Reformat {stan} to stan

R/create.R

@@ -145,7 +145,7 @@ create_shifted_cases <- function(reported_cases, shift,
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Converts the `future` argument from [rt_opts()] into arguments that can be
-#' passed to `{stan}`.
+#' passed to stan.
 #'
 #' @param future A character string or integer. This argument indicates how to
 #' set future Rt values. Supported options are to project using the Rt model
@@ -185,7 +185,7 @@ create_future_rt <- function(future = "latest", delay = 0) {
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Takes the output from [rt_opts()] and converts it into a list understood by
-#' `{stan}`.
+#' stan.
 #' @param rt A list of options as generated by [rt_opts()] defining Rt
 #' estimation. Defaults to [rt_opts()]. Set to `NULL` to switch to using back
 #' calculation rather than generating infections using Rt.
@@ -257,7 +257,7 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Takes the output of [backcalc_opts()] and converts it into a list understood
-#' by `{stan}`.
+#' by stan.
 #'
 #' @param backcalc A list of options as generated by [backcalc_opts()] to
 #' define the back calculation. Defaults to [backcalc_opts()].
@@ -285,7 +285,7 @@ create_backcalc_data <- function(backcalc = backcalc_opts()) {
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Takes the output of [gp_opts()] and converts it into a list understood by
-#' `{stan}`.
+#' stan.
 #' @param gp A list of options as generated by [gp_opts()] to define the
 #' Gaussian process. Defaults to [gp_opts()]. Set to `NULL` to disable the
 #' Gaussian process.
@@ -357,12 +357,12 @@ create_gp_data <- function(gp = gp_opts(), data) {
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Takes the output of [obs_opts()] and converts it into a list understood
-#' by `{stan}`.
+#' by stan.
 #' @param obs A list of options as generated by [obs_opts()] defining the
 #' observation model. Defaults to [obs_opts()].
 #' @param dates A vector of dates used to calculate the day of the week.
 #' @seealso [obs_opts()]
-#' @return A list of settings ready to be passed to `{stan}` defining
+#' @return A list of settings ready to be passed to stan defining
 #' the Observation Model
 #' @export
 #' @author Sam Abbott
@@ -409,8 +409,8 @@ create_obs_model <- function(obs = obs_opts(), dates) {
 #'
 #' @description`r lifecycle::badge("stable")`
 #' Takes the output of [stan_opts()] and converts it into a list understood by
-#' `{stan}`. Internally calls the other `create_` family of functions to
-#' construct a single list for input into `{stan}` with all data required
+#' stan. Internally calls the other `create_` family of functions to
+#' construct a single list for input into stan with all data required
 #' present.
 #'
 #' @param shifted_cases A `<data.frame>` of delay shifted cases
@@ -500,7 +500,7 @@ create_stan_data <- function(reported_cases, seeding_time,
 #' @description `r lifecycle::badge("stable")`
 #' Uses the output of [create_stan_data()] to create a function which can be
 #' used to sample from the prior distributions (or as close as possible) for
-#' parameters. Used in order to initialise each `{stan}` chain within a range of
+#' parameters. Used in order to initialise each stan chain within a range of
 #' plausible values.
 #' @param data A list of data as produced by [create_stan_data()].
 #' @return An initial condition generating function
@@ -608,7 +608,7 @@ create_initial_conditions <- function(data) {
 #' to [stan_opts()]. Can be used to override `data`, `init`, and `verbose`
 #' settings if desired.
 #'
-#' @param data A list of `{stan}` data as created by [create_stan_data()]
+#' @param data A list of stan data as created by [create_stan_data()]
 #'
 #' @param init Initial conditions passed to `{rstan}`. Defaults to "random" but
 #' can also be a function (as supplied by [create_initial_conditions()]).
@@ -618,7 +618,7 @@ create_initial_conditions <- function(data) {
 #'
 #' @importFrom utils modifyList
 #'
-#' @return A list of `{stan}` arguments
+#' @return A list of stan arguments
 #' @author Sam Abbott
 #' @export
 #' @examples

R/dist.R

@@ -177,7 +177,7 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Fits an integer adjusted exponential, gamma or lognormal distribution using
-#' `{stan}`.
+#' stan.
 #' @param values Numeric vector of values
 #'
 #' @param samples Numeric, number of samples to take. Must be >= 1000.
@@ -196,7 +196,7 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #' @param verbose Logical, defaults to FALSE. Should verbose progress messages
 #' be printed.
 #'
-#' @return A `{stan}` fit of an interval censored distribution
+#' @return A stan fit of an interval censored distribution
 #' @author Sam Abbott
 #' @export
 #' @examples
@@ -614,7 +614,7 @@ estimate_delay <- function(delays, ...) {
 #'
 #' @description `r lifecycle::badge("soft-deprecated")`
 #' Convolves cases by a PMF function. This function will soon be removed or
-#' replaced with a more robust `{stan}` implementation.
+#' replaced with a more robust stan implementation.
 #'
 #' @param cases A `<data.frame>` of cases (in date order) with the following
 #' variables: `date` and `cases`.

R/extract.R

@@ -1,7 +1,7 @@
 #' Extract Samples for a Parameter from a Stan model
 #'
 #' @description `r lifecycle::badge("stable")`
-#' Extracts a single from a list of `{stan}` output and returns it as a
+#' Extracts a single from a list of stan output and returns it as a
 #' `<data.table>`.
 #
 #' @param param Character string indicating the parameter to extract
@@ -57,10 +57,10 @@ extract_static_parameter <- function(param, samples) {
 #' Extract Parameter Samples from a Stan Model
 #'
 #' @description `r lifecycle::badge("stable")`
-#' Extracts a custom set of parameters from a `{stan}` object and adds
+#' Extracts a custom set of parameters from a stan object and adds
 #' stratification and dates where appropriate.
 #'
-#' @param stan_fit A fit `{stan}` model as returned by [rstan::sampling()].
+#' @param stan_fit A fit stan model as returned by [rstan::sampling()].
 #'
 #' @param data A list of the data supplied to the [rstan::sampling()] call.
 #'

R/regional_epinow.R

@@ -296,7 +296,7 @@ clean_regions <- function(reported_cases, non_zero_points) {
 #'
 #' @description `r lifecycle::badge("maturing")`
 #' Internal function that handles calling [epinow()]. Future work will extend
-#' this function to better handle `{stan}` logs and allow the user to modify
+#' this function to better handle stan logs and allow the user to modify
 #' settings between regions.
 #'
 #' @param target_region Character string indicating the region being evaluated

R/utilities.R

@@ -106,7 +106,7 @@ map_prob_change <- function(var) {
 #'
 #' @description `r lifecycle::badge("questioning")`
 #' See [here](https://www.medrxiv.org/content/10.1101/2020.01.30.20019877v3.full.pdf) # nolint
-#' for justification. Now handled internally by `{stan}` so may be removed in
+#' for justification. Now handled internally by stan so may be removed in
 #' future updates if no user demand.
 #' @param r Numeric, rate of growth estimates.
 #'
@@ -146,7 +146,7 @@ R_to_growth <- function(R, gamma_mean, gamma_sd) {
 #' Allocate Delays into Required Stan Format
 #'
 #' @description `r lifecycle::badge("stable")`
-#' Allocate delays for `{stan}`. Used in [delay_opts()].
+#' Allocate delays for stan. Used in [delay_opts()].
 #' @param delay_var List of numeric delays
 #' @param no_delays Numeric, number of delays
 #' @return A numeric array
@@ -236,7 +236,7 @@ match_output_arguments <- function(input_args = NULL,
 #' Expose internal package stan functions in R
 #'
 #' @description `r lifecycle::badge("stable")`
-#' his function exposes internal `{stan}` functions in R from a user
+#' his function exposes internal stan functions in R from a user
 #' supplied list of target files. Allows for testing of stan functions in R and
 #' potentially user use in R code.
 #'