @@ gamma <- dist_spec( ) print(gamma) } -\author{ -Sebastian Funk -} diff --git a/man/rstan_opts.Rd b/man/rstan_opts.Rd index b60a77645..297c2723a 100644 --- a/man/rstan_opts.Rd +++ b/man/rstan_opts.Rd @@ -28,6 +28,3 @@ Deprecated; specify options in \code{\link[=stan_opts]{stan_opts()}} instead. \seealso{ \code{\link[=rstan_sampling_opts]{rstan_sampling_opts()}} \code{\link[=rstan_vb_opts]{rstan_vb_opts()}} } -\author{ -Sam Abbott -} diff --git a/man/rstan_sampling_opts.Rd b/man/rstan_sampling_opts.Rd index 7d1c92465..567e134a2 100644 --- a/man/rstan_sampling_opts.Rd +++ b/man/rstan_sampling_opts.Rd @@ -60,6 +60,3 @@ A list of arguments to pass to \code{\link[rstan:stanmodel-method-sampling]{rsta \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Deprecated; use \code{\link[=stan_sampling_opts]{stan_sampling_opts()}} instead. } -\author{ -Sam Abbott -} diff --git a/man/rstan_vb_opts.Rd b/man/rstan_vb_opts.Rd index 7f353928a..0ffec4c2a 100644 --- a/man/rstan_vb_opts.Rd +++ b/man/rstan_vb_opts.Rd @@ -26,6 +26,3 @@ A list of arguments to pass to \code{\link[rstan:stanmodel-method-vb]{rstan::vb( \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Deprecated; use \code{\link[=stan_vb_opts]{stan_vb_opts()}} instead. } -\author{ -Sam Abbott -} diff --git a/man/rt_opts.Rd b/man/rt_opts.Rd index 7e828d572..d8842e0d8 100644 --- a/man/rt_opts.Rd +++ b/man/rt_opts.Rd @@ -74,6 +74,3 @@ rt_opts(prior = list(mean = 2, sd = 1)) # add a weekly random walk rt_opts(rw = 7) } -\author{ -Sam Abbott -} diff --git a/man/save_estimate_infections.Rd b/man/save_estimate_infections.Rd index 79c5ccb8e..91cc68bc5 100644 --- a/man/save_estimate_infections.Rd +++ b/man/save_estimate_infections.Rd @@ -32,6 +32,3 @@ Saves output from \code{estimate_infections} to a target directory. \seealso{ estimate_infections } -\author{ -Sam Abbott -} diff --git a/man/save_input.Rd b/man/save_input.Rd index 1b6adf692..61f4bae95 100644 --- a/man/save_input.Rd +++ b/man/save_input.Rd @@ -20,6 +20,3 @@ No return value, called for side effects \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} Saves observed data to a target location if given. } -\author{ -Sam Abbott -} diff --git a/man/secondary_opts.Rd b/man/secondary_opts.Rd index 6d41ea516..63cf5eb64 100644 --- a/man/secondary_opts.Rd +++ b/man/secondary_opts.Rd @@ -53,6 +53,3 @@ secondary_opts("prevalence") \seealso{ \code{\link[=estimate_secondary]{estimate_secondary()}} } -\author{ -Sam Abbott -} diff --git a/man/simulate_infections.Rd b/man/simulate_infections.Rd index 0f6b6ab12..a78d859fe 100644 --- a/man/simulate_infections.Rd +++ b/man/simulate_infections.Rd @@ -98,6 +98,3 @@ option will be removed in version 2.1.0. ) } } -\author{ -Sebastian Funk -} diff --git a/man/simulate_secondary.Rd b/man/simulate_secondary.Rd index f926807d7..d7edb9304 100644 --- a/man/simulate_secondary.Rd +++ b/man/simulate_secondary.Rd @@ -84,8 +84,3 @@ cases \seealso{ estimate_secondary } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/stan_model.Rd b/man/stan_model.Rd index edd371a96..49eea5fc5 100644 --- a/man/stan_model.Rd +++ b/man/stan_model.Rd @@ -25,7 +25,4 @@ A stan model object (either \code{rstan::stanmodel} or \description{ Return a stan model object for the appropriate backend } -\author{ -Sebastian Funk -} \keyword{internal} diff --git a/man/stan_opts.Rd b/man/stan_opts.Rd index f911c089f..daaa4ae23 100644 --- a/man/stan_opts.Rd +++ b/man/stan_opts.Rd @@ -73,8 +73,3 @@ stan_opts(method = "vb") \seealso{ \code{\link[=stan_sampling_opts]{stan_sampling_opts()}} \code{\link[=stan_vb_opts]{stan_vb_opts()}} } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/stan_sampling_opts.Rd b/man/stan_sampling_opts.Rd index d67c6e0b3..767695df5 100644 --- a/man/stan_sampling_opts.Rd +++ b/man/stan_sampling_opts.Rd @@ -69,8 +69,3 @@ defaults. \examples{ stan_sampling_opts(samples = 2000) } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/stan_vb_opts.Rd b/man/stan_vb_opts.Rd index cb4936929..197d8c592 100644 --- a/man/stan_vb_opts.Rd +++ b/man/stan_vb_opts.Rd @@ -32,8 +32,3 @@ defaults. \examples{ stan_vb_opts(samples = 1000) } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/trunc_opts.Rd b/man/trunc_opts.Rd index a449cede4..871980a91 100644 --- a/man/trunc_opts.Rd +++ b/man/trunc_opts.Rd @@ -32,8 +32,3 @@ trunc_opts(dist = dist_spec(mean = 3, sd = 2, max = 10)) \code{\link[=convert_to_logmean]{convert_to_logmean()}} \code{\link[=convert_to_logsd]{convert_to_logsd()}} \code{\link[=bootstrapped_dist_fit]{bootstrapped_dist_fit()}} \code{\link[=dist_spec]{dist_spec()}} } -\author{ -Sam Abbott - -Sebastian Funk -} diff --git a/man/update_horizon.Rd b/man/update_horizon.Rd index c34538fd5..e45a555a2 100644 --- a/man/update_horizon.Rd +++ b/man/update_horizon.Rd @@ -24,6 +24,3 @@ Numeric forecast horizon adjusted for the users intention Makes sure that a forecast is returned for the user specified time period beyond the target date. } -\author{ -Sam Abbott -} diff --git a/man/update_secondary_args.Rd b/man/update_secondary_args.Rd index 14c4344ba..fa2b7c2ee 100644 --- a/man/update_secondary_args.Rd +++ b/man/update_secondary_args.Rd @@ -35,6 +35,3 @@ priors <- data.frame(variable = "frac_obs", mean = 3, sd = 1) data <- list(obs_scale_mean = 4, obs_scale_sd = 3) update_secondary_args(data, priors) } -\author{ -Sam Abbott -}