diff --git a/R/deprecated.R b/R/deprecated.R
index 06f47257e..25f9a3ad3 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -26,158 +26,19 @@
 #' @inheritParams sample_approx_dist
 #' @importFrom data.table setorder data.table data.table
 #' @importFrom lubridate wday
-#' @examples
-#' \donttest{
-#' # This function is deprecated and its functionality can now be accessed
-#' # from [simulate_secondary()].
-#' # Here are some examples of how to use [simulate_secondary()] to replace
-#' # adjust_infection_to_report().
-#'
-#' # Old (using adjust_infection_to_report()):
-#' # Define example case data
-#' cases <- data.table::copy(example_confirmed)
-#' cases <- cases[, cases := as.integer(confirm)]
-#' # Define a simple reporting delay distribution
-#' delay_def <- lognorm_dist_def(
-#'  mean = 5, mean_sd = 1, sd = 3, sd_sd = 1,
-#'  max_value = 30, samples = 1, to_log = TRUE
-#' )
-#' report <- adjust_infection_to_report(
-#'  cases,
-#'  delay_defs = list(delay_def),
-#'  reporting_model = function(n) rpois(length(n), n)
-#' )
-#' print(report)
-#'
-#' # New (using simulate_secondary()):
-#' cases <- data.table::copy(example_confirmed)
-#' cases <- cases[, primary := as.integer(confirm)]
-#' uncertain_delay <- LogNormal(
-#'  mean = Normal(5, 1), sd = Normal(3, 1),
-#'  max = 30
-#' )
-#' delay <- fix_dist(uncertain_delay, strategy = "sample")
-#' report <- simulate_secondary(
-#'  cases,
-#'  delays = delay_opts(delay),
-#'  obs = obs_opts(family = "poisson")
-#' )
-#' print(report)
-#' }
 adjust_infection_to_report <- function(infections, delay_defs,
                                        reporting_model, reporting_effect,
                                        type = "sample",
                                        truncate_future = TRUE) {
-  deprecate_warn(
+  deprecate_stop(
     when = "1.5.0",
     what = "adjust_infection_to_report()",
     with = "simulate_secondary()",
     details = c(
       "See equivalent examples using `simulate_secondary()`",
-      "in ?adjust_infection_to_report.",
-      "This function will be removed completely in the next version."
+      "in ?adjust_infection_to_report."
     )
   )
-  # Reset DT Defaults on Exit
-  set_dt_single_thread()
-
-  ## deprecated
-  sample_single_dist <- function(input, delay_def) {
-    ## Define sample delay fn
-    sample_delay_fn <- function(n, ...) {
-      EpiNow2::dist_skel(
-        n = n,
-        model = delay_def$model[[1]],
-        params = delay_def$params[[1]],
-        max_value = delay_def$max_value[[1]],
-        ...
-      )
-    }
-
-
-    ## Infection to onset
-    out <- suppressWarnings(EpiNow2::sample_approx_dist(
-      cases = input,
-      dist_fn = sample_delay_fn,
-      max_value = delay_def$max_value,
-      direction = "forwards",
-      type = type,
-      truncate_future = FALSE
-    ))
-
-    return(out)
-  }
-
-  sample_dist_spec <- function(input, delay_def) {
-    ## Define sample delay fn
-    sample_delay_fn <- function(n, dist, cum, ...) {
-      fixed_dist <- discretise(fix_dist(delay_def, strategy = "sample"))
-      if (dist) {
-        fixed_dist[[1]]$pmf[n + 1]
-      } else {
-        sample(seq_along(fixed_dist[[1]]$pmf) - 1, size = n, replace = TRUE)
-      }
-    }
-
-    ## Infection to onset
-    out <- suppressWarnings(EpiNow2::sample_approx_dist(
-      cases = input,
-      dist_fn = sample_delay_fn,
-      max_value = max(delay_def),
-      direction = "forwards",
-      type = type,
-      truncate_future = FALSE
-    ))
-
-    return(out)
-  }
-
-  if (is(delay_defs, "dist_spec")) {
-    report <- sample_dist_spec(infections, extract_single_dist(delay_defs, 1))
-    if (length(delay_defs) > 1) {
-      for (def in seq(2, length(delay_defs))) {
-        report <- sample_dist_spec(report, extract_single_dist(delay_defs, def))
-      }
-    }
-  } else {
-    deprecate_warn(
-      "1.5.0",
-      "adjust_infection_to_report(delay_defs = 'should be a dist_spec')",
-      details = "Specifying this as a list of data tables is deprecated."
-    )
-    report <- sample_single_dist(infections, delay_defs[[1]])
-    if (length(delay_defs) > 1) {
-      for (def in 2:length(delay_defs)) {
-        report <- sample_single_dist(report, delay_defs[[def]])
-      }
-    }
-  }
-  ## Add a weekly reporting effect if present
-  if (!missing(reporting_effect)) {
-    reporting_effect <- data.table::data.table(
-      day = 1:7,
-      effect = reporting_effect
-    )
-
-    report <- report[, day := lubridate::wday(date, week_start = 1)]
-    report <- report[reporting_effect, on = "day"]
-    report <- report[, cases := as.integer(cases * effect)][
-      ,
-      `:=`(effect = NULL, day = NULL)
-    ]
-
-    report <- data.table::setorder(report, date)
-  }
-
-  if (!missing(reporting_model)) {
-    report <- report[, cases := reporting_model(cases)]
-  }
-
-  ## Truncate reported cases by maximum infection date
-  if (type == "sample" && truncate_future) {
-    report <- report[date <= max(infections$date)]
-  }
-  return(report)
 }
 
 #' Specify a distribution.
@@ -202,14 +63,6 @@ adjust_infection_to_report <- function(infections, delay_defs,
 #' @param max Numeric, maximum value of the distribution. The distribution will
 #' be truncated at this value. Default: `Inf`, i.e. no maximum.
 #'
-#' @param mean Deprecated; use `params_mean` instead.
-#'
-#' @param sd Deprecated; use `params_mean` instead.
-#'
-#' @param mean_sd Deprecated; use `params_sd` instead.
-#'
-#' @param sd_sd Deprecated; use `params_sd` instead.
-#'
 #' @param pmf Numeric, a vector of values that represent the (nonparametric)
 #' probability mass function of the delay (starting with 0); defaults to an
 #' empty vector corresponding to a parametric specification of the distribution
@@ -223,87 +76,18 @@ dist_spec <- function(distribution = c(
                         "lognormal", "normal", "gamma", "fixed", "empty"
                       ),
                       params_mean = numeric(0), params_sd = numeric(0),
-                      mean, sd = 0, mean_sd = 0, sd_sd = 0,
                       max = Inf, pmf = numeric(0), fixed = FALSE) {
 
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     "1.5.0",
     "dist_spec()",
     details = c(
       paste0(
         "Please use distribution functions such as `Gamma()` or `Lognormal()` ",
         "instead."
-      ),
-      "The function will become internal only in the next version."
+      )
     )
   )
-  ## check for deprecated parameters
-  if (!missing(fixed)) {
-    lifecycle::deprecate_warn(
-      "1.5.0",
-      "dist_spec(fixed)",
-      "fix_dist()"
-    )
-    params_sd <- NULL
-  }
-  ## check for deprecated parameters
-  if (!all(missing(mean), missing(sd), missing(mean_sd), missing(sd_sd)) &&
-      (length(params_mean) > 0 || length(params_sd) > 0)) {
-    stop("Distributional parameters should not be given as `mean`, `sd`, etc. ",
-         "in addition to `params_mean` or `params_sd`")
-  }
-  distribution <- match.arg(distribution)
-  ## check if distribution is given as empty and warn about deprecation if so
-  if (distribution == "empty") {
-    deprecate_warn(
-      "1.5.0",
-      "dist_spec(distribution = 'must not be \"empty\"')",
-      details = "Please use `Fixed(0)` instead."
-    )
-  }
-
-  if (!all(missing(mean), missing(sd), missing(mean_sd), missing(sd_sd))) {
-    if (sd == 0 && mean_sd == 0 && sd_sd == 0) {
-      distribution <- "fixed"
-    }
-    ## deprecated arguments given
-    if (distribution == "lognormal") {
-      params_mean <- c(meanlog = mean, sdlog = sd)
-      params_sd <- c(meanlog = mean_sd, sdlog = sd_sd)
-    } else if (distribution == "gamma") {
-      temp_dist <- Gamma(
-        mean = Normal(mean, mean_sd),
-        sd = Normal(sd, sd_sd)
-      )
-      params_mean <- vapply(get_parameters(temp_dist), mean, numeric(1))
-      params_sd <- vapply(get_parameters(temp_dist), sd_dist, numeric(1))
-    } else if (distribution == "normal") {
-      params_mean <- c(mean = mean, sd = sd)
-      params_sd <- c(mean = mean_sd, sd = sd_sd)
-    } else if (distribution == "fixed") {
-      params_mean <- mean
-    }
-  }
-  if (length(pmf) > 0) {
-    if (!all(
-      missing(mean), missing(sd), missing(mean_sd), missing(sd_sd),
-      missing(params_mean), missing(params_sd)
-    )) {
-      stop("Distributional parameters should not be given in addition to `pmf`")
-    }
-    distribution <- "nonparametric"
-    parameters <- list(pmf = pmf)
-  } else {
-    if (length(params_sd) == 0) {
-      params_sd <- rep(0, length(params_mean))
-    }
-    parameters <- lapply(seq_along(params_mean), function(id) {
-      Normal(params_mean[id], params_sd[id])
-    })
-    names(parameters) <- natural_params(distribution)
-    parameters$max <- max
-  }
-  return(new_dist_spec(parameters, distribution))
 }
 
 #' Generate a Gamma Distribution Definition Based on Parameter Estimates
@@ -327,71 +111,14 @@ dist_spec <- function(distribution = c(
 #' @export
 #' @inheritParams dist_skel
 #' @inheritParams lognorm_dist_def
-#' @examples
-#' # using estimated shape and scale
-#' def <- gamma_dist_def(
-#'   shape = 5.807, shape_sd = 0.2,
-#'   scale = 0.9, scale_sd = 0.05,
-#'   max_value = 20, samples = 10
-#' )
-#' print(def)
-#' def$params[[1]]
-#'
-#' # using mean and sd
-#' def <- gamma_dist_def(
-#'   mean = 3, mean_sd = 0.5,
-#'   sd = 3, sd_sd = 0.1,
-#'   max_value = 20, samples = 10
-#' )
-#' print(def)
-#' def$params[[1]]
 gamma_dist_def <- function(shape, shape_sd,
                            scale, scale_sd,
                            mean, mean_sd,
                            sd, sd_sd,
                            max_value, samples) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "gamma_dist_def()", "Gamma()",
-    "The function will be removed completely in the next version."
-  )
-
-  if (missing(shape) && missing(scale) && !missing(mean) && !missing(sd)) {
-    if (!missing(mean_sd)) {
-      mean <- truncnorm::rtruncnorm(samples, a = 0, mean = mean, sd = mean_sd)
-    }
-    if (!missing(sd_sd)) {
-      sd <- truncnorm::rtruncnorm(samples, a = 0, mean = sd, sd = sd_sd)
-    }
-    scale <- sd^2 / mean
-    shape <- mean / scale
-  } else {
-    if (!missing(shape_sd)) {
-      shape <- truncnorm::rtruncnorm(
-        samples,
-        a = 0, mean = shape, sd = shape_sd
-      )
-    }
-    if (!missing(scale_sd)) {
-      scale <- 1 / truncnorm::rtruncnorm(
-        samples,
-        a = 0, mean = scale, sd = scale_sd
-      )
-    }
-  }
-
-  rate <- 1 / scale
-
-  dist <- data.table::data.table(
-    model = rep("gamma", samples),
-    params = purrr::list_transpose(
-      list(
-        shape = shape,
-        rate = rate
-      )
-    ),
-    max_value = rep(max_value, samples)
+  lifecycle::deprecate_stop(
+    "1.5.0", "gamma_dist_def()", "Gamma()"
   )
-  return(dist)
 }
 
 #' Generate initial conditions by fitting to cumulative cases
@@ -427,50 +154,10 @@ gamma_dist_def <- function(shape, shape_sd,
 init_cumulative_fit <- function(args, samples = 50, warmup = 50,
                                 id = "init", verbose = FALSE,
                                 backend = "rstan") {
-  deprecate_warn(
+  deprecate_stop(
     when = "1.5.0",
     what = "init_cumulative_fit()"
   )
-  futile.logger::flog.debug(
-    "%s: Fitting to cumulative data to initialise chains", id,
-    name = "EpiNow2.epinow.estimate_infections.fit"
-  )
-  # copy main run settings and override to use only 100 iterations and a single
-  # chain
-  initial_args <- create_stan_args(
-    stan = stan_opts(
-      args$object,
-      samples = samples,
-      warmup = warmup,
-      control = list(adapt_delta = 0.9, max_treedepth = 13),
-      chains = 1,
-      cores = 2,
-      backend = backend,
-      open_progress = FALSE,
-      show_messages = FALSE
-    ),
-    data = args$data, init = args$init
-  )
-  # change observations to be cumulative in order to protect against noise and
-  # give an approximate fit (though for Rt constrained to be > 1)
-  initial_args$data$cases <- cumsum(initial_args$data$cases)
-  initial_args$data$shifted_cases <- cumsum(initial_args$data$shifted_cases)
-
-  # initial fit
-  if (verbose) {
-    fit <- fit_model(initial_args, id = "init_cumulative")
-  } else {
-    out <- tempfile(tmpdir = tempdir(check = TRUE))
-    capture.output(
-      {
-        fit <- fit_model(initial_args, id = "init_cumulative")
-      },
-      type = c("output", "message"),
-      split = FALSE,
-      file = out
-    )
-  }
-  return(fit)
 }
 
 #' Generate a Log Normal Distribution Definition Based on Parameter Estimates
@@ -497,75 +184,13 @@ init_cumulative_fit <- function(args, samples = 50, warmup = 50,
 #' @export
 #' @keywords internal
 #' @inheritParams dist_skel
-#' @examples
-#' def <- lognorm_dist_def(
-#'   mean = 1.621, mean_sd = 0.0640,
-#'   sd = 0.418, sd_sd = 0.0691,
-#'   max_value = 20, samples = 10
-#' )
-#' print(def)
-#' def$params[[1]]
-#'
-#' def <- lognorm_dist_def(
-#'   mean = 5, mean_sd = 1,
-#'   sd = 3, sd_sd = 1,
-#'   max_value = 20, samples = 10,
-#'   to_log = TRUE
-#' )
-#' print(def)
-#' def$params[[1]]
 lognorm_dist_def <- function(mean, mean_sd,
                              sd, sd_sd,
                              max_value, samples,
                              to_log = FALSE) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "lognorm_dist_def()", "LogNormal()",
-    "The function will be removed completely in the next version."
+  lifecycle::deprecate_stop(
+    "1.5.0", "lognorm_dist_def()", "LogNormal()"
   )
-
-  transform_mean <- function(mu, sig) {
-    mean_location <- log(mu^2 / sqrt(sig^2 + mu^2))
-    mean_location
-  }
-
-  transform_sd <- function(mu, sig) {
-    mean_shape <- sqrt(log(1 + (sig^2 / mu^2)))
-    mean_shape
-  }
-
-  if (missing(mean_sd)) {
-    sampled_means <- mean
-  } else {
-    sampled_means <- truncnorm::rtruncnorm(
-      samples,
-      a = 0, mean = mean, sd = mean_sd
-    )
-  }
-
-  if (missing(sd_sd)) {
-    sampled_sds <- sd
-  } else {
-    sampled_sds <- truncnorm::rtruncnorm(samples, a = 0, mean = sd, sd = sd_sd)
-  }
-  means <- sampled_means
-  sds <- sampled_sds
-
-  if (to_log) {
-    means <- mapply(transform_mean, sampled_means, sampled_sds)
-    sds <- mapply(transform_sd, sampled_means, sampled_sds)
-  }
-
-  dist <- data.table::data.table(
-    model = rep("lognormal", samples),
-    params = purrr::list_transpose(
-      list(
-        meanlog = means,
-        sdlog = sds
-      )
-    ),
-    max_value = rep(max_value, samples)
-  )
-  return(dist)
 }
 
 #' Report case counts by date of report
@@ -598,110 +223,27 @@ lognorm_dist_def <- function(mean, mean_sd,
 #' @inheritParams adjust_infection_to_report
 #' @importFrom data.table data.table rbindlist
 #' @importFrom future.apply future_lapply
-#' @examples
-#' \donttest{
-#' # This function is deprecated and its functionality can now be accessed
-#' # from [simulate_secondary()].
-#' # Here are some examples of how to use [simulate_secondary()] to replace
-#' # report_cases().
-#' # Old (using report_cases()):
-#' # Define case data
-#' cases <- example_confirmed[1:40]
-#' cases <- cases[, cases := as.integer(confirm)]
-#' cases <- cases[, confirm := NULL][, sample := 1]
-#' reported_cases <- report_cases(
-#'  case_estimates = cases,
-#'  delays = delay_opts(example_incubation_period + example_reporting_delay),
-#'  type = "sample"
-#' )
-#' print(reported_cases$samples)
-#'
-#' # New (using simulate_secondary()):
-#' cases <- example_confirmed[1:40]
-#' cases <- cases[, primary := as.integer(confirm)]
-#' report <- simulate_secondary(
-#'  cases,
-#'  delays = delay_opts(
-#'    fix_dist(example_incubation_period + example_reporting_delay)
-#'  ),
-#'  obs = obs_opts(family = "poisson")
-#' )
-#' print(report)
-#' }
 report_cases <- function(case_estimates,
                          case_forecast = NULL,
                          delays,
                          type = "sample",
                          reporting_effect,
                          CrIs = c(0.2, 0.5, 0.9)) {
-  deprecate_warn(
+  deprecate_stop(
     when = "1.5.0",
     what = "report_cases()",
     with = "simulate_secondary()",
     details = c(
       "See equivalent examples using `simulate_secondary()`",
-      "in ?report_cases.",
-      "This function will be removed completely in the next version."
-    )
-  )
-  samples <- length(unique(case_estimates$sample))
-
-  # add a null reporting effect if missing
-  if (missing(reporting_effect)) {
-    reporting_effect <- data.table::data.table(
-      sample = list(1:samples),
-      effect = rep(1, 7),
-      day = 1:7
+      "in ?report_cases."
     )
-    reporting_effect <- reporting_effect[,
-      .(sample = unlist(sample)), by = .(effect, day)
-    ]
-  }
-  # filter and sum nowcast to use only upscaled cases by date of infection
-  infections <- data.table::copy(case_estimates)
-
-  # add in case forecast if present
-  if (!is.null(case_forecast)) {
-    infections <- data.table::rbindlist(list(
-      infections,
-      case_forecast[, .(date, sample, cases = as.integer(cases))]
-    ), use.names = TRUE)
-  }
-
-  ## For each sample map to report date
-  report <- future.apply::future_lapply(1:max(infections$sample),
-    function(id) {
-      suppressWarnings(
-        EpiNow2::adjust_infection_to_report(infections[sample == id],
-          delay_defs = delays,
-          type = type,
-          reporting_effect = reporting_effect[sample == id, ]$effect
-        )
-      )
-    },
-    future.seed = TRUE
   )
-
-  report <- data.table::rbindlist(report, idcol = "sample")
-
-  out <- list()
-  # bind all samples together
-  out$samples <- report
-  # summarise samples
-  out$summarised <- calc_summary_measures(
-    report[, value := cases][, cases := NULL],
-    summarise_by = "date",
-    order_by = "date",
-    CrIs = CrIs
-  )
-  return(out)
 }
 
 #' Approximate Sampling a Distribution using Counts
 #'
 #' @description `r lifecycle::badge("deprecated")`
-#' Convolves cases by a PMF function. This function will soon be removed or
-#' replaced with a more robust stan implementation.
+#' Deprecated; Convolves cases by a PMF function.
 #'
 #' @param cases A `<data.frame>` of cases (in date order) with the following
 #' variables: `date` and `cases`.
@@ -732,60 +274,6 @@ report_cases <- function(case_estimates,
 #' @importFrom purrr map_dfc
 #' @importFrom data.table data.table setorder
 #' @importFrom lubridate days
-#' @examples
-#' \donttest{
-#' cases <- example_confirmed
-#' cases <- cases[, cases := as.integer(confirm)]
-#' print(cases)
-#'
-#' # total cases
-#' sum(cases$cases)
-#'
-#' delay_fn <- function(n, dist, cum) {
-#'   if (dist) {
-#'     pgamma(n + 0.9999, 2, 1) - pgamma(n - 1e-5, 2, 1)
-#'   } else {
-#'     as.integer(rgamma(n, 2, 1))
-#'   }
-#' }
-#'
-#' onsets <- sample_approx_dist(
-#'   cases = cases,
-#'   dist_fn = delay_fn
-#' )
-#'
-#' # estimated onset distribution
-#' print(onsets)
-#'
-#' # check that sum is equal to reported cases
-#' total_onsets <- median(
-#'   purrr::map_dbl(
-#'     1:10,
-#'     ~ sum(sample_approx_dist(
-#'       cases = cases,
-#'       dist_fn = delay_fn
-#'     )$cases)
-#'   )
-#' )
-#' total_onsets
-#'
-#'
-#' # map from onset cases to reported
-#' reports <- sample_approx_dist(
-#'   cases = cases,
-#'   dist_fn = delay_fn,
-#'   direction = "forwards"
-#' )
-#'
-#'
-#' # map from onset cases to reported using a mean shift
-#' reports <- sample_approx_dist(
-#'   cases = cases,
-#'   dist_fn = delay_fn,
-#'   direction = "forwards",
-#'   type = "median"
-#' )
-#' }
 sample_approx_dist <- function(cases = NULL,
                                dist_fn = NULL,
                                max_value = 120,
@@ -793,97 +281,168 @@ sample_approx_dist <- function(cases = NULL,
                                direction = "backwards",
                                type = "sample",
                                truncate_future = TRUE) {
-  deprecate_warn(
+  deprecate_stop(
     "1.5.0",
-    "sample_approx_dist()",
-    details = "The function will be removed completely in the next version."
+    "sample_approx_dist()"
   )
-  if (type == "sample") {
-    if (direction == "backwards") {
-      direction_fn <- rev
-    } else if (direction == "forwards") {
-      direction_fn <- function(x) {
-        x
-      }
-    }
-    # reverse cases so starts with current first
-    reversed_cases <- direction_fn(cases$cases)
-    reversed_cases[is.na(reversed_cases)] <- 0
-    # draw from the density fn of the dist
-    draw <- dist_fn(0:max_value, dist = TRUE, cum = FALSE)
+}
 
-    # approximate cases
-    mapped_cases <- do.call(cbind, purrr::map(
-      seq_along(reversed_cases),
-      ~ c(
-        rep(0, . - 1),
-        stats::rbinom(
-          length(draw),
-          rep(reversed_cases[.], length(draw)),
-          draw
-        ),
-        rep(0, length(reversed_cases) - .)
+#' Get a Literature Distribution
+#'
+#'
+#' @description `r lifecycle::badge("deprecated")`
+#'
+#' This function has been deprecated. Please specify a distribution
+#' using functions such as [Gamma()] or [LogNormal()] instead.
+#'
+#' @param data A `<data.table>` in the format of `generation_times`.
+#'
+#' @param disease A character string indicating the disease of interest.
+#'
+#' @param source A character string indicating the source of interest.
+#'
+#' @param max_value Numeric, the maximum value to allow. Defaults to 14 days.
+#'
+#' @param fixed Logical, defaults to `FALSE`. Should distributions be supplied
+#' as fixed values (vs with uncertainty)?
+#'
+#' @return A list defining a distribution
+#'
+#' @seealso [dist_spec()]
+#' @export
+#' @keywords internal
+get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) {
+  lifecycle::deprecate_stop(
+    "1.5.0", "get_dist()",
+    details = c(
+      paste(
+        "Please use distribution functions such as `Gamma()` or `Lognormal()`",
+        "instead."
       )
-    ))
-
+    )
+  )
+}
 
-    # set dates order based on direction mapping
-    if (direction == "backwards") {
-      dates <- seq(min(cases$date) - lubridate::days(length(draw) - 1),
-        max(cases$date),
-        by = "days"
-      )
-    } else if (direction == "forwards") {
-      dates <- seq(min(cases$date),
-        max(cases$date) + lubridate::days(length(draw) - 1),
-        by = "days"
+#' Get a Literature Distribution for the Generation Time
+#'
+#' @description `r lifecycle::badge("deprecated")`
+#'
+#' Extracts a literature distribution from `generation_times`.
+#' This function has been deprecated. Please specify a distribution
+#' using functions such as [Gamma()] or [LogNormal()] instead.
+#'
+#' @inheritParams get_dist
+#' @inherit get_dist
+#' @export
+#' @seealso [dist_spec()]
+#' @keywords internal
+get_generation_time <- function(disease, source, max_value = 14,
+                                fixed = FALSE) {
+  lifecycle::deprecate_stop(
+    "1.5.0", "get_generation_time()",
+    details = c(
+      paste(
+        "Please use distribution functions such as `Gamma()` or `Lognormal()`",
+        "instead."
+      ),
+      paste(
+        "To obtain the previous estimate by Ganyani et al. (2020) use",
+        "`example_generation_time`."
       )
-    }
-
-    # summarises movements and sample for placement of non-integer cases
-    case_sum <- direction_fn(rowSums(mapped_cases))
-    floor_case_sum <- floor(case_sum)
-    sample_cases <- floor_case_sum +
-      as.numeric((runif(seq_along(case_sum)) < (case_sum - floor_case_sum)))
-
-    # summarise imputed onsets and build output data.table
-    mapped_cases <- data.table::data.table(
-      date = dates,
-      cases = sample_cases
     )
+  )
+}
 
-    # filter out all zero cases until first recorded case
-    mapped_cases <- data.table::setorder(mapped_cases, date)
-    mapped_cases <- mapped_cases[
-      ,
-      cum_cases := cumsum(cases)
-    ][cum_cases != 0][, cum_cases := NULL]
-  } else if (type == "median") {
-    shift <- as.integer(
-      median(as.integer(dist_fn(1000, dist = FALSE)), na.rm = TRUE)
+#'  Get a Literature Distribution for the Incubation Period
+#'
+#' @description `r lifecycle::badge("deprecated")`
+#'
+#' Extracts a literature distribution from `generation_times`.
+#' This function has been deprecated. Please specify a distribution
+#' using functions such as [Gamma()] or [LogNormal()] instead.
+#'
+#' @inheritParams get_dist
+#' @inherit get_dist
+#' @export
+#' @keywords internal
+get_incubation_period <- function(disease, source, max_value = 14,
+                                  fixed = FALSE) {
+  lifecycle::deprecate_stop(
+    "1.5.0", "get_incubation_period()",
+    details = c(
+      paste(
+        "Please use distribution functions such as `Gamma()` or `Lognormal()`",
+        "instead."
+      ),
+     paste(
+      "To obtain the previous estimate by Ganyani et al. (2020) use",
+      "`example_incubation_period`."
+     )
     )
+  )
+}
 
-    if (direction == "backwards") {
-      mapped_cases <- data.table::copy(cases)[
-        ,
-        date := date - lubridate::days(shift)
-      ]
-    } else if (direction == "forwards") {
-      mapped_cases <- data.table::copy(cases)[
-        ,
-        date := date + lubridate::days(shift)
-      ]
-    }
-  }
+#' Rstan Sampling Options
+#'
+#' @description `r lifecycle::badge("deprecated")`
+#' Deprecated; use [stan_sampling_opts()] instead.
+#' @inheritParams stan_sampling_opts
+#' @return A list of arguments to pass to [rstan::sampling()].
+#' @export
+rstan_sampling_opts <- function(cores = getOption("mc.cores", 1L),
+                                warmup = 250,
+                                samples = 2000,
+                                chains = 4,
+                                control = list(),
+                                save_warmup = FALSE,
+                                seed = as.integer(runif(1, 1, 1e8)),
+                                future = FALSE,
+                                max_execution_time = Inf,
+                                ...) {
+  lifecycle::deprecate_stop(
+    "1.5.0", "rstan_sampling_opts()",
+    "stan_sampling_opts()"
+  )
+}
 
-  if (!is.null(earliest_allowed_mapped)) {
-    mapped_cases <- mapped_cases[date >= as.Date(earliest_allowed_mapped)]
-  }
+#' Rstan Variational Bayes Options
+#'
+#' @description `r lifecycle::badge("deprecated")`
+#' Deprecated; use [stan_vb_opts()] instead.
+#' @inheritParams stan_vb_opts
+#' @return A list of arguments to pass to [rstan::vb()].
+#' @export
+rstan_vb_opts <- function(samples = 2000,
+                          trials = 10,
+                          iter = 10000, ...) {
+  lifecycle::deprecate_stop(
+    "1.5.0", "rstan_vb_opts()",
+    "stan_vb_opts()"
+  )
+}
 
-  # filter out future cases
-  if (direction == "forwards" && truncate_future) {
-    max_date <- max(cases$date)
-    mapped_cases <- mapped_cases[date <= max_date]
-  }
-  return(mapped_cases)
+#' Rstan Options
+#'
+#' @description `r lifecycle::badge("deprecated")`
+#' Deprecated; specify options in [stan_opts()] instead.
+#'
+#' @param object Stan model object. By default uses the compiled package
+#' default.
+#'
+#' @param method A character string, defaulting to sampling. Currently supports
+#' [rstan::sampling()] ("sampling") or [rstan::vb()].
+#'
+#' @param ... Additional parameters to pass  underlying option functions.
+#' @importFrom rlang arg_match
+#' @return A list of arguments to pass to the appropriate rstan functions.
+#' @export
+#' @inheritParams rstan_sampling_opts
+#' @seealso [rstan_sampling_opts()] [rstan_vb_opts()]
+rstan_opts <- function(object = NULL,
+                       samples = 2000,
+                       method = c("sampling", "vb"), ...) {
+  lifecycle::deprecate_stop(
+    "1.5.0", "rstan_opts()",
+    "stan_opts()"
+  )
 }
diff --git a/R/dist_spec.R b/R/dist_spec.R
index 08513d18f..48f717257 100644
--- a/R/dist_spec.R
+++ b/R/dist_spec.R
@@ -185,10 +185,10 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #'
 #' @description `r lifecycle::badge("experimental")`
 #' @return A delay distribution representing the sum of the two delays
-#' @param e1 The first delay distribution (of type [dist_spec()]) to
+#' @param e1 The first delay distribution (of type <dist_spec>) to
 #' combine.
 #'
-#' @param e2 The second delay distribution (of type [dist_spec()]) to
+#' @param e2 The second delay distribution (of type <dist_spec>) to
 #' combine.
 #' @method + dist_spec
 #' @export
@@ -214,7 +214,7 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #' This combines the parameters so that they can be fed as multiple delay
 #' distributions to [epinow()] or [estimate_infections()].
 #'
-#' @param ... The delay distributions (from calls to [dist_spec()]) to combine
+#' @param ... The delay distributions to combine
 #' @return Combined delay distributions (with class `<dist_spec>`)
 #' @method c dist_spec
 #' @export
@@ -248,7 +248,7 @@ c.dist_spec <- function(...) {
 #'
 #' @description `r lifecycle::badge("experimental")`
 #' This works out the mean of all the (parametric / nonparametric) delay
-#' distributions combined in the passed [dist_spec()] (ignoring any uncertainty
+#' distributions combined in the passed <dist_spec> (ignoring any uncertainty
 #' in parameters)
 #'
 #' @param x The `<dist_spec>` to use
@@ -312,9 +312,9 @@ mean.dist_spec <- function(x, ..., ignore_uncertainty = FALSE) {
 #'
 #' @description `r lifecycle::badge("experimental")`
 #' This works out the standard deviation of all the (parametric /
-#' nonparametric) delay distributions combined in the passed [dist_spec()].
+#' nonparametric) delay distributions combined in the passed <dist_spec>.
 #'
-#' @param x The [dist_spec()] to use
+#' @param x The <dist_spec> to use
 #' @return A vector of standard deviations.
 #' @importFrom utils head
 #' @keywords internal
@@ -370,10 +370,10 @@ sd_dist <- function(x) {
 #'
 #' @description `r lifecycle::badge("experimental")`
 #' This works out the maximum of all the (parametric / nonparametric) delay
-#' distributions combined in the passed [dist_spec()] (ignoring any uncertainty
+#' distributions combined in the passed <dist_spec> (ignoring any uncertainty
 #' in parameters)
 #'
-#' @param x The [dist_spec()] to use
+#' @param x The <dist_spec> to use
 #' @param ... Not used
 #' @return A vector of means.
 #' @method max dist_spec
@@ -554,7 +554,7 @@ apply_tolerance <- function(x, tolerance) {
 #'
 #' @description `r lifecycle::badge("experimental")`
 #' This displays the parameters of the uncertain and probability mass
-#' functions of fixed delay distributions combined in the passed [dist_spec()].
+#' functions of fixed delay distributions combined in the passed <dist_spec>.
 #' @param x The `<dist_spec>` to use
 #' @param ... Not used
 #' @return invisible
@@ -1186,7 +1186,7 @@ get_pmf <- function(x, id = NULL) {
   return(x[[id]]$pmf)
 }
 
-##' Get the distribution of a [dist_spec()]
+##' Get the distribution of a <dist_spec>
 ##'
 ##' @inheritParams get_dist_spec_id
 ##' @description `r lifecycle::badge("experimental")`
diff --git a/R/epinow.R b/R/epinow.R
index 906c1f803..c4b239423 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -63,7 +63,7 @@
 #'
 #' # estimate Rt and nowcast/forecast cases by date of infection
 #' out <- epinow(
-#'   reported_cases = reported_cases,
+#'   data = reported_cases,
 #'   generation_time = generation_time_opts(generation_time),
 #'   rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
 #'   delays = delay_opts(incubation_period + reporting_delay)
@@ -98,20 +98,12 @@ epinow <- function(data,
                    target_folder = NULL, target_date,
                    logs = tempdir(), id = "epinow", verbose = interactive(),
                    reported_cases) {
-  # Warning for deprecated arguments
   if (!missing(reported_cases)) {
-    if (!missing(data)) {
-      stop("Can't have `reported_cases` and `data` arguments. ",
-           "Use `data` instead."
-      )
-    }
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "1.5.0",
       "epinow(reported_cases)",
-      "epinow(data)",
-      "The argument will be removed completely in the next version."
+      "epinow(data)"
     )
-    data <- reported_cases
   }
   # Check inputs
   assert_logical(return_output)
diff --git a/R/estimate_delay.R b/R/estimate_delay.R
index e45e1c53b..5b076efd0 100644
--- a/R/estimate_delay.R
+++ b/R/estimate_delay.R
@@ -183,16 +183,13 @@ bootstrapped_dist_fit <- function(values, dist = "lognormal",
 
     fit <- EpiNow2::dist_fit(values, samples = samples, dist = dist)
 
-
     out <- list()
     if (dist == "lognormal") {
-      out$mean_samples <- sample(extract(fit)$mu, samples)
-      out$sd_samples <- sample(extract(fit)$sigma, samples)
+      out$meanlog <- sample(extract(fit)$mu, samples)
+      out$sdlog <- sample(extract(fit)$sigma, samples)
     } else if (dist == "gamma") {
-      alpha_samples <- sample(extract(fit)$alpha, samples)
-      beta_samples <- sample(extract(fit)$beta, samples)
-      out$mean_samples <- alpha_samples / beta_samples
-      out$sd_samples <- sqrt(alpha_samples) / beta_samples
+      out$shape <- sample(extract(fit)$alpha, samples)
+      out$rate <- sample(extract(fit)$beta, samples)
     }
     return(out)
   }
@@ -224,17 +221,16 @@ bootstrapped_dist_fit <- function(values, dist = "lognormal",
     dist_samples <- purrr::map(dist_samples, unlist)
   }
 
-  out <- list()
-  out$mean <- mean(dist_samples$mean_samples)
-  out$mean_sd <- sd(dist_samples$mean_samples)
-  out$sd <- mean(dist_samples$sd_sample)
-  out$sd_sd <- sd(dist_samples$sd_samples)
+  params <- lapply(dist_samples, function(x) {
+    Normal(mean = mean(x), sd = sd(x))
+  })
+
   if (!missing(max_value)) {
-    out$max <- max_value
+    params$max <- max_value
   } else {
-    out$max <- max(values)
+    params$max <- max(values)
   }
-  return(do.call(dist_spec, out))
+  return(new_dist_spec(params = params, distribution = dist))
 }
 
 #' Estimate a Delay Distribution
diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index b5e9f6f6d..11bced120 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -129,18 +129,11 @@ estimate_infections <- function(data,
                                 reported_cases) {
   # Deprecate reported_cases in favour of data
   if (!missing(reported_cases)) {
-     if (!missing(data)) {
-      stop("Can't have `reported_cases` and `data` arguments. ",
-           "Use `data` instead."
-      )
-     }
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "1.5.0",
       "estimate_infections(reported_cases)",
-      "estimate_infections(data)",
-      "The argument will be removed completely in the next version."
+      "estimate_infections(data)"
     )
-    data <- reported_cases
   }
   # Validate inputs
   check_reports_valid(data, model = "estimate_infections")
diff --git a/R/estimate_secondary.R b/R/estimate_secondary.R
index e3eeb1e5b..adf5488d0 100644
--- a/R/estimate_secondary.R
+++ b/R/estimate_secondary.R
@@ -159,16 +159,11 @@ estimate_secondary <- function(data,
                                reports) {
   # Deprecate reported_cases in favour of data
   if (!missing(reports)) {
-     if (!missing(data)) {
-      stop("Can't have `reported` and `data` arguments. Use `data` instead.")
-    }
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "1.5.0",
       "estimate_secondary(reports)",
-      "estimate_secondary(data)",
-      "The argument will be removed completely in the next version."
+      "estimate_secondary(data)"
     )
-    data <- reports
   }
   # Validate the inputs
   check_reports_valid(data, model = "estimate_secondary")
diff --git a/R/estimate_truncation.R b/R/estimate_truncation.R
index 55fd8271c..e15fe38ca 100644
--- a/R/estimate_truncation.R
+++ b/R/estimate_truncation.R
@@ -42,12 +42,6 @@
 #'
 #' @param obs Deprecated; use `data` instead.
 #'
-#' @param max_truncation Deprecated; use `truncation` instead.
-#'
-#' @param trunc_max Deprecated; use `truncation` instead.
-#'
-#' @param trunc_dist Deprecated; use `truncation` instead.
-#'
 #' @param model A compiled stan model to override the default model. May be
 #' useful for package developers or those developing extensions.
 #'
@@ -111,8 +105,7 @@
 #' plot(out)
 #' options(old_opts)
 #' }
-estimate_truncation <- function(data, max_truncation, trunc_max = 10,
-                                trunc_dist = "lognormal",
+estimate_truncation <- function(data,
                                 truncation = trunc_opts(
                                   LogNormal(
                                     meanlog = Normal(0, 1),
@@ -131,16 +124,11 @@ estimate_truncation <- function(data, max_truncation, trunc_max = 10,
                                 obs) {
 
   if (!missing(obs)) {
-     if (!missing(data)) {
-      stop("Can't have `obs` and `data` arguments. Use `data` instead.")
-    }
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "1.5.0",
       "estimate_truncation(obs)",
-      "estimate_truncation(data)",
-      "The argument will be removed completely in the next version."
+      "estimate_truncation(data)"
     )
-    data <- obs
   }
   if (!is.null(model)) {
     lifecycle::deprecate_stop(
@@ -150,11 +138,10 @@ estimate_truncation <- function(data, max_truncation, trunc_max = 10,
     )
   }
   if (!missing(weigh_delay_priors)) {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "1.5.0",
       "estimate_truncation(weigh_delay_priors)",
-      "trunc_opts(weight_prior)",
-      detail = "This argument will be removed completely in the next version"
+      "trunc_opts(weight_prior)"
     )
   }
    # Validate inputs
@@ -167,68 +154,6 @@ estimate_truncation <- function(data, max_truncation, trunc_max = 10,
   assert_logical(weigh_delay_priors)
   assert_logical(verbose)
 
-  ## code block to remove in next EpiNow2 version
-  construct_trunc <- FALSE
-  if (!missing(trunc_max)) {
-    if (!missing(truncation)) {
-      stop(
-        "`trunc_max` and `truncation` arguments are both given. ",
-        "Use only `truncation` instead.")
-    }
-    if (!missing(max_truncation)) {
-      stop(
-        "`max_truncation` and `trunc_max` arguments are both given. ",
-        "Use only `truncation` instead.")
-    }
-    deprecate_stop(
-      "1.4.0",
-      "estimate_truncation(trunc_max)",
-      "estimate_truncation(truncation)"
-    )
-    construct_trunc <- TRUE
-  }
-  if (!missing(max_truncation)) {
-    if (!missing(truncation)) {
-      stop(
-        "`max_truncation` and `truncation` arguments are both given. ",
-        "Use only `truncation` instead.")
-    }
-    deprecate_stop(
-      "1.4.0",
-      "estimate_truncation(max_truncation)",
-      "estimate_truncation(truncation)"
-    )
-    trunc_max <- max_truncation
-    construct_trunc <- TRUE
-  }
-  if (!missing(trunc_dist)) {
-    trunc_dist <- arg_match(trunc_dist)
-    if (!missing(truncation)) {
-      stop(
-        "`trunc_dist` and `truncation` arguments are both given. ",
-        "Use only `truncation` instead.")
-    }
-    deprecate_stop(
-      "1.4.0",
-      "estimate_truncation(trunc_dist)",
-      "estimate_truncation(truncation)"
-    )
-    construct_trunc <- TRUE
-  }
-  if (construct_trunc) {
-    params_mean <- c(0, 1)
-    params_sd <- c(1, 1)
-    parameters <- lapply(seq_along(params_mean), function(id) {
-      Normal(params_mean, params_sd)
-    })
-    names(parameters) <- natural_params(trunc_dist)
-    parameters$max <- trunc_max
-    truncation <- new_dist_spec(
-      params = parameters,
-      distribution = trunc_dist
-    )
-  }
-
   # combine into ordered matrix
   dirty_obs <- purrr::map(data, data.table::as.data.table)
   dirty_obs <- purrr::map(dirty_obs,
diff --git a/R/get.R b/R/get.R
index 913a1bfea..f3c9d4130 100644
--- a/R/get.R
+++ b/R/get.R
@@ -154,134 +154,6 @@ get_regional_results <- function(regional_output,
   return(out)
 }
 
-#' Get a Literature Distribution
-#'
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#'
-#' This function has been deprecated. Please specify a distribution
-#' using functions such as [Gamma()] or [LogNormal()] instead.
-#'
-#' @param data A `<data.table>` in the format of `generation_times`.
-#'
-#' @param disease A character string indicating the disease of interest.
-#'
-#' @param source A character string indicating the source of interest.
-#'
-#' @param max_value Numeric, the maximum value to allow. Defaults to 14 days.
-#'
-#' @param fixed Logical, defaults to `FALSE`. Should distributions be supplied
-#' as fixed values (vs with uncertainty)?
-#'
-#' @return A list defining a distribution
-#'
-#' @seealso [dist_spec()]
-#' @export
-#' @keywords internal
-get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "get_dist()",
-    details = c(
-      paste(
-        "Please use distribution functions such as `Gamma()` or `Lognormal()`",
-        "instead."
-      ),
-      "The function will be removed completely in the next version."
-    )
-  )
-  target_disease <- disease
-  target_source <- source
-  data <- data[disease == target_disease][source == target_source]
-  if (fixed) {
-    data$sd <- 0
-    data$sd_sd <- 0
-  }
-  parameters <- list(
-    Normal(data$mean, data$mean_sd),
-    Normal(data$sd, data$sd_sd)
-  )
-  if (data$dist == "gamma") {
-    names(parameters) <- c("mean", "sd")
-  } else {
-    names(parameters) <- c("meanlog", "sdlog")
-  }
-  parameters$max <- max_value
-  return(new_dist_spec(
-    params = parameters,
-    distribution = data$dist
-  ))
-}
-#' Get a Literature Distribution for the Generation Time
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#'
-#' Extracts a literature distribution from `generation_times`.
-#' This function has been deprecated. Please specify a distribution
-#' using functions such as [Gamma()] or [LogNormal()] instead.
-#'
-#' @inheritParams get_dist
-#' @inherit get_dist
-#' @export
-#' @seealso [dist_spec()]
-#' @keywords internal
-get_generation_time <- function(disease, source, max_value = 14,
-                                fixed = FALSE) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "get_generation_time()",
-    details = c(
-      paste(
-        "Please use distribution functions such as `Gamma()` or `Lognormal()`",
-        "instead."
-      ),
-      "The function will be removed completely in the next version.",
-      paste(
-        "To obtain the previous estimate by Ganyani et al. (2020) use",
-        "`example_generation_time`."
-      )
-    )
-  )
-  dist <- get_dist(EpiNow2::generation_times,
-    disease = disease, source = source,
-    max_value = max_value, fixed = fixed
-  )
-
-  return(dist)
-}
-#'  Get a Literature Distribution for the Incubation Period
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#'
-#' Extracts a literature distribution from `generation_times`.
-#' This function has been deprecated. Please specify a distribution
-#' using functions such as [Gamma()] or [LogNormal()] instead.
-#'
-#' @inheritParams get_dist
-#' @inherit get_dist
-#' @export
-#' @keywords internal
-get_incubation_period <- function(disease, source, max_value = 14,
-                                  fixed = FALSE) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "get_incubation_period()",
-    details = c(
-      paste(
-        "Please use distribution functions such as `Gamma()` or `Lognormal()`",
-        "instead."
-      ),
-      "The function will be removed completely in the next version.",
-     paste(
-      "To obtain the previous estimate by Ganyani et al. (2020) use",
-      "`example_incubation_period`."
-     )
-    )
-  )
-  dist <- get_dist(EpiNow2::incubation_periods,
-    disease = disease, source = source,
-    max_value = max_value, fixed = fixed
-  )
-
-  return(dist)
-}
 #' Get Regions with Most Reported Cases
 #'
 #' @description `r lifecycle::badge("stable")`
diff --git a/R/opts.R b/R/opts.R
index 3d212614d..11af0a9a3 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -44,52 +44,18 @@
 generation_time_opts <- function(dist = Fixed(1), ...,
                                  disease, source, max = 14, fixed = FALSE,
                                  tolerance = 0.001, weight_prior = TRUE) {
-  deprecated_options_given <- FALSE
   dot_options <- list(...)
 
-  ## check consistent options are given
-  type_options <- (length(dot_options) > 0) + ## distributional parameters
-    (!missing(disease) && !missing(source)) ## from included distributions
-  if (type_options > 1) {
+  if ((length(dot_options) > 0) ||
+      (!missing(disease) && !missing(source)) ||
+      (!is(dist, "dist_spec"))) {
     stop(
-      "Generation time can be given either as distributional options ",
-      "or as a combination of disease and source, but not both."
-    )
-  }
-  if (length(dot_options) > 0) {
-    if (is(dist, "dist_spec")) { ## dist not specified
-      dot_options$distribution <- "gamma"
-    }
-    ## set max
-    if (!("max" %in% names(dot_options))) {
-      dot_options$max <- max
-    }
-    ## set default of mean=1 for backwards compatibility
-    if (!("mean" %in% names(dot_options))) {
-      dot_options$mean <- 1
-    }
-    dist <- do.call(dist_spec, dot_options)
-    if (fixed) dist <- fix_dist(dist)
-    deprecated_options_given <- TRUE
-  } else if (!missing(disease) && !missing(source)) {
-    dist <- get_generation_time(disease, source, max, fixed)
-    dist$fixed <- fixed
-    deprecated_options_given <- TRUE
-  }
-  if (!is(dist, "dist_spec")) {
-    if (is.list(dist) && length(dot_options) == 0) {
-      dist <- do.call(dist_spec, dist)
-    }
-    deprecated_options_given <- TRUE
-  }
-  if (deprecated_options_given) {
-    warning(
       "The generation time distribution should be given to ",
       "`generation_time_opts` using a `dist_spec`. ",
       "This behaviour has changed from previous versions of `EpiNow2` and ",
       "any code using it may need to be updated as any other ways of ",
-      "specifying the generation time are deprecated and will be removed in ",
-      "the next version. For examples and more ",
+      "specifying the generation time are deprecated.",
+      "For examples and more ",
       "information, see the relevant documentation pages using ",
       "`?generation_time_opts`")
   }
@@ -189,7 +155,7 @@ secondary_opts <- function(type = c("incidence", "prevalence"), ...) {
 #' @inheritParams generation_time_opts
 #' @return A `<delay_opts>` object summarising the input delay distributions.
 #' @seealso [convert_to_logmean()] [convert_to_logsd()]
-#' [bootstrapped_dist_fit()] [dist_spec()]
+#' [bootstrapped_dist_fit()] \code{\link{Distributions}}
 #' @export
 #' @examples
 #' # no delays
@@ -209,27 +175,14 @@ delay_opts <- function(dist = Fixed(0), ..., fixed = FALSE, tolerance = 0.001,
                        weight_prior = TRUE) {
   dot_options <- list(...)
   if (!is(dist, "dist_spec")) { ## could be old syntax
-    if (is.list(dist)) {
-      ## combine lists if more than one given
-      dot_options <- c(list(dist), dot_options)
-      dist <- lapply(dot_options, do.call, what = dist_spec)
-      if (length(dist) > 1) {
-        for (i in seq(2, length(dist))) {
-          dist[[1]] <- dist[[1]] + dist[[i]]
-        }
-      }
-      dist <- dist[[1]]
-    } else {
-      stop("`dist` should be given as result of a call to `dist_spec`.")
-    }
-    warning(
+    stop(
       "Delay distributions must be of given either using a call to ",
       "`dist_spec` or one of the `get_...` functions such as ",
       "`get_incubation_period`. ",
       "This behaviour has changed from previous versions of `EpiNow2` and ",
       "any code using it may need to be updated as any other ways of ",
-      "specifying delays are deprecated and will be removed in ",
-      "the next version. For examples and more ",
+      "specifying delays are deprecated. ",
+      "For examples and more ",
       "information, see the relevant documentation pages using ",
       "`?delay_opts`."
     )
@@ -268,7 +221,7 @@ delay_opts <- function(dist = Fixed(0), ..., fixed = FALSE, tolerance = 0.001,
 #' distribution.
 #'
 #' @seealso [convert_to_logmean()] [convert_to_logsd()]
-#' [bootstrapped_dist_fit()] [dist_spec()]
+#' [bootstrapped_dist_fit()] \code{\link{Distributions}}
 #' @export
 #' @examples
 #' # no truncation
@@ -279,10 +232,7 @@ delay_opts <- function(dist = Fixed(0), ..., fixed = FALSE, tolerance = 0.001,
 trunc_opts <- function(dist = Fixed(0), tolerance = 0.001,
                        weight_prior = FALSE) {
   if (!is(dist, "dist_spec")) {
-    if (is.list(dist)) {
-      dist <- do.call(dist_spec, dist)
-    }
-    warning(
+    stop(
       "Truncation distributions must be of given either using a call to ",
       "`dist_spec` or one of the `get_...` functions. ",
       "This behaviour has changed from previous versions of `EpiNow2` and ",
@@ -583,11 +533,10 @@ obs_opts <- function(family = c("negbin", "poisson"),
   }
 
   if (length(phi) == 2 && is.numeric(phi)) {
-    warning(
+    stop(
       "Specifying `phi` as a length 2 vector is deprecated. Mean and SD ",
       "should be given as list elements."
     )
-    phi <- list(mean = phi[1], sd = phi[2])
   }
   obs <- list(
     family = arg_match(family),
@@ -614,33 +563,6 @@ obs_opts <- function(family = c("negbin", "poisson"),
   return(obs)
 }
 
-#' Rstan Sampling Options
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#' Deprecated; use [stan_sampling_opts()] instead.
-#' @inheritParams stan_sampling_opts
-#' @return A list of arguments to pass to [rstan::sampling()].
-#' @export
-rstan_sampling_opts <- function(cores = getOption("mc.cores", 1L),
-                                warmup = 250,
-                                samples = 2000,
-                                chains = 4,
-                                control = list(),
-                                save_warmup = FALSE,
-                                seed = as.integer(runif(1, 1, 1e8)),
-                                future = FALSE,
-                                max_execution_time = Inf,
-                                ...) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "rstan_sampling_opts()",
-    "stan_sampling_opts()"
-  )
-  return(stan_sampling_opts(
-    cores, warmup, samples, chains, control, save_warmup, seed, future,
-    max_execution_time, backend = "rstan", ...
-  ))
-}
-
 #' Stan Sampling Options
 #'
 #' @description `r lifecycle::badge("stable")`
@@ -738,23 +660,6 @@ stan_sampling_opts <- function(cores = getOption("mc.cores", 1L),
   return(opts)
 }
 
-#' Rstan Variational Bayes Options
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#' Deprecated; use [stan_vb_opts()] instead.
-#' @inheritParams stan_vb_opts
-#' @return A list of arguments to pass to [rstan::vb()].
-#' @export
-rstan_vb_opts <- function(samples = 2000,
-                          trials = 10,
-                          iter = 10000, ...) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "rstan_vb_opts()",
-    "stan_vb_opts()"
-  )
-  return(stan_vb_opts(samples, trials, iter, ...))
-}
-
 #' Stan Variational Bayes Options
 #'
 #' @description `r lifecycle::badge("stable")`
@@ -846,51 +751,6 @@ stan_pathfinder_opts <- function(backend = "cmdstanr",
   return(opts)
 }
 
-#' Rstan Options
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#' Deprecated; specify options in [stan_opts()] instead.
-#'
-#' @param object Stan model object. By default uses the compiled package
-#' default.
-#'
-#' @param method A character string, defaulting to sampling. Currently supports
-#' [rstan::sampling()] ("sampling") or [rstan::vb()].
-#'
-#' @param ... Additional parameters to pass  underlying option functions.
-#' @importFrom rlang arg_match
-#' @return A list of arguments to pass to the appropriate rstan functions.
-#' @export
-#' @inheritParams rstan_sampling_opts
-#' @seealso [rstan_sampling_opts()] [rstan_vb_opts()]
-rstan_opts <- function(object = NULL,
-                       samples = 2000,
-                       method = c("sampling", "vb"), ...) {
-  lifecycle::deprecate_warn(
-    "1.5.0", "rstan_opts()",
-    "stan_opts()"
-  )
-  method <- arg_match(method)
-  # shared everywhere opts
-  if (is.null(object)) {
-    object <- stanmodels$estimate_infections
-  }
-  opts <- list(
-    object = object,
-    method = method
-  )
-  if (method == "sampling") {
-    opts <- c(
-      opts, stan_sampling_opts(samples = samples, backend = "rstan", ...)
-    )
-  } else if (method == "vb") {
-    opts <- c(
-      opts, stan_vb_opts(samples = samples, ...)
-    )
-  }
-  return(opts)
-}
-
 #' Stan Options
 #'
 #' @description `r lifecycle::badge("stable")`
@@ -911,21 +771,8 @@ rstan_opts <- function(object = NULL,
 #' @param backend Character string indicating the backend to use for fitting
 #' stan models. Supported arguments are "rstan" (default) or "cmdstanr".
 #'
-#' @param init_fit `r lifecycle::badge("experimental")`
-#' Character string or `stanfit` object, defaults to NULL. Should an initial
-#' fit be used to initialise the full fit. An example scenario would be using a
-#' national level fit to parametrise regional level fits. Optionally a
-#' character string can be passed with the currently supported option being
-#' "cumulative". This fits the model to cumulative cases and may be useful for
-#' certain data sets where the sampler gets stuck or struggles to initialise.
-#' See [init_cumulative_fit()] for details.
-#'
-#' This implementation is based on the approach taken in
-#' [epidemia](https://github.com/ImperialCollegeLondon/epidemia/) authored by
-#' James Scott.
-#'
-#' This argument is deprecated and the default (NULL) will be used from
-#' the next version.
+#' @param init_fit `r lifecycle::badge("deprecated")`
+#' This argument is deprecated.
 #'
 #' @param return_fit Logical, defaults to TRUE. Should the fit stan model be
 #' returned.
@@ -1001,16 +848,10 @@ stan_opts <- function(object = NULL,
   }
 
   if (!is.null(init_fit)) {
-    deprecate_warn(
+    deprecate_stop(
       when = "1.5.0",
-      what = "stan_opts(init_fit)",
-      details = paste("This argument is deprecated and the default (NULL)",
-                      "will be used from the next version.")
+      what = "stan_opts(init_fit)"
     )
-    if (is.character(init_fit)) {
-      init_fit <- arg_match(init_fit, values = "cumulative")
-    }
-    opts$init_fit <- init_fit
   }
   opts <- c(opts, list(return_fit = return_fit))
   attr(opts, "class") <- c("stan_opts", class(opts))
diff --git a/R/regional_epinow.R b/R/regional_epinow.R
index 070e75c32..23ccb52eb 100644
--- a/R/regional_epinow.R
+++ b/R/regional_epinow.R
@@ -113,20 +113,12 @@ regional_epinow <- function(data,
                             verbose = FALSE,
                             logs = tempdir(check = TRUE), ...,
                             reported_cases) {
-  # Warning for deprecated arguments
   if (!missing(reported_cases)) {
-     if (!missing(data)) {
-       stop("Can't have `reported_cases` and `data` arguments. ",
-            "Use `data` instead."
-       )
-    }
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "1.5.0",
       "regional_epinow(reported_cases)",
-      "regional_epinow(data)",
-      "The argument will be removed completely in the next version."
+      "regional_epinow(data)"
     )
-    data <- reported_cases
   }
   # supported output
   output <- match_output_arguments(output,
diff --git a/R/simulate_infections.R b/R/simulate_infections.R
index 0bd4631bd..59ddd950c 100644
--- a/R/simulate_infections.R
+++ b/R/simulate_infections.R
@@ -8,10 +8,6 @@
 #' standard deviation of delays or observation scaling, must be fixed.
 #' Uncertain parameters are not allowed.
 #'
-#' A previous function called [simulate_infections()] that simulates from a
-#' given model fit has been renamed [forecast_infections()]. Using
-#' [simulate_infections()] with existing estimates is now deprecated. This
-#' option will be removed in the next version.
 #' @param R a data frame of reproduction numbers (column `R`) by date (column
 #'   `date`). Column `R` must be numeric and `date` must be in date format. If
 #'   not all days between the first and last day in the `date` are present,
@@ -75,16 +71,11 @@ simulate_infections <- function(estimates, R, initial_infections,
                                 pop = 0, ...) {
   ## deprecated usage
   if (!missing(estimates)) {
-    deprecate_warn(
+    deprecate_stop(
       "1.5.0",
       "simulate_infections(estimates)",
-      "forecast_infections()",
-      details = paste0(
-        "The `estimates` option will be removed from [simulate_infections()] ",
-        "in the next version."
-      )
+      "forecast_infections()"
     )
-    return(forecast_infections(estimates = estimates, ...))
   }
 
   ## check inputs
diff --git a/R/simulate_secondary.R b/R/simulate_secondary.R
index ed1aabb58..956f8470b 100644
--- a/R/simulate_secondary.R
+++ b/R/simulate_secondary.R
@@ -41,7 +41,6 @@ simulate_secondary <- function(primary,
                                CrIs = c(0.2, 0.5, 0.9),
                                backend = "rstan",
                                ...) {
-  ## deprecated usage
   assert_data_frame(primary, any.missing = FALSE)
   assert_subset(c("date", "primary"), colnames(primary))
   assert_date(primary$date)
diff --git a/man/adjust_infection_to_report.Rd b/man/adjust_infection_to_report.Rd
index decaa3a95..7171307c5 100644
--- a/man/adjust_infection_to_report.Rd
+++ b/man/adjust_infection_to_report.Rd
@@ -46,43 +46,4 @@ A \code{data.table} containing a \code{date} variable (date of report) and a
 Maps from cases by date of infection to date of report via date of
 onset.
 }
-\examples{
-\donttest{
-# This function is deprecated and its functionality can now be accessed
-# from [simulate_secondary()].
-# Here are some examples of how to use [simulate_secondary()] to replace
-# adjust_infection_to_report().
-
-# Old (using adjust_infection_to_report()):
-# Define example case data
-cases <- data.table::copy(example_confirmed)
-cases <- cases[, cases := as.integer(confirm)]
-# Define a simple reporting delay distribution
-delay_def <- lognorm_dist_def(
- mean = 5, mean_sd = 1, sd = 3, sd_sd = 1,
- max_value = 30, samples = 1, to_log = TRUE
-)
-report <- adjust_infection_to_report(
- cases,
- delay_defs = list(delay_def),
- reporting_model = function(n) rpois(length(n), n)
-)
-print(report)
-
-# New (using simulate_secondary()):
-cases <- data.table::copy(example_confirmed)
-cases <- cases[, primary := as.integer(confirm)]
-uncertain_delay <- LogNormal(
- mean = Normal(5, 1), sd = Normal(3, 1),
- max = 30
-)
-delay <- fix_dist(uncertain_delay, strategy = "sample")
-report <- simulate_secondary(
- cases,
- delays = delay_opts(delay),
- obs = obs_opts(family = "poisson")
-)
-print(report)
-}
-}
 \keyword{internal}
diff --git a/man/c.dist_spec.Rd b/man/c.dist_spec.Rd
index 9c8415679..7f926b5a5 100644
--- a/man/c.dist_spec.Rd
+++ b/man/c.dist_spec.Rd
@@ -7,7 +7,7 @@
 \method{c}{dist_spec}(...)
 }
 \arguments{
-\item{...}{The delay distributions (from calls to \code{\link[=dist_spec]{dist_spec()}}) to combine}
+\item{...}{The delay distributions to combine}
 }
 \value{
 Combined delay distributions (with class \verb{<dist_spec>})
diff --git a/man/delay_opts.Rd b/man/delay_opts.Rd
index ea5c8dccd..d6e2dc381 100644
--- a/man/delay_opts.Rd
+++ b/man/delay_opts.Rd
@@ -54,5 +54,5 @@ delay_opts(delay + delay)
 }
 \seealso{
 \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()}}
+\code{\link[=bootstrapped_dist_fit]{bootstrapped_dist_fit()}} \code{\link{Distributions}}
 }
diff --git a/man/dist_spec.Rd b/man/dist_spec.Rd
index 0af001f4a..6eeb683aa 100644
--- a/man/dist_spec.Rd
+++ b/man/dist_spec.Rd
@@ -8,10 +8,6 @@ dist_spec(
   distribution = c("lognormal", "normal", "gamma", "fixed", "empty"),
   params_mean = numeric(0),
   params_sd = numeric(0),
-  mean,
-  sd = 0,
-  mean_sd = 0,
-  sd_sd = 0,
   max = Inf,
   pmf = numeric(0),
   fixed = FALSE
@@ -29,14 +25,6 @@ distribution as defined in [natural_params().}
 \item{params_sd}{Numeric. Standard deviations of the parameters of the
 distribution as defined in [natural_params().}
 
-\item{mean}{Deprecated; use \code{params_mean} instead.}
-
-\item{sd}{Deprecated; use \code{params_mean} instead.}
-
-\item{mean_sd}{Deprecated; use \code{params_sd} instead.}
-
-\item{sd_sd}{Deprecated; use \code{params_sd} instead.}
-
 \item{max}{Numeric, maximum value of the distribution. The distribution will
 be truncated at this value. Default: \code{Inf}, i.e. no maximum.}
 
diff --git a/man/epinow.Rd b/man/epinow.Rd
index b191cc5e1..c44770f93 100644
--- a/man/epinow.Rd
+++ b/man/epinow.Rd
@@ -156,7 +156,7 @@ reported_cases <- example_confirmed[1:40]
 
 # estimate Rt and nowcast/forecast cases by date of infection
 out <- epinow(
-  reported_cases = reported_cases,
+  data = reported_cases,
   generation_time = generation_time_opts(generation_time),
   rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
   delays = delay_opts(incubation_period + reporting_delay)
diff --git a/man/estimate_truncation.Rd b/man/estimate_truncation.Rd
index d0c5dc323..ffe91f243 100644
--- a/man/estimate_truncation.Rd
+++ b/man/estimate_truncation.Rd
@@ -6,9 +6,6 @@
 \usage{
 estimate_truncation(
   data,
-  max_truncation,
-  trunc_max = 10,
-  trunc_dist = "lognormal",
   truncation = trunc_opts(LogNormal(meanlog = Normal(0, 1), sdlog = Normal(1, 1), max =
     10)),
   model = NULL,
@@ -28,12 +25,6 @@ and a confirm (numeric) variable. Each data set should be a snapshot
 of the reported data over time. All data sets must contain a complete vector
 of dates.}
 
-\item{max_truncation}{Deprecated; use \code{truncation} instead.}
-
-\item{trunc_max}{Deprecated; use \code{truncation} instead.}
-
-\item{trunc_dist}{Deprecated; use \code{truncation} instead.}
-
 \item{truncation}{A call to \code{\link[=trunc_opts]{trunc_opts()}} defining the truncation of
 the observed data. Defaults to \code{\link[=trunc_opts]{trunc_opts()}}, i.e. no truncation.  See the
 \code{\link[=estimate_truncation]{estimate_truncation()}} help file for an approach to estimating this from
diff --git a/man/gamma_dist_def.Rd b/man/gamma_dist_def.Rd
index 760e60bb4..0ae5ea187 100644
--- a/man/gamma_dist_def.Rd
+++ b/man/gamma_dist_def.Rd
@@ -46,23 +46,4 @@ A \verb{<data.table>} defining the distribution as used by \code{\link[=dist_ske
 \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[=Gamma]{Gamma()}} instead to define a gamma distribution.
 }
-\examples{
-# using estimated shape and scale
-def <- gamma_dist_def(
-  shape = 5.807, shape_sd = 0.2,
-  scale = 0.9, scale_sd = 0.05,
-  max_value = 20, samples = 10
-)
-print(def)
-def$params[[1]]
-
-# using mean and sd
-def <- gamma_dist_def(
-  mean = 3, mean_sd = 0.5,
-  sd = 3, sd_sd = 0.1,
-  max_value = 20, samples = 10
-)
-print(def)
-def$params[[1]]
-}
 \keyword{internal}
diff --git a/man/get_dist.Rd b/man/get_dist.Rd
index 36a20357c..132a06c4b 100644
--- a/man/get_dist.Rd
+++ b/man/get_dist.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/get.R
+% Please edit documentation in R/deprecated.R
 \name{get_dist}
 \alias{get_dist}
 \title{Get a Literature Distribution}
diff --git a/man/get_distribution.Rd b/man/get_distribution.Rd
index 904cefe3c..28dfb930a 100644
--- a/man/get_distribution.Rd
+++ b/man/get_distribution.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/dist_spec.R
 \name{get_distribution}
 \alias{get_distribution}
-\title{Get the distribution of a \code{\link[=dist_spec]{dist_spec()}}}
+\title{Get the distribution of a <dist_spec>}
 \usage{
 get_distribution(x, id = NULL)
 }
diff --git a/man/get_generation_time.Rd b/man/get_generation_time.Rd
index 6dc2db796..b222e1ab0 100644
--- a/man/get_generation_time.Rd
+++ b/man/get_generation_time.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/get.R
+% Please edit documentation in R/deprecated.R
 \name{get_generation_time}
 \alias{get_generation_time}
 \title{Get a Literature Distribution for the Generation Time}
diff --git a/man/get_incubation_period.Rd b/man/get_incubation_period.Rd
index accfaaa1d..07b0b2a0c 100644
--- a/man/get_incubation_period.Rd
+++ b/man/get_incubation_period.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/get.R
+% Please edit documentation in R/deprecated.R
 \name{get_incubation_period}
 \alias{get_incubation_period}
 \title{Get a Literature Distribution for the Incubation Period}
diff --git a/man/lognorm_dist_def.Rd b/man/lognorm_dist_def.Rd
index 5eb9b031a..bcf35d3bf 100644
--- a/man/lognorm_dist_def.Rd
+++ b/man/lognorm_dist_def.Rd
@@ -31,22 +31,4 @@ Generates a distribution definition when only parameter estimates
 are available for log normal distributed parameters. See \code{\link[=rlnorm]{rlnorm()}} for
 distribution information.
 }
-\examples{
-def <- lognorm_dist_def(
-  mean = 1.621, mean_sd = 0.0640,
-  sd = 0.418, sd_sd = 0.0691,
-  max_value = 20, samples = 10
-)
-print(def)
-def$params[[1]]
-
-def <- lognorm_dist_def(
-  mean = 5, mean_sd = 1,
-  sd = 3, sd_sd = 1,
-  max_value = 20, samples = 10,
-  to_log = TRUE
-)
-print(def)
-def$params[[1]]
-}
 \keyword{internal}
diff --git a/man/max.dist_spec.Rd b/man/max.dist_spec.Rd
index 5e4aed9e9..c81f811ef 100644
--- a/man/max.dist_spec.Rd
+++ b/man/max.dist_spec.Rd
@@ -7,7 +7,7 @@
 \method{max}{dist_spec}(x, ...)
 }
 \arguments{
-\item{x}{The \code{\link[=dist_spec]{dist_spec()}} to use}
+\item{x}{The <dist_spec> to use}
 
 \item{...}{Not used}
 }
@@ -17,7 +17,7 @@ A vector of means.
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 This works out the maximum of all the (parametric / nonparametric) delay
-distributions combined in the passed \code{\link[=dist_spec]{dist_spec()}} (ignoring any uncertainty
+distributions combined in the passed <dist_spec> (ignoring any uncertainty
 in parameters)
 }
 \examples{
diff --git a/man/mean.dist_spec.Rd b/man/mean.dist_spec.Rd
index fe38f65bf..f517df066 100644
--- a/man/mean.dist_spec.Rd
+++ b/man/mean.dist_spec.Rd
@@ -18,7 +18,7 @@ parameters will be returned as NA.}
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 This works out the mean of all the (parametric / nonparametric) delay
-distributions combined in the passed \code{\link[=dist_spec]{dist_spec()}} (ignoring any uncertainty
+distributions combined in the passed <dist_spec> (ignoring any uncertainty
 in parameters)
 }
 \examples{
diff --git a/man/plus-.dist_spec.Rd b/man/plus-.dist_spec.Rd
index 7692bafbe..16e967faa 100644
--- a/man/plus-.dist_spec.Rd
+++ b/man/plus-.dist_spec.Rd
@@ -7,10 +7,10 @@
 \method{+}{dist_spec}(e1, e2)
 }
 \arguments{
-\item{e1}{The first delay distribution (of type \code{\link[=dist_spec]{dist_spec()}}) to
+\item{e1}{The first delay distribution (of type <dist_spec>) to
 combine.}
 
-\item{e2}{The second delay distribution (of type \code{\link[=dist_spec]{dist_spec()}}) to
+\item{e2}{The second delay distribution (of type <dist_spec>) to
 combine.}
 }
 \value{
diff --git a/man/print.dist_spec.Rd b/man/print.dist_spec.Rd
index 21dbba464..c3ea43cfb 100644
--- a/man/print.dist_spec.Rd
+++ b/man/print.dist_spec.Rd
@@ -17,7 +17,7 @@ invisible
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 This displays the parameters of the uncertain and probability mass
-functions of fixed delay distributions combined in the passed \code{\link[=dist_spec]{dist_spec()}}.
+functions of fixed delay distributions combined in the passed <dist_spec>.
 }
 \examples{
 #' # A fixed lognormal distribution with mean 5 and sd 1.
diff --git a/man/report_cases.Rd b/man/report_cases.Rd
index a729a7c6b..500d233e7 100644
--- a/man/report_cases.Rd
+++ b/man/report_cases.Rd
@@ -48,35 +48,4 @@ Convolves latent infections to reported cases via an observation model.
 Likely to be removed/replaced in later releases by functionality drawing on
 the \code{stan} implementation.
 }
-\examples{
-\donttest{
-# This function is deprecated and its functionality can now be accessed
-# from [simulate_secondary()].
-# Here are some examples of how to use [simulate_secondary()] to replace
-# report_cases().
-# Old (using report_cases()):
-# Define case data
-cases <- example_confirmed[1:40]
-cases <- cases[, cases := as.integer(confirm)]
-cases <- cases[, confirm := NULL][, sample := 1]
-reported_cases <- report_cases(
- case_estimates = cases,
- delays = delay_opts(example_incubation_period + example_reporting_delay),
- type = "sample"
-)
-print(reported_cases$samples)
-
-# New (using simulate_secondary()):
-cases <- example_confirmed[1:40]
-cases <- cases[, primary := as.integer(confirm)]
-report <- simulate_secondary(
- cases,
- delays = delay_opts(
-   fix_dist(example_incubation_period + example_reporting_delay)
- ),
- obs = obs_opts(family = "poisson")
-)
-print(report)
-}
-}
 \keyword{internal}
diff --git a/man/rstan_opts.Rd b/man/rstan_opts.Rd
index f13484bd4..985ed4ce2 100644
--- a/man/rstan_opts.Rd
+++ b/man/rstan_opts.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/opts.R
+% Please edit documentation in R/deprecated.R
 \name{rstan_opts}
 \alias{rstan_opts}
 \title{Rstan Options}
diff --git a/man/rstan_sampling_opts.Rd b/man/rstan_sampling_opts.Rd
index 567e134a2..a1889d609 100644
--- a/man/rstan_sampling_opts.Rd
+++ b/man/rstan_sampling_opts.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/opts.R
+% Please edit documentation in R/deprecated.R
 \name{rstan_sampling_opts}
 \alias{rstan_sampling_opts}
 \title{Rstan Sampling Options}
diff --git a/man/rstan_vb_opts.Rd b/man/rstan_vb_opts.Rd
index 0ffec4c2a..9d8c9c14a 100644
--- a/man/rstan_vb_opts.Rd
+++ b/man/rstan_vb_opts.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/opts.R
+% Please edit documentation in R/deprecated.R
 \name{rstan_vb_opts}
 \alias{rstan_vb_opts}
 \title{Rstan Variational Bayes Options}
diff --git a/man/sample_approx_dist.Rd b/man/sample_approx_dist.Rd
index 6ac8adfdb..431ad97f7 100644
--- a/man/sample_approx_dist.Rd
+++ b/man/sample_approx_dist.Rd
@@ -43,62 +43,6 @@ A \verb{<data.table>} of cases by date of onset
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
-Convolves cases by a PMF function. This function will soon be removed or
-replaced with a more robust stan implementation.
-}
-\examples{
-\donttest{
-cases <- example_confirmed
-cases <- cases[, cases := as.integer(confirm)]
-print(cases)
-
-# total cases
-sum(cases$cases)
-
-delay_fn <- function(n, dist, cum) {
-  if (dist) {
-    pgamma(n + 0.9999, 2, 1) - pgamma(n - 1e-5, 2, 1)
-  } else {
-    as.integer(rgamma(n, 2, 1))
-  }
-}
-
-onsets <- sample_approx_dist(
-  cases = cases,
-  dist_fn = delay_fn
-)
-
-# estimated onset distribution
-print(onsets)
-
-# check that sum is equal to reported cases
-total_onsets <- median(
-  purrr::map_dbl(
-    1:10,
-    ~ sum(sample_approx_dist(
-      cases = cases,
-      dist_fn = delay_fn
-    )$cases)
-  )
-)
-total_onsets
-
-
-# map from onset cases to reported
-reports <- sample_approx_dist(
-  cases = cases,
-  dist_fn = delay_fn,
-  direction = "forwards"
-)
-
-
-# map from onset cases to reported using a mean shift
-reports <- sample_approx_dist(
-  cases = cases,
-  dist_fn = delay_fn,
-  direction = "forwards",
-  type = "median"
-)
-}
+Deprecated; Convolves cases by a PMF function.
 }
 \keyword{internal}
diff --git a/man/sd_dist.Rd b/man/sd_dist.Rd
index be8ef17f6..303d21a22 100644
--- a/man/sd_dist.Rd
+++ b/man/sd_dist.Rd
@@ -7,7 +7,7 @@
 sd_dist(x)
 }
 \arguments{
-\item{x}{The \code{\link[=dist_spec]{dist_spec()}} to use}
+\item{x}{The <dist_spec> to use}
 }
 \value{
 A vector of standard deviations.
@@ -15,7 +15,7 @@ A vector of standard deviations.
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 This works out the standard deviation of all the (parametric /
-nonparametric) delay distributions combined in the passed \code{\link[=dist_spec]{dist_spec()}}.
+nonparametric) delay distributions combined in the passed <dist_spec>.
 }
 \examples{
 \dontrun{
diff --git a/man/simulate_infections.Rd b/man/simulate_infections.Rd
index b3ac1147a..1853b67ec 100644
--- a/man/simulate_infections.Rd
+++ b/man/simulate_infections.Rd
@@ -94,11 +94,6 @@ model can be specified using the same options as in \code{\link[=estimate_infect
 In order to simulate, all parameters that are specified such as the mean and
 standard deviation of delays or observation scaling, must be fixed.
 Uncertain parameters are not allowed.
-
-A previous function called \code{\link[=simulate_infections]{simulate_infections()}} that simulates from a
-given model fit has been renamed \code{\link[=forecast_infections]{forecast_infections()}}. Using
-\code{\link[=simulate_infections]{simulate_infections()}} with existing estimates is now deprecated. This
-option will be removed in the next version.
 }
 \examples{
 \donttest{
diff --git a/man/stan_opts.Rd b/man/stan_opts.Rd
index 828f1940b..6d02872a8 100644
--- a/man/stan_opts.Rd
+++ b/man/stan_opts.Rd
@@ -31,21 +31,8 @@ laplace algorithm ("laplace") or pathfinder ("pathfinder").}
 \item{backend}{Character string indicating the backend to use for fitting
 stan models. Supported arguments are "rstan" (default) or "cmdstanr".}
 
-\item{init_fit}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
-Character string or \code{stanfit} object, defaults to NULL. Should an initial
-fit be used to initialise the full fit. An example scenario would be using a
-national level fit to parametrise regional level fits. Optionally a
-character string can be passed with the currently supported option being
-"cumulative". This fits the model to cumulative cases and may be useful for
-certain data sets where the sampler gets stuck or struggles to initialise.
-See \code{\link[=init_cumulative_fit]{init_cumulative_fit()}} for details.
-
-This implementation is based on the approach taken in
-\href{https://github.com/ImperialCollegeLondon/epidemia/}{epidemia} authored by
-James Scott.
-
-This argument is deprecated and the default (NULL) will be used from
-the next version.}
+\item{init_fit}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
+This argument is deprecated.}
 
 \item{return_fit}{Logical, defaults to TRUE. Should the fit stan model be
 returned.}
diff --git a/man/trunc_opts.Rd b/man/trunc_opts.Rd
index 4ea435246..7205e3566 100644
--- a/man/trunc_opts.Rd
+++ b/man/trunc_opts.Rd
@@ -41,5 +41,5 @@ trunc_opts(dist = LogNormal(mean = 3, sd = 2, max = 10))
 }
 \seealso{
 \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()}}
+\code{\link[=bootstrapped_dist_fit]{bootstrapped_dist_fit()}} \code{\link{Distributions}}
 }
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index a5d565846..e5e31d564 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -16,6 +16,3 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
 }
 
 withr::defer(future::plan("sequential"), teardown_env())
-
-## process warning once as previous behaviour has been deprecated
-dummy <- suppressWarnings(dist_spec(mean = 0, sd = 1, max = 5))
diff --git a/tests/testthat/test-adjust_infection_to_report.R b/tests/testthat/test-adjust_infection_to_report.R
deleted file mode 100644
index 078e7c7c1..000000000
--- a/tests/testthat/test-adjust_infection_to_report.R
+++ /dev/null
@@ -1,41 +0,0 @@
-
-# define example cases
-cases <- data.table::copy(example_confirmed)[, cases := as.integer(confirm)]
-
-# define a single report delay distribution
-delay <- LogNormal(
-  meanlog = Normal(1.4, 0.3), sdlog = Normal(0.6, 0.2), max = 30
-)
-
-test_that("adjust_infection_to_report can correctly handle a simple mapping", {
-  reports <- suppressWarnings(adjust_infection_to_report(
-    cases,
-    delay_defs = example_incubation_period + delay
-  ))
-  expect_true(nrow(reports) > 80)
-  expect_true(all(!is.infinite(reports$cases)))
-  expect_true(all(!is.na(reports$cases)))
-})
-
-test_that("adjust_infection_to_report can correctly handle a mapping with a day
-           of the week effect", {
-  reports <- suppressWarnings(adjust_infection_to_report(
-    cases,
-    delay_defs = example_incubation_period + delay,
-    reporting_effect = c(1.1, rep(1, 4), 0.95, 0.95)
-  ))
-  expect_true(nrow(reports) > 80)
-  expect_true(all(!is.infinite(reports$cases)))
-  expect_true(all(!is.na(reports$cases)))
-})
-
-test_that("deprecated functions are deprecated", {
-  # define example cases
-  cases <- data.table::copy(example_confirmed)[, cases := as.integer(confirm)]
-  expect_deprecated(
-    adjust_infection_to_report(
-      cases,
-      delay_defs = example_incubation_period + delay,
-    )
-  )
-})
diff --git a/tests/testthat/test-create_obs_model.R b/tests/testthat/test-create_obs_model.R
index b2940a284..b704ca54d 100644
--- a/tests/testthat/test-create_obs_model.R
+++ b/tests/testthat/test-create_obs_model.R
@@ -67,10 +67,3 @@ test_that("create_obs_model can be used with a user set phi", {
   expect_equal(obs$phi_sd, 0)
   expect_error(obs_opts(phi = c("Hi", "World")))
 })
-
-test_that("using a vector for phi in create_obs_model is deprecated", {
-  expect_warning(
-    create_obs_model(dates = dates, obs = obs_opts(phi = c(10, 0.1))),
-    "deprecated"
-  )
-})
diff --git a/tests/testthat/test-dist.R b/tests/testthat/test-dist.R
index 826bb04e6..1fce67f51 100644
--- a/tests/testthat/test-dist.R
+++ b/tests/testthat/test-dist.R
@@ -19,24 +19,3 @@ test_that("distributions are the same in R and stan", {
   expect_equal(pmf_r_lognormal, pmf_stan_lognormal)
   expect_equal(pmf_r_gamma, pmf_stan_gamma)
 })
-
-test_that("deprecated functions are deprecated", {
-  delay_fn <- function(n, dist, cum) {
-      pgamma(n + 0.9999, 2, 1) - pgamma(n - 1e-5, 2, 1)
-  }
-  expect_deprecated(
-    sample_approx_dist(
-      cases = example_confirmed[1:5],
-      dist_fn = delay_fn,
-      direction = "forwards",
-      type = "median"
-    )
-  )
-  args <- list(mean = 3, mean_sd = 0, sd = 2, sd_sd = 0, max_value = 15)
-  expect_deprecated(
-    do.call(lognorm_dist_def, (c(args, list(samples = 1))))$params[[1]]
-  )
-  expect_deprecated(
-    do.call(gamma_dist_def, (c(args, list(samples = 1))))$params[[1]]
-  )
-})
diff --git a/tests/testthat/test-dist_spec.R b/tests/testthat/test-dist_spec.R
index c961c0c3e..597160835 100644
--- a/tests/testthat/test-dist_spec.R
+++ b/tests/testthat/test-dist_spec.R
@@ -294,7 +294,3 @@ test_that("get functions report errors", {
     Gamma(mean = 4, sd = 1), Gamma(mean = 4, sd = 1)
   )), "must be specified")
 })
-
-test_that("deprecated functions are deprecated", {
-  expect_deprecated(dist_spec(params_mean = c(1.6, 0.6), max = 19))
-})
diff --git a/tests/testthat/test-epinow.R b/tests/testthat/test-epinow.R
index 50264ef18..b1857ebb5 100644
--- a/tests/testthat/test-epinow.R
+++ b/tests/testthat/test-epinow.R
@@ -198,14 +198,3 @@ test_that("epinow fails if given variational inference arguments when using NUTs
     )
   ))))
 })
-
-test_that("deprecated arguments are recognised", {
-  expect_deprecated(
-    x <- capture.output(suppressMessages(
-      epinow(
-        reported_cases = reported_cases,
-        generation_time = generation_time_opts(Fixed(1))
-      )
-    ))
-  )
-})
diff --git a/tests/testthat/test-estimate_secondary.R b/tests/testthat/test-estimate_secondary.R
index b09020bb3..d4c64e948 100644
--- a/tests/testthat/test-estimate_secondary.R
+++ b/tests/testthat/test-estimate_secondary.R
@@ -229,9 +229,3 @@ test_that("estimate_secondary works with zero_threshold set", {
   expect_s3_class(out, "estimate_secondary")
   expect_named(out, c("predictions", "posterior", "data", "fit"))
 })
-
-test_that("deprecated arguments are recognised", {
-  expect_deprecated(
-    estimate_secondary(reports = inc_cases)
-  )
-})
\ No newline at end of file
diff --git a/tests/testthat/test-estimate_truncation.R b/tests/testthat/test-estimate_truncation.R
index ccd7382ac..e0851d5cb 100644
--- a/tests/testthat/test-estimate_truncation.R
+++ b/tests/testthat/test-estimate_truncation.R
@@ -84,21 +84,4 @@ test_that("estimate_truncation works with zero_threshold set", {
   expect_s3_class(out$dist, "dist_spec")
 })
 
-test_that("deprecated arguments are recognised", {
-  expect_error(estimate_truncation(example_truncated,
-    verbose = FALSE, trunc_max = 10
-  ), "deprecated")
-  expect_error(estimate_truncation(example_truncated,
-    verbose = FALSE, max_truncation = 10
-  ), "deprecated")
-  expect_error(estimate_truncation(example_truncated,
-    verbose = FALSE, trunc_dist = "lognormal"
-  ), "deprecated")
-  expect_deprecated(
-    estimate_truncation(obs = example_truncated,
-      verbose = FALSE
-    )
-  )
-})
-
 options(old_opts)
diff --git a/tests/testthat/test-forecast-infections.R b/tests/testthat/test-forecast-infections.R
index 3bd49b509..d43c81eaf 100644
--- a/tests/testthat/test-forecast-infections.R
+++ b/tests/testthat/test-forecast-infections.R
@@ -78,9 +78,3 @@ test_that("forecast_infections works to simulate a passed in estimate_infections
   sims_sample <- forecast_infections(out, R_samples)
   expect_equal(names(sims_sample), c("samples", "summarised", "observations"))
 })
-
-test_that("simulate_infections with a given estimate is deprecated", {
-  expect_deprecated(
-    sims <- simulate_infections(out)
-  )
-})
diff --git a/tests/testthat/test-get_dist.R b/tests/testthat/test-get_dist.R
deleted file mode 100644
index 97cafd400..000000000
--- a/tests/testthat/test-get_dist.R
+++ /dev/null
@@ -1,6 +0,0 @@
-test_that("get_dist is deprecated", {
-  data <- data.table::data.table(mean = 1, mean_sd = 1, sd = 1, sd_sd = 1, source = "test", disease = "test", dist = "lognormal")
-  expect_deprecated(
-    get_dist(data, disease = "test", source = "test")
-  )
-})
diff --git a/tests/testthat/test-opts.R b/tests/testthat/test-opts.R
deleted file mode 100644
index e53f812be..000000000
--- a/tests/testthat/test-opts.R
+++ /dev/null
@@ -1,7 +0,0 @@
-test_that("default generation time options produce a warning", {
-  expect_warning(generation_time_opts(), "1 day")
-})
-
-test_that("deprecated arguments are caught", {
-  expect_deprecated(stan_opts(init_fit = "cumulative"))
-})
diff --git a/tests/testthat/test-regional_epinow.R b/tests/testthat/test-regional_epinow.R
index 412bab8c6..830899bb1 100644
--- a/tests/testthat/test-regional_epinow.R
+++ b/tests/testthat/test-regional_epinow.R
@@ -109,11 +109,3 @@ test_that("regional_epinow produces expected output when run with region specifi
   df_non_zero(out$regional$realland$summary)
   expect_equal(names(out$regional$realland$plots), c("summary", "infections", "reports", "R", "growth_rate"))
 })
-
-test_that("deprecated arguments are recognised", {
-  expect_deprecated(
-    regional_epinow(
-      reported_cases = cases,
-      generation_time = generation_time_opts(Fixed(1))
-  ))
-})
diff --git a/tests/testthat/test-report_cases.R b/tests/testthat/test-report_cases.R
deleted file mode 100644
index e530ff746..000000000
--- a/tests/testthat/test-report_cases.R
+++ /dev/null
@@ -1,37 +0,0 @@
-test_that("report_cases can simulate infections forward", {
-  set.seed(123)
-  # define example cases
-  cases <- example_confirmed[1:10]
-
-  # Instead of running them model we use example
-  # data for speed in this example.
-  cases <- cases[, cases := as.integer(confirm)]
-  cases <- cases[, confirm := NULL][, sample := 1]
-  reported_cases <- suppressWarnings(report_cases(
-    case_estimates = cases,
-    delays = delay_opts(example_incubation_period + example_reporting_delay),
-    type = "sample"
-  ))
-  expect_equal(class(reported_cases), "list")
-  expect_equal(class(reported_cases$samples), c("data.table", "data.frame"))
-  expect_equal(class(reported_cases$summarised), c("data.table", "data.frame"))
-  expect_equal(nrow(reported_cases$summarised), 7)
-  expect_equal(class(reported_cases$summarised$median), "numeric")
-  set.seed(Sys.time())
-})
-
-test_that("deprecated functions are deprecated", {
-  cases <- example_confirmed[1:40]
-  # get example delays
-  #' # Instead of running them model we use example
-  #' # data for speed in this example.
-  cases <- cases[, cases := as.integer(confirm)]
-  cases <- cases[, confirm := NULL][, sample := 1]
-  expect_deprecated(
-    report_cases(
-      case_estimates = cases,
-      delays = delay_opts(example_incubation_period + example_reporting_delay),
-      type = "sample"
-    )
-  )
-})