remove author tags [ci skip]

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

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

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 `<data.frame>` 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

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 `<data.table>` 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 `<dist_spec>` 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 `<dist_spec>` 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 `<dist_spec>`)
-#' @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 `<dist_spec>` 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 `<dist_spec>` 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 `<dist_spec>` has any uncertainty, it is removed and the
 ##' corresponding distribution converted into a fixed one.
 ##' @return A `<dist_spec>` object without uncertainty
-##' @author Sebastian Funk
 ##' @export
 ##' @param x A `<dist_spec>` object
 ##' @param strategy Character; either "mean" (use the mean estimates of the

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,

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

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()

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 `<data.frame>` 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

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