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Change expected type of reported_cases argument to numeric #594

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Merged
merged 5 commits into from
Mar 4, 2024
Merged

Change expected type of reported_cases argument to numeric #594

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8ad321d
Revise doc to state expected type as numeric not integer
jamesmbaazam Mar 4, 2024
06153e0
Add NEWS item
jamesmbaazam Mar 4, 2024
6634ed7
Revise NEWS item
jamesmbaazam Mar 4, 2024
0e40b27
Remove tune_inv_gamma function after deprecation
jamesmbaazam Mar 4, 2024
6ba20fc
Merge branch 'main' into improve-reported-cases-doc
sbfnk Mar 4, 2024
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Remove tune_inv_gamma function after deprecation
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@jamesmbaazam
jamesmbaazam committed Mar 4, 2024
commit 0e40b27fcb554ec2520dae1e51f5a87e2c0d90e8
1 change: 0 additions & 1 deletion NAMESPACE
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Expand Up @@ -99,7 +99,6 @@ export(stan_vb_opts)
export(summarise_key_measures)
export(summarise_results)
export(trunc_opts)
export(tune_inv_gamma)
export(update_horizon)
export(update_list)
export(update_secondary_args)
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33 changes: 0 additions & 33 deletions R/dist.R
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Expand Up @@ -796,39 +796,6 @@ sample_approx_dist <- function(cases = NULL,
return(mapped_cases)
}

#' Tune an Inverse Gamma to Achieve the Target Truncation
#'
#' @description `r lifecycle::badge("deprecated")`
#' Allows an inverse gamma distribution to be. tuned so that less than 0.01 of
#' its probability mass function falls outside of the specified bounds. This is
#' required when using an inverse gamma prior, for example for a Gaussian
#' process. As no inverse gamma priors are currently in use and this function
#' has some stability issues it has been deprecated.
#'
#' @param lower Numeric, defaults to 2. Lower truncation bound.
#'
#' @param upper Numeric, defaults to 21. Upper truncation bound.
#'
#' @return A list of alpha and beta values that describe a inverse gamma
#' distribution that achieves the target truncation.
#' @export
#'
#' @keywords internal
#'
tune_inv_gamma <- function(lower = 2, upper = 21) {
lifecycle::deprecate_stop(
"1.3.6", "tune_inv_gamma()",
details = paste0(
"As no inverse gamma priors are currently in use and this function has ",
"some stability issues it has been deprecated. Please let the package ",
"authors know if deprecating this function has caused any issues. ",
"For the last active version of the function see the one contained ",
"in version 1.3.5 at ",
"https://github.com/epiforecasts/EpiNow2/blob/bad836ebd650ace73ad1ead887fd0eae98c52dd6/R/dist.R#L739" # nolint
)
)
}

#' Specify a distribution.
#'
#' @description `r lifecycle::badge("stable")`
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26 changes: 0 additions & 26 deletions man/tune_inv_gamma.Rd
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