diff --git a/DESCRIPTION b/DESCRIPTION index c82fc7401..bd62a84c0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -108,4 +108,3 @@ LinkingTo: rstan (>= 2.21.1), StanHeaders (>= 2.21.0-5) Language: en-GB -RdMacros: lifecycle diff --git a/R/adjust.R b/R/adjust.R index 1f98c8c3f..078c58840 100644 --- a/R/adjust.R +++ b/R/adjust.R @@ -1,6 +1,6 @@ #' Adjust from Case Counts by Infection Date to Date of Report #' -#' @description \lifecycle{soft-deprecated} +#' @description `r lifecycle::badge("soft-deprecated")` #' Maps from cases by date of infection to date of report via date of #' onset. #' @param infections `data.table` containing a `date` variable and a numeric `cases` variable. diff --git a/R/create.R b/R/create.R index 27471ed14..1e729d7e0 100644 --- a/R/create.R +++ b/R/create.R @@ -1,5 +1,5 @@ #' Create Clean Reported Cases -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Cleans a data frame of reported cases by replacing missing dates with 0 cases and applies an optional #' threshold at which point 0 cases are replaced with a moving average of observed cases. See `zero_threshold` #' for details. @@ -40,7 +40,7 @@ create_clean_reported_cases <- function(reported_cases, horizon, zero_threshold #' Create Delay Shifted Cases #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' This functions creates a data frame of reported cases that has been smoothed using #' a rolling average (with a period set by `smoothing_window`) and shifted back in time #' by some delay. It is used by `estimate_infections` to generate the mean shifted prior @@ -86,7 +86,7 @@ create_shifted_cases <- function(reported_cases, shift, #' Construct the Required Future Rt assumption #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Converts the `future` argument from `rt_opts()` into arguments that can be 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 ("project"), to use the latest estimate based on partial data ("latest"), @@ -114,7 +114,7 @@ create_future_rt <- function(future = "latest", delay = 0) { #' Create Time-varying Reproduction Number Data #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Takes the output from `rt_opts()` and converts it into a list understood by #' `stan`. #' @param rt A list of options as generated by `rt_opts()` defining Rt estimation. @@ -178,7 +178,7 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL, } #' Create Back Calculation Data #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Takes the output of `backcalc_opts()` and converts it into a list understood by `stan`. #' @param backcalc A list of options as generated by `backcalc_opts()` to define the #' back calculation. Defaults to `backcalc_opts()`. @@ -208,7 +208,7 @@ create_backcalc_data <- function(backcalc = backcalc_opts) { } #' Create Gaussian Process Data #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Takes the output of `gp_opts()` and converts it into a list understood by `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 @@ -273,7 +273,7 @@ create_gp_data <- function(gp = gp_opts(), data) { #' Create Observation Model Settings #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Takes the output of `obs_opts()` and converts it into a list understood by `stan`. #' @param obs A list of options as generated by `obs_opts()` defining the #' observation model. Defaults to `obs_opts()`. @@ -306,12 +306,12 @@ create_obs_model <- function(obs = obs_opts()) { } #' Create Stan Data Required for estimate_infections #' -#' @description \lifecycle{stable} +#' @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 present. #' @param shifted_cases A dataframe of delay shifted cases -#' @param truncation \lifecycle{experimental} A list of options as generated by `trunc_opts()` +#' @param truncation `r lifecycle::badge("experimental")` A list of options as generated by `trunc_opts()` #' defining the truncation of observed data. Defaults to `trunc_opts()`. See `estimate_truncation()` #' for an approach to estimating truncation from data. #' @inheritParams create_gp_data @@ -383,7 +383,7 @@ create_stan_data <- function(reported_cases, generation_time, } #' Create Initial Conditions Generating Function -#' @description \lifecycle{stable} +#' @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 plausible values. @@ -447,7 +447,7 @@ create_initial_conditions <- function(data) { #' Create a List of Stan Arguments #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Generates a list of arguments as required by `rstan::sampling` or `rstan::vb` by combining the required options, #' with data, and type of initialisation. Initialisation defaults to random but it is expected that `create_initial_conditions` #' will be used. diff --git a/R/data.R b/R/data.R index 02a2ea868..8e4c6c342 100644 --- a/R/data.R +++ b/R/data.R @@ -1,6 +1,6 @@ #' Literature Estimates of Generation Times #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Generation time estimates. See here for details: #' https://github.com/epiforecasts/EpiNow2/blob/master/data-raw/generation-time.R #' @format A `data.table` of summarising the distribution @@ -8,7 +8,7 @@ #' Literature Estimates of Incubation Periods #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Incubation period estimates. See here for details: #' https://github.com/epiforecasts/EpiNow2/blob/master/data-raw/incubation-period.R #' @format A `data.table` of summarising the distribution @@ -17,7 +17,7 @@ #' Example Confirmed Case Data Set #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' An example data frame of observed cases #' @format A data frame containing cases reported on each date. "example_confirmed" \ No newline at end of file diff --git a/R/dist.R b/R/dist.R index 329321ec0..20fa73832 100644 --- a/R/dist.R +++ b/R/dist.R @@ -1,6 +1,6 @@ #' Distribution Skeleton #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' This function acts as a skeleton for a truncated distribution defined by #' model type, maximum value and model parameters. It is designed to be used with the #' output from `get_dist`. @@ -121,7 +121,7 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model, #' Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Fits an integer adjusted exponential, gamma or lognormal distribution using #' `stan`. #' @param values Numeric vector of values @@ -212,7 +212,7 @@ dist_fit <- function(values = NULL, samples = NULL, cores = 1, #' Generate a Gamma Distribution Definition Based on Parameter Estimates #' -#' @description \lifecycle{soft-deprecated} +#' @description `r lifecycle::badge("soft-deprecated")` #' Generates a distribution definition when only parameter estimates #' are available for gamma distributed parameters. See `rgamma` for distribution information. #' @param shape Numeric, shape parameter of the gamma distribution. @@ -268,7 +268,7 @@ gamma_dist_def <- function(shape, shape_sd, #' Generate a Log Normal Distribution Definition Based on Parameter Estimates #' -#' @description \lifecycle{soft-deprecated} +#' @description `r lifecycle::badge("soft-deprecated")` #' Generates a distribution definition when only parameter estimates #' are available for log normal distributed parameters. See `rlnorm` for distribution information. #' @param mean Numeric, log mean parameter of the gamma distribution. @@ -334,7 +334,7 @@ lognorm_dist_def <- function(mean, mean_sd, #' Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Fits an integer adjusted distribution to a subsampled bootstrap of data and then integrates #' the posterior samples into a single set of summary statistics. Can be used to generate a robust #' reporting delay that accounts for the fact the underlying delay likely varies over time or that @@ -432,7 +432,7 @@ bootstrapped_dist_fit <- function(values, dist = "lognormal", #' Estimate a Delay Distribution #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Estimate a log normal delay distribution from a vector of integer delays. #' Currently this function is a simple wrapper for `bootstrapped_dist_fit`. #' @param delays Integer vector of delays @@ -452,7 +452,7 @@ estimate_delay <- function(delays, ...) { #' Approximate Sampling a Distribution using Counts #' -#' @description \lifecycle{soft-deprecated} +#' @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. #' @param cases A dataframe of cases (in date order) with the following variables: @@ -595,7 +595,7 @@ sample_approx_dist <- function(cases = NULL, #' Tune an Inverse Gamma to Achieve the Target Truncation #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' 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 diff --git a/R/epinow-internal.R b/R/epinow-internal.R index a7ac0fa25..08e9ed064 100644 --- a/R/epinow-internal.R +++ b/R/epinow-internal.R @@ -1,6 +1,6 @@ #' Updates Forecast Horizon Based on Input Data and Target #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Makes sure that a forecast is returned for the user specified #' time period beyond the target date. #' @inheritParams setup_target_folder @@ -16,7 +16,7 @@ update_horizon <- function(horizon, target_date, reported_cases) { #' Save Observed Data #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Saves observed data to a target location if given. #' @inheritParams setup_target_folder #' @inheritParams epinow @@ -36,7 +36,7 @@ save_input <- function(reported_cases, target_folder) { #' Save Estimated Infections #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Saves output from `estimate_infections` to a target directory. #' @param estimates List of data frames as output by `estimate_infections` #' @param samples Logical, defaults to TRUE. Should samples be saved @@ -65,7 +65,7 @@ save_estimate_infections <- function(estimates, target_folder = NULL, #' Save Forecast Infections #' -#' @description \lifecycle{experimental} +#' @description `r lifecycle::badge("experimental")` #' Saves the output from `forecast_infections` to a target directory. #' @param forecast A list of data frames as output by `forecast_infections` #' @inheritParams save_estimate_infections @@ -85,7 +85,7 @@ save_forecast_infections <- function(forecast, target_folder = NULL, samples = T #' Estimate Cases by Report Date #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Either extracts or converts reported cases from an input data table. For output from #' `estimate_infections` this is a simple filtering step but for output from `forecast_infection` #' this is currently an approximate convolution. This step is likely to be updated/deprecated @@ -158,7 +158,7 @@ estimates_by_report_date <- function(estimates, forecast, delays, CrIs = c(0.2, #' Copy Results From Dated Folder to Latest #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Copies output from the dated folder to a latest folder. May be undergo changes in later releases. #' @param latest_folder Character string containing the path to the latest target folder. #' As produced by `setup_target_folder`. @@ -188,7 +188,7 @@ copy_results_to_latest <- function(target_folder = NULL, latest_folder = NULL) { #' Construct Output #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Combines the output produced internally by `epinow` into a single list. #' @param estimated_reported_cases A list of dataframes as produced by #' `estimates_by_report_date`. diff --git a/R/epinow.R b/R/epinow.R index 69b70f8bb..d1ce8f6ac 100644 --- a/R/epinow.R +++ b/R/epinow.R @@ -1,6 +1,6 @@ #' Real-time Rt Estimation, Forecasting and Reporting #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' This function wraps the functionality of `estimate_infections()` and `forecast_infections()` in order #' to estimate Rt and cases by date of infection, forecast into these infections into the future. It also contains #' additional functionality to convert forecasts to date of report and produce summary output useful for reporting diff --git a/R/estimate_infections.R b/R/estimate_infections.R index e59960daa..9e3c65aa7 100644 --- a/R/estimate_infections.R +++ b/R/estimate_infections.R @@ -1,6 +1,6 @@ #' Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Uses a non-parametric approach to reconstruct cases by date of infection from reported #' cases. It uses either a generative Rt model or non-parametric back calculation to estimate underlying #' latent infections and then maps these infections to observed cases via uncertain reporting delays and a flexible @@ -256,7 +256,7 @@ estimate_infections <- function(reported_cases, #' Fit a Stan Model using the NUTs sampler #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Fits a stan model using `rstan::sampling`. Provides the optional ability to run chains using #' `future` with error catching, timeouts and merging of completed chains. #' @param args List of stan arguments @@ -365,7 +365,7 @@ fit_model_with_nuts <- function(args, future = FALSE, max_execution_time = Inf, #' Fit a Stan Model using Variational Inference #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Fits a stan model using variational inference. #' @inheritParams fit_model_with_nuts #' @importFrom futile.logger flog.debug flog.info flog.error @@ -425,7 +425,7 @@ fit_model_with_vb <- function(args, future = FALSE, id = "stan", verbose = FALSE #' Format Posterior Samples #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Summaries posterior samples and adds additional custom variables. #' @param posterior_samples A list of posterior samples as returned by `extract_parameter_samples` #' @param horizon Numeric, forecast horizon diff --git a/R/estimate_truncation.R b/R/estimate_truncation.R index 2b1ae55af..c51427e94 100644 --- a/R/estimate_truncation.R +++ b/R/estimate_truncation.R @@ -1,6 +1,6 @@ #' Estimate Truncation of Observed Data #' -#' @description \lifecycle{experimental} +#' @description `r lifecycle::badge("experimental")` #' Estimates a truncation distribution from multiple snapshots of the same #' data source over time. This distribution can then be used in `regional_epinow`, #' `epinow`, and `estimate_infections` to adjust for truncated data. See [here](https://gist.github.com/seabbs/176b0c7f83eab1a7192a25b28bbd116a) @@ -198,8 +198,8 @@ estimate_truncation <- function(obs, max_truncation = 10, #' Plot method for estimate_truncation #' -#' @description \lifecycle{experimental} -#' \code{plot} method for class "estimate_truncation". Returns +#' @description `r lifecycle::badge("experimental")` +#' `plot` method for class "estimate_truncation". Returns #' a plot faceted over each dataset used in fitting with the latest #' observations as columns, the data observed at the time (and so truncated) #' as dots and the truncation adjusted estimates as a ribbon. diff --git a/R/extract.R b/R/extract.R index 99bd4dd11..9e8ed8596 100644 --- a/R/extract.R +++ b/R/extract.R @@ -1,6 +1,6 @@ #' Extract Samples for a Parameter from a Stan model #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' 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 #' @param samples Extracted stan model (using `rstan::extract`) @@ -41,7 +41,7 @@ extract_static_parameter <- function(param, samples) { #' Extract Parameter Samples from a Stan Model #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' 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` diff --git a/R/forecast_infections.R b/R/forecast_infections.R index 0b79821d1..a55c69e95 100644 --- a/R/forecast_infections.R +++ b/R/forecast_infections.R @@ -1,6 +1,6 @@ #' Forecast Infections and the Time-Varying Reproduction Number #' -#' @description \lifecycle{experimental} +#' @description `r lifecycle::badge("experimental")` #' Provides optional tools for forecasting cases and Rt estimates using the timeseries methods #' (via the `EpiSoon` package). It requires the `Episoon` package. Installation instructions for the EpiSoon package are #' available [here](https://epiforecasts.io/EpiSoon/). diff --git a/R/get.R b/R/get.R index efa5a6f0c..d00239764 100644 --- a/R/get.R +++ b/R/get.R @@ -1,6 +1,6 @@ #' Get Folders with Results #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' @param results_dir A character string giving the directory in which results #' are stored (as produced by `regional_rt_pipeline`). #' @return A named character vector containing the results to plot. @@ -19,7 +19,7 @@ get_regions <- function(results_dir) { } #' Get a Single Raw Result #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' @param file Character string giving the result files name. #' @param region Character string giving the region of interest. #' @param date Target date (in the format `"yyyy-mm-dd`). @@ -34,7 +34,7 @@ get_raw_result <- function(file, region, date, } #' Get Combined Regional Results #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Summarises results across regions either from input or from disk. See the examples for #' details. #' @param regional_output A list of output as produced by `regional_epinow` and stored in the @@ -154,7 +154,7 @@ get_regional_results <- function(regional_output, #' Get a Literature Distribution #' #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Search a data frame for a distribution and return it in the format expected #' by `delay_opts` and the `generation_time` argument of `epinow` and `estimate_infections`. #' @param data A `data.table` in the format of `generation_times`. @@ -175,7 +175,7 @@ get_dist <- function(data, disease, source, max_value = 15) { } #' Get a Literature Distribution for the Generation Time #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Extracts a literature distribution from `generation_times` #' @inheritParams get_dist #' @inherit get_dist @@ -191,7 +191,7 @@ get_generation_time <- function(disease, source, max_value = 15) { } #' Get a Literature Distribution for the Incubation Period #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Extracts a literature distribution from `incubation_periods` #' @inheritParams get_dist #' @inherit get_dist @@ -207,7 +207,7 @@ get_incubation_period <- function(disease, source, max_value = 15) { } #' Get Regions with Most Reported Cases #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Extract a vector of regions with the most reported cases in a set time window. #' @param time_window Numeric, number of days to include from latest date in data. #' Defaults to 7 days. diff --git a/R/map.R b/R/map.R index 4f4b98649..c0e2e0483 100644 --- a/R/map.R +++ b/R/map.R @@ -1,7 +1,7 @@ #' Generate a global map for a single variable. #' #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' This general purpose function can be used to generate a global map for a single variable. It has few defaults but #' the data supplied must contain a \code{country} variable for linking to mapping data. This function requires the #' installation of the `rnaturalearth` package. Status of this function is currently questioning as it is uncertain @@ -120,7 +120,7 @@ global_map <- function(data = NULL, variable = NULL, #' Generate a country map for a single variable. #' #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' This general purpose function can be used to generate a country map for a single variable. It has few defaults but #' the data supplied must contain a \code{region_code} variable for linking to mapping data. This function requires #' the installation of the `rnaturalearth` package. Status of this function is currently questioning as it is uncertain @@ -228,7 +228,7 @@ country_map <- function(data = NULL, country = NULL, #' Custom Map Theme #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Applies a custom map theme to be used with `global_map`, `country_map`, and other `ggplot2` maps. Status of #' this function is currently questioning as it is uncertain if it is in use. Future releases may depreciate it. #' @param map `ggplot2` map object diff --git a/R/opts.R b/R/opts.R index c1c681b57..7f5167d19 100644 --- a/R/opts.R +++ b/R/opts.R @@ -38,7 +38,7 @@ delay_opts <- function(...) { #' Truncation Distribution Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Returns a truncation distribution formatted for usage by downstream functions. See #' `estimate_truncation` for an approach to estimate this distribution. #' @param dist A list defining the truncation distribution, defaults to `NULL` in which @@ -64,7 +64,7 @@ trunc_opts <- function(dist = NULL) { #' Time-Varying Reproduction Number Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the optional arguments for the time-varying reproduction number. #' Custom settings can be supplied which override the defaults. #' @param prior List containing named numeric elements "mean" and "sd". The mean and @@ -130,7 +130,7 @@ rt_opts <- function(prior = list(mean = 1, sd = 1), #' Back Calculation Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the optional arguments for the back calculation #' of cases. Only used if `rt = NULL`. #' @param prior_window Integer, defaults to 7 days. The mean smoothing window to apply @@ -157,7 +157,7 @@ backcalc_opts <- function(prior_window = 7, rt_window = 1) { #' Approximate Gaussian Process Settings #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the structure of the approximate Gaussian #' process. Custom settings can be supplied which override the defaults. #' @param ls_mean Numeric, defaults to 21 days. The mean of the lognormal length scale. @@ -217,7 +217,7 @@ gp_opts <- function(basis_prop = 0.2, #' Observation Model Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the structure of the observation #' model. Custom settings can be supplied which override the defaults. #' @param family Character string defining the observation model. Options are @@ -263,7 +263,7 @@ obs_opts <- function(family = "negbin", #' Rstan Sampling Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the arguments passed to #' `rstan::sampling`. Custom settings can be supplied which override the defaults. #' @param cores Number of cores to use when executing the chains in parallel, @@ -320,7 +320,7 @@ rstan_sampling_opts <- function(cores = getOption("mc.cores", 1L), #' Rstan Variational Bayes Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the arguments passed to #' `rstan::vb`. Custom settings can be supplied which override the defaults. #' @param samples Numeric, default 2000. Overall number of approximate posterior @@ -348,7 +348,7 @@ rstan_vb_opts <- function(samples = 2000, #' Rstan Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the arguments passed to underlying `rstan` #' functions via `rstan_sampling_opts` and `rstan_vb_opts`.Custom settings can be supplied #' which override the defaults. @@ -387,7 +387,7 @@ rstan_opts <- function(object = NULL, #' Stan Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Defines a list specifying the arguments passed to underlying stan #' backend functions via `rstan_sampling_opts` and `rstan_vb_opts`. Custom settings #' can be supplied which override the defaults. @@ -420,7 +420,7 @@ stan_opts <- function(samples = 2000, #' Return an _opts List per Region #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Define a list of `_opts` to pass to `regional_epinow` `_opts` accepting arguments. #' This is useful when different settings are needed between regions within a single #' `regional_epinow` call. Using `opts_list` the defaults can be applied to all regions @@ -462,7 +462,7 @@ opts_list <- function(opts, reported_cases, ...) { #' Filter Options for a Target Region #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' A helper function that allows the selection of region specific settings if #' present and otherwise applies the overarching settings #' @param opts Either a list of calls to an `_opts` function or a single diff --git a/R/plot.R b/R/plot.R index 752bb3dd3..ee9aeed17 100644 --- a/R/plot.R +++ b/R/plot.R @@ -1,6 +1,6 @@ #' Plot EpiNow2 Credible Intervals #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Adds lineranges for user specified credible intervals #' @param plot A `ggplot2` plot #' @param CrIs Numeric list of credible intervals present in the data. As produced @@ -31,7 +31,7 @@ plot_CrIs <- function(plot, CrIs, alpha, size) { #' Plot Estimates #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Allows users to plot the output from `estimate_infections` easily. In future releases it #' may be depreciated in favour of increasing the functionality of the S3 plot methods. #' @param estimate A data.table of estimates containing the following variables: date, type @@ -170,7 +170,7 @@ plot_estimates <- function(estimate, reported, ylab = "Cases", hline, #' Plot a Summary of the Latest Results #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Used to return a summary plot across regions (using results generated by `summarise_results`). #' May be depreciated in later releases in favour of enhanced S3 methods. #' @param summary_results A data.table as returned by `summarise_results` (the `data` object). @@ -274,8 +274,8 @@ plot_summary <- function(summary_results, #' Plot method for estimate_infections #' -#' @description \lifecycle{maturing} -#' \code{plot} method for class "estimate_infections". +#' @description `r lifecycle::badge("maturing")` +#' `plot` method for class "estimate_infections". #' @param x A list of output as produced by `estimate_infections` #' @param type A character vector indicating the name of plots to return. Defaults #' to "summary" with supported options being "infections", "reports", "R", "growth_rate", @@ -308,8 +308,8 @@ plot.estimate_infections <- function(x, type = "summary", ...) { #' Plot method for epinow #' -#' @description \lifecycle{maturing} -#' \code{plot} method for class "epinow". +#' @description `r lifecycle::badge("maturing")` +#' `plot` method for class "epinow". #' @param x A list of output as produced by `epinow` #' @inheritParams plot.estimate_infections #' @seealso plot plot.estimate_infections report_plots estimate_infections diff --git a/R/regional_epinow.R b/R/regional_epinow.R index 38216a45a..d3baf82e1 100644 --- a/R/regional_epinow.R +++ b/R/regional_epinow.R @@ -1,6 +1,6 @@ #' Real-time Rt Estimation, Forecasting and Reporting by Region #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Efficiently runs `epinow()` across multiple regions in an efficient manner and conducts basic data checks and #' cleaning such as removing regions with fewer than `non_zero_points` as these are unlikely to produce reasonable #' results whilst consuming significant resources. See the documentation for `epinow` for further information. @@ -207,7 +207,7 @@ regional_epinow <- function(reported_cases, #' Clean Regions #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Removes regions with insufficient time points, and provides logging information on the #' input. #' @seealso regional_epinow @@ -244,7 +244,7 @@ clean_regions <- function(reported_cases, non_zero_points) { #' Run epinow with Regional Processing Code #' -#' @description \lifecycle{maturing} +#' @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 settings between #' regions. @@ -327,7 +327,7 @@ run_region <- function(target_region, #' Process regional estimate #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Internal function that removes output that is not required, and returns logging #' information. #' @param out List of output returned by `epinow` @@ -364,7 +364,7 @@ process_region <- function(out, target_region, timing, #' Process all Region Estimates #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Internal function that processes the output from multiple `epinow` runs, adds #' summary logging information. #' @param regional_out A list of output from multiple runs of `regional_epinow` diff --git a/R/report.R b/R/report.R index 14cb893f7..557720111 100644 --- a/R/report.R +++ b/R/report.R @@ -1,6 +1,6 @@ #' Report case counts by date of report #' -#' @description \lifecycle{soft-deprecated} +#' @description `r lifecycle::badge("soft-deprecated")` #' Convolves latent infections to reported cases via an observation model. Likely to be removed/replaced #' in later releases by functionality drawing on the `stan` implementation. #' @param case_estimates A data.table of case estimates with the following variables: date, sample, cases @@ -98,7 +98,7 @@ report_cases <- function(case_estimates, #' Provide Summary Statistics for Estimated Infections and Rt -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Creates a snapshot summary of estimates. May be removed in later releases as S3 methods are #' enhanced. #' @param summarised_estimates A data.table of summarised estimates containing the following variables: @@ -180,7 +180,7 @@ report_summary <- function(summarised_estimates, #' Report plots #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Returns key summary plots for estimates. May be depreciated in later releases as current S3 methods #' are enhanced. #' @param summarised_estimates A data.table of summarised estimates containing the following variables: diff --git a/R/setup.R b/R/setup.R index 0e978e750..1dd5350a2 100644 --- a/R/setup.R +++ b/R/setup.R @@ -1,6 +1,6 @@ #' Setup Logging #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Sets up `futile.logger` logging, which is integrated into `EpiNow2`. See the #' documentation for `futile.logger` for full details. By default `EpiNow2` prints all logs at #' the "INFO" level and returns them to the console. Usage of logging is currently being explored @@ -49,7 +49,7 @@ setup_logging <- function(threshold = "INFO", file = NULL, #' Setup Default Logging #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Sets up default logging. Usage of logging is currently being explored as the current setup #' cannot log stan errors or progress. #' @param logs Character path indicating the target folder in which to store log @@ -94,7 +94,7 @@ setup_default_logging <- function(logs = tempdir(), } #' Set up Future Backend -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' A utility function that aims to streamline the set up #' of the required future backend with sensible defaults for most users of `regional_epinow`. #' More advanced users are recommended to setup their own `future` backend based on their @@ -147,7 +147,7 @@ setup_future <- function(reported_cases, strategies = c("multiprocess", "multipr } #' Convert to Data Table -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Convenience function that sets the number of `data.table` cores to 1 and #' maps input to be a `data.table` #' @inheritParams estimate_infections @@ -162,7 +162,7 @@ setup_dt <- function(reported_cases) { #' Setup Target Folder for Saving #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Sets up a folders for saving results #' @param target_date Date, defaults to maximum found in the data if not specified. #' @param target_folder Character string specifying where to save results (will create if not present). diff --git a/R/simulate.R b/R/simulate.R index 50bc5cf80..28589f4cb 100644 --- a/R/simulate.R +++ b/R/simulate.R @@ -1,6 +1,6 @@ #' Simulate Cases by Date of Infection, Onset and Report #' -#' \@description \lifecycle{questioning} +#' \@description `r lifecycle::badge("questioning")` #' Simulate cases from a single Rt trace, an initial number of cases, and a reporting model #' This functionality has largely been superseded by `simulate_infections` and will likely to replaced #' or updated to depend on `stan` code. diff --git a/R/simulate_infections.R b/R/simulate_infections.R index a87e3876e..d86364f57 100644 --- a/R/simulate_infections.R +++ b/R/simulate_infections.R @@ -1,6 +1,6 @@ #' Simulate infections using a given trajectory of the time-varying reproduction number #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' This function simulates infections using an existing fit to observed cases but with a modified #' time-varying reproduction number. This can be used to explore forecast models or past counterfactuals. #' Simulations can be run in parallel using `future::plan`. diff --git a/R/summarise.R b/R/summarise.R index a55d215ee..44ff8c492 100644 --- a/R/summarise.R +++ b/R/summarise.R @@ -1,6 +1,6 @@ #' Summarise Real-time Results #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' Used internally by `regional_summary` to produce a summary table of results. May be streamlined in later #' releases. #' @param regions An character string containing the list of regions to extract results for @@ -91,7 +91,7 @@ summarise_results <- function(regions, #' Regional Summary Output #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Used to produce summary output either internally in `regional_epinow` or externally. #' @param summary_dir A character string giving the directory #' in which to store summary of results. @@ -323,7 +323,7 @@ regional_summary <- function(regional_output = NULL, #' Summarise rt and cases #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Produces summarised data frames of output across regions. Used internally by `regional_summary`. #' @param regional_results A list of dataframes as produced by `get_regional_results` #' @param results_dir Character string indicating the directory from which to extract results. @@ -387,7 +387,7 @@ summarise_key_measures <- function(regional_results = NULL, #' Summarise Regional Runtimes #' -#' @description \lifecycle{maturing} +#' @description `r lifecycle::badge("maturing")` #' Used internally by `regional_epinow` to summarise region run times. #' @seealso regional_summary regional_epinow #' @inheritParams regional_summary @@ -462,7 +462,7 @@ regional_runtimes <- function(regional_output = NULL, #' Calculate Credible Interval #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Adds symmetric a credible interval based on quantiles. #' @param samples A data.table containing at least a value variable #' @param summarise_by A character vector of variables to group by. @@ -494,7 +494,7 @@ calc_CrI <- function(samples, summarise_by = c(), CrI = 0.9) { #' Calculate Credible Intervals #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Adds symmetric credible intervals based on quantiles. #' @param CrIs Numeric vector of credible intervals to calculate. #' @inheritParams calc_CrI @@ -544,7 +544,7 @@ extract_CrIs <- function(summarised) { #' Calculate Summary Statistics #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Calculate summary statistics from a data frame by group. Currently supports the #' mean, median and standard deviation. #' @return A data.table containing the upper and lower bounds for the specified credible interval @@ -569,7 +569,7 @@ calc_summary_stats <- function(samples, summarise_by = c()) { #' Calculate All Summary Measures #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Calculate summary statistics and credible intervals from a data frame by group. #' @param order_by A character vector of parameters to order by, defaults to all `summarise_by` #' variables. @@ -609,7 +609,7 @@ calc_summary_measures <- function(samples, #' Summary output from epinow #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' \code{summary} method for class "epinow". #' @param object A list of output as produced by "epinow". #' @param output A character string of output to summarise. Defaults to "estimates" @@ -644,7 +644,7 @@ summary.epinow <- function(object, output = "estimates", #' Summary output from estimate_infections #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' \code{summary} method for class "estimate_infections". #' @param object A list of output as produced by "estimate_infections". #' @param type A character vector of data types to return. Defaults to "snapshot" diff --git a/R/utilities.R b/R/utilities.R index 9e0e6ad21..e988883e6 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -1,6 +1,6 @@ #' Clean Nowcasts for a Supplied Date #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' This function removes nowcasts in the format produced by `EpiNow2` from a target #' directory for the date supplied. #' @param date Date object. Defaults to today's date @@ -32,7 +32,7 @@ clean_nowcasts <- function(date = NULL, nowcast_dir = ".") { #' Format Credible Intervals #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Combines a list of values into formatted credible intervals. #' @param value List of value to map into a string. Requires, #' `point`, `lower`, and `upper.` @@ -56,7 +56,7 @@ make_conf <- function(value, CrI = 90, reverse = FALSE) { #' Categorise the Probability of Change for Rt #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Categorises a numeric variable into "Increasing" (< 0.05), #' "Likely increasing" (<0.2), "Unsure" (< 0.8), "Likely decreasing" (< 0.95), "Decreasing" (<= 1) #' @param var Numeric variable to be categorised @@ -81,7 +81,7 @@ map_prob_change <- function(var) { #' Convert Growth Rates to Reproduction numbers. #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' See [here](https://www.medrxiv.org/content/10.1101/2020.01.30.20019877v3.full.pdf) #' for justification. Now handled internally by stan so may be removed in future updates if #' no user demand. @@ -100,7 +100,7 @@ growth_to_R <- function(r, gamma_mean, gamma_sd) { #' Convert Reproduction Numbers to Growth Rates #' -#' @description \lifecycle{questioning} +#' @description `r lifecycle::badge("questioning")` #' See [here](https://www.medrxiv.org/content/10.1101/2020.01.30.20019877v3.full.pdf) #' for justification. Now handled internally by stan so may be removed in future updates if #' no user demand. @@ -119,7 +119,7 @@ R_to_growth <- function(R, gamma_mean, gamma_sd) { #' Allocate Delays into Required Stan Format #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Allocate delays for stan. Used in `delay_opts`. #' @param delay_var List of numeric delays #' @param no_delays Numeric, number of delays @@ -135,7 +135,7 @@ allocate_delays <- function(delay_var, no_delays) { #' Allocate Empty Parameters to a List #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Allocate missing parameters to be empty two dimensional arrays. Used #' internally by `simulate_infections.` #' @param data A list of parameters @@ -155,7 +155,7 @@ allocate_empty <- function(data, params) { } #' Match User Supplied Arguments with Supported Options #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Match user supplied arguments with supported options and return a logical list for #' internal usage #' @param input_args A character vector of input arguments (can be partial). @@ -220,7 +220,7 @@ match_output_arguments <- function(input_args = c(), #' Expose internal package stan functions in R #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' 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. @@ -252,7 +252,7 @@ expose_stan_fns <- function(files, target_dir, ...) { #' Convert mean and sd to log mean for a log normal distribution #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Convert from mean and standard deviation to the log mean of the #' lognormal distribution. Useful for defining distributions supported by #' `estimate_infections`, `epinow`, and `regional_epinow`. @@ -271,7 +271,7 @@ convert_to_logmean <- function(mean, sd){ #' Convert mean and sd to log standard deviation for a log normal distribution #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Convert from mean and standard deviation to the log standard deviation of the #' lognormal distribution. Useful for defining distributions supported by #' `estimate_infections`, `epinow`, and `regional_epinow`. @@ -291,7 +291,7 @@ convert_to_logsd <- function(mean, sd) { #' Update a List #' -#' @description \lifecycle{stable} +#' @description `r lifecycle::badge("stable")` #' Used to handle updating settings in a list. For example when making #' changes to `opts_list` output. #' @param defaults A list of default settings diff --git a/man/R_to_growth.Rd b/man/R_to_growth.Rd index 65905c1e5..297d6fcc5 100644 --- a/man/R_to_growth.Rd +++ b/man/R_to_growth.Rd @@ -17,7 +17,7 @@ R_to_growth(R, gamma_mean, gamma_sd) Numeric vector of reproduction number estimates } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} See \href{https://www.medrxiv.org/content/10.1101/2020.01.30.20019877v3.full.pdf}{here} for justification. Now handled internally by stan so may be removed in future updates if no user demand. diff --git a/man/adjust_infection_to_report.Rd b/man/adjust_infection_to_report.Rd index 8351b1663..02851d9bf 100644 --- a/man/adjust_infection_to_report.Rd +++ b/man/adjust_infection_to_report.Rd @@ -36,7 +36,7 @@ A \code{data.table} containing a \code{date} variable (date of report) and a \co a third variable \code{reference} which indicates what the date variable refers to. } \description{ -\lifecycle{soft-deprecated} +\ifelse{html}{\figure{lifecycle-soft-deprecated.svg}{options: alt='Soft-deprecated lifecycle'}}{\strong{Soft-deprecated}} Maps from cases by date of infection to date of report via date of onset. } diff --git a/man/allocate_delays.Rd b/man/allocate_delays.Rd index cd3007285..06afb9cd0 100644 --- a/man/allocate_delays.Rd +++ b/man/allocate_delays.Rd @@ -15,6 +15,6 @@ allocate_delays(delay_var, no_delays) A numeric array } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Allocate delays for stan. Used in \code{delay_opts}. } diff --git a/man/allocate_empty.Rd b/man/allocate_empty.Rd index 0d7908973..35a6626ba 100644 --- a/man/allocate_empty.Rd +++ b/man/allocate_empty.Rd @@ -16,7 +16,7 @@ empty if missing.} A list of parameters some allocated to be empty } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Allocate missing parameters to be empty two dimensional arrays. Used internally by \code{simulate_infections.} } diff --git a/man/backcalc_opts.Rd b/man/backcalc_opts.Rd index 38c935f13..b347d7522 100644 --- a/man/backcalc_opts.Rd +++ b/man/backcalc_opts.Rd @@ -19,7 +19,7 @@ Rt. This must be odd so that the central estimate is included.} A list of back calculation settings } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the optional arguments for the back calculation of cases. Only used if \code{rt = NULL}. } diff --git a/man/bootstrapped_dist_fit.Rd b/man/bootstrapped_dist_fit.Rd index 494061711..cf1b6c8b4 100644 --- a/man/bootstrapped_dist_fit.Rd +++ b/man/bootstrapped_dist_fit.Rd @@ -37,7 +37,7 @@ allow (added to output but does impact fitting).} A list summarising the bootstrapped distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Fits an integer adjusted distribution to a subsampled bootstrap of data and then integrates the posterior samples into a single set of summary statistics. Can be used to generate a robust reporting delay that accounts for the fact the underlying delay likely varies over time or that diff --git a/man/calc_CrI.Rd b/man/calc_CrI.Rd index 4a814e0a9..8de738e39 100644 --- a/man/calc_CrI.Rd +++ b/man/calc_CrI.Rd @@ -18,7 +18,7 @@ Defaults to 0.9.} A data.table containing the upper and lower bounds for the specified credible interval } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Adds symmetric a credible interval based on quantiles. } \examples{ diff --git a/man/calc_CrIs.Rd b/man/calc_CrIs.Rd index ef4a3412d..c5b3f0aa0 100644 --- a/man/calc_CrIs.Rd +++ b/man/calc_CrIs.Rd @@ -18,7 +18,7 @@ A data.table containing the \code{summarise_by} variables and the specified lowe credible intervals } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Adds symmetric credible intervals based on quantiles. } \examples{ diff --git a/man/calc_summary_measures.Rd b/man/calc_summary_measures.Rd index 196ca20bc..55c70dacf 100644 --- a/man/calc_summary_measures.Rd +++ b/man/calc_summary_measures.Rd @@ -25,7 +25,7 @@ variables.} A data.table containing summary statistics by group. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Calculate summary statistics and credible intervals from a data frame by group. } \examples{ diff --git a/man/calc_summary_stats.Rd b/man/calc_summary_stats.Rd index c475f59ad..86224bcda 100644 --- a/man/calc_summary_stats.Rd +++ b/man/calc_summary_stats.Rd @@ -15,7 +15,7 @@ calc_summary_stats(samples, summarise_by = c()) A data.table containing the upper and lower bounds for the specified credible interval } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Calculate summary statistics from a data frame by group. Currently supports the mean, median and standard deviation. } diff --git a/man/clean_nowcasts.Rd b/man/clean_nowcasts.Rd index 40f8628ce..9f536dfcc 100644 --- a/man/clean_nowcasts.Rd +++ b/man/clean_nowcasts.Rd @@ -13,7 +13,7 @@ clean_nowcasts(date = NULL, nowcast_dir = ".") to the current directory.} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} This function removes nowcasts in the format produced by \code{EpiNow2} from a target directory for the date supplied. } diff --git a/man/clean_regions.Rd b/man/clean_regions.Rd index 5fb227094..494a14ac2 100644 --- a/man/clean_regions.Rd +++ b/man/clean_regions.Rd @@ -16,7 +16,7 @@ that region to be evaluated. Defaults to 7.} A dataframe of cleaned regional data } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Removes regions with insufficient time points, and provides logging information on the input. } diff --git a/man/construct_output.Rd b/man/construct_output.Rd index 2831f1a05..18b003ba6 100644 --- a/man/construct_output.Rd +++ b/man/construct_output.Rd @@ -31,6 +31,6 @@ construct_output( A list of output as returned by \code{epinow} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Combines the output produced internally by \code{epinow} into a single list. } diff --git a/man/convert_to_logmean.Rd b/man/convert_to_logmean.Rd index f4b628a91..5a68c1ccf 100644 --- a/man/convert_to_logmean.Rd +++ b/man/convert_to_logmean.Rd @@ -15,7 +15,7 @@ convert_to_logmean(mean, sd) The log mean of a lognormal distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Convert from mean and standard deviation to the log mean of the lognormal distribution. Useful for defining distributions supported by \code{estimate_infections}, \code{epinow}, and \code{regional_epinow}. diff --git a/man/convert_to_logsd.Rd b/man/convert_to_logsd.Rd index e6009d290..c87422436 100644 --- a/man/convert_to_logsd.Rd +++ b/man/convert_to_logsd.Rd @@ -15,7 +15,7 @@ convert_to_logsd(mean, sd) The log standard deviation of a lognormal distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Convert from mean and standard deviation to the log standard deviation of the lognormal distribution. Useful for defining distributions supported by \code{estimate_infections}, \code{epinow}, and \code{regional_epinow}. diff --git a/man/copy_results_to_latest.Rd b/man/copy_results_to_latest.Rd index c1534c632..d1ebfebd7 100644 --- a/man/copy_results_to_latest.Rd +++ b/man/copy_results_to_latest.Rd @@ -13,6 +13,6 @@ copy_results_to_latest(target_folder = NULL, latest_folder = NULL) As produced by \code{setup_target_folder}.} } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Copies output from the dated folder to a latest folder. May be undergo changes in later releases. } diff --git a/man/country_map.Rd b/man/country_map.Rd index 8876e8b25..ef63e4b89 100644 --- a/man/country_map.Rd +++ b/man/country_map.Rd @@ -46,7 +46,7 @@ expects the possible values to be "Increasing", "Likely increasing", "Likely dec A \code{ggplot2} object containing a country map. } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} This general purpose function can be used to generate a country map for a single variable. It has few defaults but the data supplied must contain a \code{region_code} variable for linking to mapping data. This function requires the installation of the \code{rnaturalearth} package. Status of this function is currently questioning as it is uncertain diff --git a/man/create_backcalc_data.Rd b/man/create_backcalc_data.Rd index 1ad8560f1..ccebac585 100644 --- a/man/create_backcalc_data.Rd +++ b/man/create_backcalc_data.Rd @@ -14,7 +14,7 @@ back calculation. Defaults to \code{backcalc_opts()}.} A list of settings defining the Gaussian process } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Takes the output of \code{backcalc_opts()} and converts it into a list understood by \code{stan}. } \examples{ diff --git a/man/create_clean_reported_cases.Rd b/man/create_clean_reported_cases.Rd index 30ff43a4d..313b02a9d 100644 --- a/man/create_clean_reported_cases.Rd +++ b/man/create_clean_reported_cases.Rd @@ -20,7 +20,7 @@ then the zero is replaced with the} A cleaned data frame of reported cases } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Cleans a data frame of reported cases by replacing missing dates with 0 cases and applies an optional threshold at which point 0 cases are replaced with a moving average of observed cases. See \code{zero_threshold} for details. diff --git a/man/create_future_rt.Rd b/man/create_future_rt.Rd index c9655e6b1..90d7f4561 100644 --- a/man/create_future_rt.Rd +++ b/man/create_future_rt.Rd @@ -18,6 +18,6 @@ from this many days into the future (or past if negative) past will be used forw A list containing a logical called fixed and an integer called from } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Converts the \code{future} argument from \code{rt_opts()} into arguments that can be passed to \code{stan}. } diff --git a/man/create_gp_data.Rd b/man/create_gp_data.Rd index af3ba27a1..dc78e30a3 100644 --- a/man/create_gp_data.Rd +++ b/man/create_gp_data.Rd @@ -18,7 +18,7 @@ Gaussian process.} A list of settings defining the Gaussian process } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Takes the output of \code{gp_opts()} and converts it into a list understood by \code{stan}. } \examples{ diff --git a/man/create_initial_conditions.Rd b/man/create_initial_conditions.Rd index 8f0a59b16..39765614c 100644 --- a/man/create_initial_conditions.Rd +++ b/man/create_initial_conditions.Rd @@ -13,7 +13,7 @@ create_initial_conditions(data) An initial condition generating function } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Uses the output of \code{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 \code{stan} chain within a range of plausible values. diff --git a/man/create_obs_model.Rd b/man/create_obs_model.Rd index ff40f71f8..75470c791 100644 --- a/man/create_obs_model.Rd +++ b/man/create_obs_model.Rd @@ -15,7 +15,7 @@ A list of settings ready to be passed to stan defining the Observation Model } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Takes the output of \code{obs_opts()} and converts it into a list understood by \code{stan}. } \examples{ diff --git a/man/create_rt_data.Rd b/man/create_rt_data.Rd index 67d38e52c..0dda2627e 100644 --- a/man/create_rt_data.Rd +++ b/man/create_rt_data.Rd @@ -21,7 +21,7 @@ rather than generating infections using Rt.} A list of settings defining the time-varying reproduction number } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Takes the output from \code{rt_opts()} and converts it into a list understood by \code{stan}. } diff --git a/man/create_shifted_cases.Rd b/man/create_shifted_cases.Rd index a6dd02573..ae8d53178 100644 --- a/man/create_shifted_cases.Rd +++ b/man/create_shifted_cases.Rd @@ -21,7 +21,7 @@ to apply.} A data frame for shifted reported cases } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} This functions creates a data frame of reported cases that has been smoothed using a rolling average (with a period set by \code{smoothing_window}) and shifted back in time by some delay. It is used by \code{estimate_infections} to generate the mean shifted prior diff --git a/man/create_stan_args.Rd b/man/create_stan_args.Rd index a943e29cd..3ac03c945 100644 --- a/man/create_stan_args.Rd +++ b/man/create_stan_args.Rd @@ -26,7 +26,7 @@ as supplied by \code{create_intitial_conditions}).} A list of stan arguments } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Generates a list of arguments as required by \code{rstan::sampling} or \code{rstan::vb} by combining the required options, with data, and type of initialisation. Initialisation defaults to random but it is expected that \code{create_initial_conditions} will be used. diff --git a/man/create_stan_data.Rd b/man/create_stan_data.Rd index 3bd189f61..188e562ea 100644 --- a/man/create_stan_data.Rd +++ b/man/create_stan_data.Rd @@ -46,7 +46,7 @@ back calculation. Defaults to \code{backcalc_opts()}.} \item{shifted_cases}{A dataframe of delay shifted cases} -\item{truncation}{\lifecycle{experimental} A list of options as generated by \code{trunc_opts()} +\item{truncation}{\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} A list of options as generated by \code{trunc_opts()} defining the truncation of observed data. Defaults to \code{trunc_opts()}. See \code{estimate_truncation()} for an approach to estimating truncation from data.} } @@ -54,7 +54,7 @@ for an approach to estimating truncation from data.} A list of stan data } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Takes the output of \code{stan_opts()} and converts it into a list understood by \code{stan}. Internally calls the other \code{create_} family of functions to construct a single list for input into stan with all data required present. diff --git a/man/dist_fit.Rd b/man/dist_fit.Rd index f0f0d7f04..b1a61ceb1 100644 --- a/man/dist_fit.Rd +++ b/man/dist_fit.Rd @@ -31,7 +31,7 @@ gamma (\code{"gamma"}) and lognormal (\code{"lognorma"}) are also supported.} A \code{stan} fit of an interval censored distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Fits an integer adjusted exponential, gamma or lognormal distribution using \code{stan}. } diff --git a/man/dist_skel.Rd b/man/dist_skel.Rd index 839124256..e221ae426 100644 --- a/man/dist_skel.Rd +++ b/man/dist_skel.Rd @@ -28,7 +28,7 @@ of this range are resampled.} A vector of samples or a probability distribution. } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} This function acts as a skeleton for a truncated distribution defined by model type, maximum value and model parameters. It is designed to be used with the output from \code{get_dist}. diff --git a/man/epinow.Rd b/man/epinow.Rd index 2a9b0312c..24296c804 100644 --- a/man/epinow.Rd +++ b/man/epinow.Rd @@ -37,7 +37,7 @@ generation time (assuming a gamma distribution).} \item{delays}{A call to \code{delay_opts} defining delay distributions and options. See the documentation of \code{delay_opts} and the examples below for details.} -\item{truncation}{\lifecycle{experimental} A list of options as generated by \code{trunc_opts()} +\item{truncation}{\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} A list of options as generated by \code{trunc_opts()} defining the truncation of observed data. Defaults to \code{trunc_opts()}. See \code{estimate_truncation()} for an approach to estimating truncation from data.} @@ -95,7 +95,7 @@ to assign errors to regions. Alter the default to run with error catching.} A list of output from estimate_infections, forecast_infections, report_cases, and report_summary. } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} This function wraps the functionality of \code{estimate_infections()} and \code{forecast_infections()} in order to estimate Rt and cases by date of infection, forecast into these infections into the future. It also contains additional functionality to convert forecasts to date of report and produce summary output useful for reporting diff --git a/man/estimate_delay.Rd b/man/estimate_delay.Rd index 655fad035..2d3aeb516 100644 --- a/man/estimate_delay.Rd +++ b/man/estimate_delay.Rd @@ -15,7 +15,7 @@ estimate_delay(delays, ...) A list summarising the bootstrapped distribution } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Estimate a log normal delay distribution from a vector of integer delays. Currently this function is a simple wrapper for \code{bootstrapped_dist_fit}. } diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd index ff3d85bc2..0feff6e35 100644 --- a/man/estimate_infections.Rd +++ b/man/estimate_infections.Rd @@ -31,7 +31,7 @@ generation time (assuming a gamma distribution).} \item{delays}{A call to \code{delay_opts} defining delay distributions and options. See the documentation of \code{delay_opts} and the examples below for details.} -\item{truncation}{\lifecycle{experimental} A list of options as generated by \code{trunc_opts()} +\item{truncation}{\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} A list of options as generated by \code{trunc_opts()} defining the truncation of observed data. Defaults to \code{trunc_opts()}. See \code{estimate_truncation()} for an approach to estimating truncation from data.} @@ -63,7 +63,7 @@ to assign errors to regions. Alter the default to run with error catching.} \code{futile.logger}. See \code{setup_logging} for more detailed logging options.} } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Uses a non-parametric approach to reconstruct cases by date of infection from reported cases. It uses either a generative Rt model or non-parametric back calculation to estimate underlying latent infections and then maps these infections to observed cases via uncertain reporting delays and a flexible diff --git a/man/estimate_truncation.Rd b/man/estimate_truncation.Rd index 3f6dcb4b8..32ff8aaa0 100644 --- a/man/estimate_truncation.Rd +++ b/man/estimate_truncation.Rd @@ -40,7 +40,7 @@ observed data (\code{last_obs}, useful for plotting and validation), the data us (\code{data}) and the fit object (\code{fit}). } \description{ -\lifecycle{experimental} +\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} Estimates a truncation distribution from multiple snapshots of the same data source over time. This distribution can then be used in \code{regional_epinow}, \code{epinow}, and \code{estimate_infections} to adjust for truncated data. See \href{https://gist.github.com/seabbs/176b0c7f83eab1a7192a25b28bbd116a}{here} diff --git a/man/estimates_by_report_date.Rd b/man/estimates_by_report_date.Rd index f79154be5..6b2488b3d 100644 --- a/man/estimates_by_report_date.Rd +++ b/man/estimates_by_report_date.Rd @@ -31,7 +31,7 @@ and the examples below for details.} A list of samples and summarised estimates of estimated cases by date of report } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Either extracts or converts reported cases from an input data table. For output from \code{estimate_infections} this is a simple filtering step but for output from \code{forecast_infection} this is currently an approximate convolution. This step is likely to be updated/deprecated diff --git a/man/example_confirmed.Rd b/man/example_confirmed.Rd index 0848b736d..e83d41f50 100644 --- a/man/example_confirmed.Rd +++ b/man/example_confirmed.Rd @@ -11,7 +11,7 @@ A data frame containing cases reported on each date. example_confirmed } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} An example data frame of observed cases } \keyword{datasets} diff --git a/man/expose_stan_fns.Rd b/man/expose_stan_fns.Rd index 840dc9f3a..993187a46 100644 --- a/man/expose_stan_fns.Rd +++ b/man/expose_stan_fns.Rd @@ -14,7 +14,7 @@ expose_stan_fns(files, target_dir, ...) \item{...}{Additional arguments passed to \code{rstan::expose_stan_functions}.} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} 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. diff --git a/man/extract_parameter.Rd b/man/extract_parameter.Rd index b1a12e734..dffb7157c 100644 --- a/man/extract_parameter.Rd +++ b/man/extract_parameter.Rd @@ -18,6 +18,6 @@ a date} A data frame containing the parameter name, date, sample id and sample value } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Extracts a single from a list of \code{stan} output and returns it as a \code{data.table}. } diff --git a/man/extract_parameter_samples.Rd b/man/extract_parameter_samples.Rd index 5b5d7b839..ee057a136 100644 --- a/man/extract_parameter_samples.Rd +++ b/man/extract_parameter_samples.Rd @@ -32,7 +32,7 @@ extracted from data} A list of dataframes each containing the posterior of a parameter } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Extracts a custom set of parameters from a stan object and adds stratification and dates where appropriate. } diff --git a/man/filter_opts.Rd b/man/filter_opts.Rd index fe1e42344..9b5f2062d 100644 --- a/man/filter_opts.Rd +++ b/man/filter_opts.Rd @@ -16,7 +16,7 @@ call to an \verb{_opts} function.} A list of options } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} A helper function that allows the selection of region specific settings if present and otherwise applies the overarching settings } diff --git a/man/fit_model_with_nuts.Rd b/man/fit_model_with_nuts.Rd index a4a539d11..0dbf88d08 100644 --- a/man/fit_model_with_nuts.Rd +++ b/man/fit_model_with_nuts.Rd @@ -29,7 +29,7 @@ to assign errors to regions. Alter the default to run with error catching.} A stan model object } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Fits a stan model using \code{rstan::sampling}. Provides the optional ability to run chains using \code{future} with error catching, timeouts and merging of completed chains. } diff --git a/man/fit_model_with_vb.Rd b/man/fit_model_with_vb.Rd index 9d36c58b8..ce287b2ec 100644 --- a/man/fit_model_with_vb.Rd +++ b/man/fit_model_with_vb.Rd @@ -20,6 +20,6 @@ to assign errors to regions. Alter the default to run with error catching.} A stan model object } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Fits a stan model using variational inference. } diff --git a/man/forecast_infections.Rd b/man/forecast_infections.Rd index 8437a3dfa..38be6b0c3 100644 --- a/man/forecast_infections.Rd +++ b/man/forecast_infections.Rd @@ -45,7 +45,7 @@ A list of \code{data.tables}. The first entry ("samples") contains raw forecast summarised forecasts. } \description{ -\lifecycle{experimental} +\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} Provides optional tools for forecasting cases and Rt estimates using the timeseries methods (via the \code{EpiSoon} package). It requires the \code{Episoon} package. Installation instructions for the EpiSoon package are available \href{https://epiforecasts.io/EpiSoon/}{here}. diff --git a/man/format_fit.Rd b/man/format_fit.Rd index 2083c9eba..ac5396637 100644 --- a/man/format_fit.Rd +++ b/man/format_fit.Rd @@ -23,6 +23,6 @@ format_fit(posterior_samples, horizon, shift, burn_in, start_date, CrIs) A list of samples and summarised posterior parameter estimates } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Summaries posterior samples and adds additional custom variables. } diff --git a/man/gamma_dist_def.Rd b/man/gamma_dist_def.Rd index 9b8686a80..fac3d5f34 100644 --- a/man/gamma_dist_def.Rd +++ b/man/gamma_dist_def.Rd @@ -43,7 +43,7 @@ of this range are resampled.} A data.table defining the distribution as used by \code{dist_skel} } \description{ -\lifecycle{soft-deprecated} +\ifelse{html}{\figure{lifecycle-soft-deprecated.svg}{options: alt='Soft-deprecated lifecycle'}}{\strong{Soft-deprecated}} Generates a distribution definition when only parameter estimates are available for gamma distributed parameters. See \code{rgamma} for distribution information. } diff --git a/man/generation_times.Rd b/man/generation_times.Rd index 32d3bed3e..7f498d390 100644 --- a/man/generation_times.Rd +++ b/man/generation_times.Rd @@ -11,7 +11,7 @@ A \code{data.table} of summarising the distribution generation_times } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Generation time estimates. See here for details: https://github.com/epiforecasts/EpiNow2/blob/master/data-raw/generation-time.R } diff --git a/man/get_dist.Rd b/man/get_dist.Rd index 28538a561..6c63cf716 100644 --- a/man/get_dist.Rd +++ b/man/get_dist.Rd @@ -19,7 +19,7 @@ get_dist(data, disease, source, max_value = 15) A list defining a distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Search a data frame for a distribution and return it in the format expected by \code{delay_opts} and the \code{generation_time} argument of \code{epinow} and \code{estimate_infections}. } diff --git a/man/get_generation_time.Rd b/man/get_generation_time.Rd index c197fd7ec..022135412 100644 --- a/man/get_generation_time.Rd +++ b/man/get_generation_time.Rd @@ -17,7 +17,7 @@ get_generation_time(disease, source, max_value = 15) A list defining a distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Extracts a literature distribution from \code{generation_times} } \examples{ diff --git a/man/get_incubation_period.Rd b/man/get_incubation_period.Rd index 9a6d49862..99744644c 100644 --- a/man/get_incubation_period.Rd +++ b/man/get_incubation_period.Rd @@ -17,7 +17,7 @@ get_incubation_period(disease, source, max_value = 15) A list defining a distribution } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Extracts a literature distribution from \code{incubation_periods} } \examples{ diff --git a/man/get_raw_result.Rd b/man/get_raw_result.Rd index 7e9bdceb3..db2064024 100644 --- a/man/get_raw_result.Rd +++ b/man/get_raw_result.Rd @@ -19,5 +19,5 @@ get_raw_result(file, region, date, result_dir) An R object read in from the targeted .rds file } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} } diff --git a/man/get_regional_results.Rd b/man/get_regional_results.Rd index 786ac890b..7606ef496 100644 --- a/man/get_regional_results.Rd +++ b/man/get_regional_results.Rd @@ -30,7 +30,7 @@ data for. Defaults to "latest" which finds the latest results available.} A list of estimates, forecasts and estimated cases by date of report. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Summarises results across regions either from input or from disk. See the examples for details. } diff --git a/man/get_regions.Rd b/man/get_regions.Rd index e715387a2..eeddc07de 100644 --- a/man/get_regions.Rd +++ b/man/get_regions.Rd @@ -14,5 +14,5 @@ are stored (as produced by \code{regional_rt_pipeline}).} A named character vector containing the results to plot. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} } diff --git a/man/get_regions_with_most_reports.Rd b/man/get_regions_with_most_reports.Rd index 1f3b07b98..2026b5fce 100644 --- a/man/get_regions_with_most_reports.Rd +++ b/man/get_regions_with_most_reports.Rd @@ -18,6 +18,6 @@ Defaults to 7 days.} A character vector of regions with the highest reported cases } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Extract a vector of regions with the most reported cases in a set time window. } diff --git a/man/global_map.Rd b/man/global_map.Rd index 4d616739b..2c911419b 100644 --- a/man/global_map.Rd +++ b/man/global_map.Rd @@ -38,7 +38,7 @@ expects the possible values to be "Increasing", "Likely increasing", "Likely dec A \code{ggplot2} object containing a global map. } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} This general purpose function can be used to generate a global map for a single variable. It has few defaults but the data supplied must contain a \code{country} variable for linking to mapping data. This function requires the installation of the \code{rnaturalearth} package. Status of this function is currently questioning as it is uncertain diff --git a/man/gp_opts.Rd b/man/gp_opts.Rd index 470b806a4..87cddc648 100644 --- a/man/gp_opts.Rd +++ b/man/gp_opts.Rd @@ -51,7 +51,7 @@ in Rt and infections.} A list of settings defining the Gaussian process } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the structure of the approximate Gaussian process. Custom settings can be supplied which override the defaults. } diff --git a/man/growth_to_R.Rd b/man/growth_to_R.Rd index 21444fc0b..dbf6957ac 100644 --- a/man/growth_to_R.Rd +++ b/man/growth_to_R.Rd @@ -17,7 +17,7 @@ growth_to_R(r, gamma_mean, gamma_sd) Numeric vector of reproduction number estimates } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} See \href{https://www.medrxiv.org/content/10.1101/2020.01.30.20019877v3.full.pdf}{here} for justification. Now handled internally by stan so may be removed in future updates if no user demand. diff --git a/man/incubation_periods.Rd b/man/incubation_periods.Rd index 5d06ecb27..691de804d 100644 --- a/man/incubation_periods.Rd +++ b/man/incubation_periods.Rd @@ -11,7 +11,7 @@ A \code{data.table} of summarising the distribution incubation_periods } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Incubation period estimates. See here for details: https://github.com/epiforecasts/EpiNow2/blob/master/data-raw/incubation-period.R } diff --git a/man/lognorm_dist_def.Rd b/man/lognorm_dist_def.Rd index c62ea71e4..23ffd1e1f 100644 --- a/man/lognorm_dist_def.Rd +++ b/man/lognorm_dist_def.Rd @@ -26,7 +26,7 @@ of this range are resampled.} A data.table defining the distribution as used by \code{dist_skel} } \description{ -\lifecycle{soft-deprecated} +\ifelse{html}{\figure{lifecycle-soft-deprecated.svg}{options: alt='Soft-deprecated lifecycle'}}{\strong{Soft-deprecated}} Generates a distribution definition when only parameter estimates are available for log normal distributed parameters. See \code{rlnorm} for distribution information. } diff --git a/man/make_conf.Rd b/man/make_conf.Rd index ef3cd6b85..f1708fcda 100644 --- a/man/make_conf.Rd +++ b/man/make_conf.Rd @@ -19,7 +19,7 @@ credible interval be switched.} A character vector formatted for reporting } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Combines a list of values into formatted credible intervals. } \examples{ diff --git a/man/map_prob_change.Rd b/man/map_prob_change.Rd index 9a1fdf18f..1c1764f7f 100644 --- a/man/map_prob_change.Rd +++ b/man/map_prob_change.Rd @@ -13,7 +13,7 @@ map_prob_change(var) A character variable. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Categorises a numeric variable into "Increasing" (< 0.05), "Likely increasing" (<0.2), "Unsure" (< 0.8), "Likely decreasing" (< 0.95), "Decreasing" (<= 1) } diff --git a/man/match_output_arguments.Rd b/man/match_output_arguments.Rd index ac44f4a53..96ca303a9 100644 --- a/man/match_output_arguments.Rd +++ b/man/match_output_arguments.Rd @@ -26,7 +26,7 @@ of futile.logger for details. Supported options are "info" and "debug"} A logical vector of named output arguments } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Match user supplied arguments with supported options and return a logical list for internal usage } diff --git a/man/obs_opts.Rd b/man/obs_opts.Rd index a0ab80505..e77c758ce 100644 --- a/man/obs_opts.Rd +++ b/man/obs_opts.Rd @@ -25,7 +25,7 @@ distributed scaling factor.} A list of observation model settings. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the structure of the observation model. Custom settings can be supplied which override the defaults. } diff --git a/man/opts_list.Rd b/man/opts_list.Rd index c25a419b5..556510a47 100644 --- a/man/opts_list.Rd +++ b/man/opts_list.Rd @@ -20,7 +20,7 @@ A named list of options per region which can be passed to the \verb{_opt} accepting arguments of \code{regional_epinow} } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Define a list of \verb{_opts} to pass to \code{regional_epinow} \verb{_opts} accepting arguments. This is useful when different settings are needed between regions within a single \code{regional_epinow} call. Using \code{opts_list} the defaults can be applied to all regions diff --git a/man/plot.epinow.Rd b/man/plot.epinow.Rd index 89272ce18..78cb83fb5 100644 --- a/man/plot.epinow.Rd +++ b/man/plot.epinow.Rd @@ -19,7 +19,7 @@ to "summary" with supported options being "infections", "reports", "R", "growth List of plots as produced by \code{report_plots} } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} \code{plot} method for class "epinow". } \seealso{ diff --git a/man/plot.estimate_infections.Rd b/man/plot.estimate_infections.Rd index b6c2474ac..3b38a9d26 100644 --- a/man/plot.estimate_infections.Rd +++ b/man/plot.estimate_infections.Rd @@ -20,7 +20,7 @@ to "summary" with supported options being "infections", "reports", "R", "growth List of plots as produced by \code{report_plots} } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} \code{plot} method for class "estimate_infections". } \seealso{ diff --git a/man/plot.estimate_truncation.Rd b/man/plot.estimate_truncation.Rd index 66a2822ed..6f89e9a53 100644 --- a/man/plot.estimate_truncation.Rd +++ b/man/plot.estimate_truncation.Rd @@ -15,7 +15,7 @@ \code{ggplot2} object } \description{ -\lifecycle{experimental} +\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} \code{plot} method for class "estimate_truncation". Returns a plot faceted over each dataset used in fitting with the latest observations as columns, the data observed at the time (and so truncated) diff --git a/man/plot_CrIs.Rd b/man/plot_CrIs.Rd index c0c0196c0..379e63d13 100644 --- a/man/plot_CrIs.Rd +++ b/man/plot_CrIs.Rd @@ -20,6 +20,6 @@ by \code{extract_CrIs}} A \code{ggplot2} plot. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Adds lineranges for user specified credible intervals } diff --git a/man/plot_estimates.Rd b/man/plot_estimates.Rd index 6100f78f3..f68b9bf8f 100644 --- a/man/plot_estimates.Rd +++ b/man/plot_estimates.Rd @@ -33,7 +33,7 @@ on the maximum number of reported cases.} A \code{ggplot2} object } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Allows users to plot the output from \code{estimate_infections} easily. In future releases it may be depreciated in favour of increasing the functionality of the S3 plot methods. } diff --git a/man/plot_summary.Rd b/man/plot_summary.Rd index 8fe9c65d9..c6bdfb200 100644 --- a/man/plot_summary.Rd +++ b/man/plot_summary.Rd @@ -19,7 +19,7 @@ plot_summary(summary_results, x_lab = "Region", log_cases = FALSE, max_cases) A \code{ggplot2} object } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Used to return a summary plot across regions (using results generated by \code{summarise_results}). May be depreciated in later releases in favour of enhanced S3 methods. } diff --git a/man/process_region.Rd b/man/process_region.Rd index 0739a6d1a..780a13055 100644 --- a/man/process_region.Rd +++ b/man/process_region.Rd @@ -32,7 +32,7 @@ the completion of estimation to.} A list of processed output } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Internal function that removes output that is not required, and returns logging information. } diff --git a/man/process_regions.Rd b/man/process_regions.Rd index 2de4c090b..36b0cc7b0 100644 --- a/man/process_regions.Rd +++ b/man/process_regions.Rd @@ -15,7 +15,7 @@ process_regions(regional_out, regions) A list of all regional estimates and successful regional estimates } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Internal function that processes the output from multiple \code{epinow} runs, adds summary logging information. } diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd index 1edc7ee5d..6f54b3ec6 100644 --- a/man/regional_epinow.Rd +++ b/man/regional_epinow.Rd @@ -37,7 +37,7 @@ generation time (assuming a gamma distribution).} \item{delays}{A call to \code{delay_opts} defining delay distributions and options. See the documentation of \code{delay_opts} and the examples below for details.} -\item{truncation}{\lifecycle{experimental} A list of options as generated by \code{trunc_opts()} +\item{truncation}{\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} A list of options as generated by \code{trunc_opts()} defining the truncation of observed data. Defaults to \code{trunc_opts()}. See \code{estimate_truncation()} for an approach to estimating truncation from data.} @@ -94,7 +94,7 @@ place to start.} A list of output stratified at the top level into regional output and across region output summary output } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Efficiently runs \code{epinow()} across multiple regions in an efficient manner and conducts basic data checks and cleaning such as removing regions with fewer than \code{non_zero_points} as these are unlikely to produce reasonable results whilst consuming significant resources. See the documentation for \code{epinow} for further information. diff --git a/man/regional_runtimes.Rd b/man/regional_runtimes.Rd index f875e1b79..5d8d1a71d 100644 --- a/man/regional_runtimes.Rd +++ b/man/regional_runtimes.Rd @@ -27,7 +27,7 @@ if no directory for saving is specified.} A data.table of region run times } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Used internally by \code{regional_epinow} to summarise region run times. } \examples{ diff --git a/man/regional_summary.Rd b/man/regional_summary.Rd index 66c989bb8..cc6cae336 100644 --- a/man/regional_summary.Rd +++ b/man/regional_summary.Rd @@ -46,7 +46,7 @@ on the maximum number of reported cases.} A list of summary measures and plots } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Used to produce summary output either internally in \code{regional_epinow} or externally. } \examples{ diff --git a/man/report_cases.Rd b/man/report_cases.Rd index a784b303c..08bd83e04 100644 --- a/man/report_cases.Rd +++ b/man/report_cases.Rd @@ -36,7 +36,7 @@ A list of \code{data.table}s. The first entry contains the following variables \ being summarised across samples. } \description{ -\lifecycle{soft-deprecated} +\ifelse{html}{\figure{lifecycle-soft-deprecated.svg}{options: alt='Soft-deprecated lifecycle'}}{\strong{Soft-deprecated}} 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. } diff --git a/man/report_plots.Rd b/man/report_plots.Rd index 68b321d76..ec6b29d57 100644 --- a/man/report_plots.Rd +++ b/man/report_plots.Rd @@ -27,7 +27,7 @@ on the maximum number of reported cases.} A \code{ggplot2} object } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Returns key summary plots for estimates. May be depreciated in later releases as current S3 methods are enhanced. } diff --git a/man/report_summary.Rd b/man/report_summary.Rd index ce5ed3770..88c1975c9 100644 --- a/man/report_summary.Rd +++ b/man/report_summary.Rd @@ -26,7 +26,7 @@ variable, median, bottom, and top. It should contain the following estimates: R, A data.table containing formatted and numeric summary measures } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Creates a snapshot summary of estimates. May be removed in later releases as S3 methods are enhanced. } diff --git a/man/rstan_opts.Rd b/man/rstan_opts.Rd index ef66e555c..39104baf3 100644 --- a/man/rstan_opts.Rd +++ b/man/rstan_opts.Rd @@ -21,7 +21,7 @@ When using multiple chains iterations per chain is samples / chains.} A list of arguments to pass to the appropriate rstan functions. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the arguments passed to underlying \code{rstan} functions via \code{rstan_sampling_opts} and \code{rstan_vb_opts}.Custom settings can be supplied which override the defaults. diff --git a/man/rstan_sampling_opts.Rd b/man/rstan_sampling_opts.Rd index 37e17d130..836caebda 100644 --- a/man/rstan_sampling_opts.Rd +++ b/man/rstan_sampling_opts.Rd @@ -53,7 +53,7 @@ allowed time then estimation will fail with an informative error.} A list of arguments to pass to \code{rstan::sampling} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the arguments passed to \code{rstan::sampling}. Custom settings can be supplied which override the defaults. } diff --git a/man/rstan_vb_opts.Rd b/man/rstan_vb_opts.Rd index 623110bc1..b2b5a8fb8 100644 --- a/man/rstan_vb_opts.Rd +++ b/man/rstan_vb_opts.Rd @@ -22,7 +22,7 @@ before failing.} A list of arguments to pass to \code{rstan::vb} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the arguments passed to \code{rstan::vb}. Custom settings can be supplied which override the defaults. } diff --git a/man/rt_opts.Rd b/man/rt_opts.Rd index 5b8c000c4..37e21d6be 100644 --- a/man/rt_opts.Rd +++ b/man/rt_opts.Rd @@ -51,7 +51,7 @@ susceptible. When set to 0 no population adjustment is done.} A list of settings defining the time-varying reproduction number } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the optional arguments for the time-varying reproduction number. Custom settings can be supplied which override the defaults. } diff --git a/man/run_region.Rd b/man/run_region.Rd index c0d717205..f57878769 100644 --- a/man/run_region.Rd +++ b/man/run_region.Rd @@ -37,7 +37,7 @@ generation time (assuming a gamma distribution).} \item{delays}{A call to \code{delay_opts} defining delay distributions and options. See the documentation of \code{delay_opts} and the examples below for details.} -\item{truncation}{\lifecycle{experimental} A list of options as generated by \code{trunc_opts()} +\item{truncation}{\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} A list of options as generated by \code{trunc_opts()} defining the truncation of observed data. Defaults to \code{trunc_opts()}. See \code{estimate_truncation()} for an approach to estimating truncation from data.} @@ -91,7 +91,7 @@ progress bar.} A list of processed output as produced by \code{process_region} } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Internal function that handles calling \code{epinow}. Future work will extend this function to better handle \code{stan} logs and allow the user to modify settings between regions. diff --git a/man/sample_approx_dist.Rd b/man/sample_approx_dist.Rd index f89fdf339..f39886f6c 100644 --- a/man/sample_approx_dist.Rd +++ b/man/sample_approx_dist.Rd @@ -40,7 +40,7 @@ Defaults to \code{TRUE}.} A \code{data.table} of cases by date of onset } \description{ -\lifecycle{soft-deprecated} +\ifelse{html}{\figure{lifecycle-soft-deprecated.svg}{options: alt='Soft-deprecated lifecycle'}}{\strong{Soft-deprecated}} Convolves cases by a PMF function. This function will soon be removed or replaced with a more robust \code{stan} implementation. } diff --git a/man/save_estimate_infections.Rd b/man/save_estimate_infections.Rd index 34f33cc80..7472fddce 100644 --- a/man/save_estimate_infections.Rd +++ b/man/save_estimate_infections.Rd @@ -22,7 +22,7 @@ save_estimate_infections( be returned.} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Saves output from \code{estimate_infections} to a target directory. } \seealso{ diff --git a/man/save_forecast_infections.Rd b/man/save_forecast_infections.Rd index 9c05e502c..5c4ef9143 100644 --- a/man/save_forecast_infections.Rd +++ b/man/save_forecast_infections.Rd @@ -14,7 +14,7 @@ save_forecast_infections(forecast, target_folder = NULL, samples = TRUE) \item{samples}{Logical, defaults to TRUE. Should samples be saved} } \description{ -\lifecycle{experimental} +\ifelse{html}{\out{Experimental lifecycle}}{\strong{Experimental}} Saves the output from \code{forecast_infections} to a target directory. } \seealso{ diff --git a/man/save_input.Rd b/man/save_input.Rd index dff4af714..2094fcefb 100644 --- a/man/save_input.Rd +++ b/man/save_input.Rd @@ -13,6 +13,6 @@ in date format.} \item{target_folder}{Character string specifying where to save results (will create if not present).} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Saves observed data to a target location if given. } diff --git a/man/setup_default_logging.Rd b/man/setup_default_logging.Rd index 93932c7f9..75133585e 100644 --- a/man/setup_default_logging.Rd +++ b/man/setup_default_logging.Rd @@ -23,7 +23,7 @@ returned from \code{epinow} to the console.} \item{target_date}{Date, defaults to maximum found in the data if not specified.} } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Sets up default logging. Usage of logging is currently being explored as the current setup cannot log stan errors or progress. } diff --git a/man/setup_dt.Rd b/man/setup_dt.Rd index 6b48a7138..f128e3c0e 100644 --- a/man/setup_dt.Rd +++ b/man/setup_dt.Rd @@ -14,7 +14,7 @@ in date format.} A data table } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Convenience function that sets the number of \code{data.table} cores to 1 and maps input to be a \code{data.table} } diff --git a/man/setup_future.Rd b/man/setup_future.Rd index 675939f97..f2a0efda0 100644 --- a/man/setup_future.Rd +++ b/man/setup_future.Rd @@ -27,7 +27,7 @@ Numeric number of cores to use per worker. If greater than 1 pass to used then nothing is returned. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} A utility function that aims to streamline the set up of the required future backend with sensible defaults for most users of \code{regional_epinow}. More advanced users are recommended to setup their own \code{future} backend based on their diff --git a/man/setup_logging.Rd b/man/setup_logging.Rd index e7f6e5376..6faecaded 100644 --- a/man/setup_logging.Rd +++ b/man/setup_logging.Rd @@ -30,7 +30,7 @@ all logging for \code{epinow} and nested functions, EpiNow2.epinow.estimate_infe Nothing } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Sets up \code{futile.logger} logging, which is integrated into \code{EpiNow2}. See the documentation for \code{futile.logger} for full details. By default \code{EpiNow2} prints all logs at the "INFO" level and returns them to the console. Usage of logging is currently being explored diff --git a/man/setup_target_folder.Rd b/man/setup_target_folder.Rd index 4e72bee92..6bc2dcbf8 100644 --- a/man/setup_target_folder.Rd +++ b/man/setup_target_folder.Rd @@ -15,6 +15,6 @@ setup_target_folder(target_folder = NULL, target_date) A list containing the path to the dated folder and the latest folder } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Sets up a folders for saving results } diff --git a/man/simulate_cases.Rd b/man/simulate_cases.Rd index f9ce1cdab..685ef54ff 100644 --- a/man/simulate_cases.Rd +++ b/man/simulate_cases.Rd @@ -50,7 +50,7 @@ which approximates sampling or "median" would shift by the median of the distrib A dataframe containing three variables: \code{date}, \code{cases} and \code{reference}. } \description{ -\@description \lifecycle{questioning} +\@description \ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Simulate cases from a single Rt trace, an initial number of cases, and a reporting model This functionality has largely been superseded by \code{simulate_infections} and will likely to replaced or updated to depend on \code{stan} code. diff --git a/man/simulate_infections.Rd b/man/simulate_infections.Rd index ad1c8d7ff..77b90d137 100644 --- a/man/simulate_infections.Rd +++ b/man/simulate_infections.Rd @@ -35,7 +35,7 @@ simulations are done at once.} shown.} } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} This function simulates infections using an existing fit to observed cases but with a modified time-varying reproduction number. This can be used to explore forecast models or past counterfactuals. Simulations can be run in parallel using \code{future::plan}. diff --git a/man/stan_opts.Rd b/man/stan_opts.Rd index 892b84411..ff31e4dd4 100644 --- a/man/stan_opts.Rd +++ b/man/stan_opts.Rd @@ -21,7 +21,7 @@ Currently only "rstan" is supported.} A list of arguments to pass to the appropriate rstan functions. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Defines a list specifying the arguments passed to underlying stan backend functions via \code{rstan_sampling_opts} and \code{rstan_vb_opts}. Custom settings can be supplied which override the defaults. diff --git a/man/summarise_key_measures.Rd b/man/summarise_key_measures.Rd index 101602acb..3f099b325 100644 --- a/man/summarise_key_measures.Rd +++ b/man/summarise_key_measures.Rd @@ -28,7 +28,7 @@ data for. Defaults to "latest" which finds the latest results available.} A list of summarised Rt, cases by date of infection and cases by date of report } \description{ -\lifecycle{maturing} +\ifelse{html}{\out{Maturing lifecycle}}{\strong{Maturing}} Produces summarised data frames of output across regions. Used internally by \code{regional_summary}. } \seealso{ diff --git a/man/summarise_results.Rd b/man/summarise_results.Rd index ead43895c..f64028081 100644 --- a/man/summarise_results.Rd +++ b/man/summarise_results.Rd @@ -30,7 +30,7 @@ for this date.} A list of summary data } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Used internally by \code{regional_summary} to produce a summary table of results. May be streamlined in later releases. } diff --git a/man/summary.epinow.Rd b/man/summary.epinow.Rd index 93a718720..b88884f9f 100644 --- a/man/summary.epinow.Rd +++ b/man/summary.epinow.Rd @@ -23,7 +23,7 @@ but also supports "forecast", and "estimated_reported_cases".} Returns a data frame of summary output } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} \code{summary} method for class "epinow". } \seealso{ diff --git a/man/summary.estimate_infections.Rd b/man/summary.estimate_infections.Rd index bf7497209..6b0cf12aa 100644 --- a/man/summary.estimate_infections.Rd +++ b/man/summary.estimate_infections.Rd @@ -25,7 +25,7 @@ parameters of interest and date.} Returns a data frame of summary output } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} \code{summary} method for class "estimate_infections". } \seealso{ diff --git a/man/theme_map.Rd b/man/theme_map.Rd index 87912dbf9..7e2bff164 100644 --- a/man/theme_map.Rd +++ b/man/theme_map.Rd @@ -41,7 +41,7 @@ expects the possible values to be "Increasing", "Likely increasing", "Likely dec A \code{ggplot2} object } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} Applies a custom map theme to be used with \code{global_map}, \code{country_map}, and other \code{ggplot2} maps. Status of this function is currently questioning as it is uncertain if it is in use. Future releases may depreciate it. } diff --git a/man/trunc_opts.Rd b/man/trunc_opts.Rd index 9eccb5788..57a2b0508 100644 --- a/man/trunc_opts.Rd +++ b/man/trunc_opts.Rd @@ -16,7 +16,7 @@ for max defined in logged form).} A list summarising the input truncation distribution. } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Returns a truncation distribution formatted for usage by downstream functions. See \code{estimate_truncation} for an approach to estimate this distribution. } diff --git a/man/tune_inv_gamma.Rd b/man/tune_inv_gamma.Rd index eedbcab9f..3fb5667ce 100644 --- a/man/tune_inv_gamma.Rd +++ b/man/tune_inv_gamma.Rd @@ -16,7 +16,7 @@ A list of alpha and beta values that describe a inverse gamma distribution that achieves the target truncation. } \description{ -\lifecycle{questioning} +\ifelse{html}{\out{Questioning lifecycle}}{\strong{Questioning}} 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 diff --git a/man/update_horizon.Rd b/man/update_horizon.Rd index 2307dbd44..22abb7f00 100644 --- a/man/update_horizon.Rd +++ b/man/update_horizon.Rd @@ -18,7 +18,7 @@ in date format.} Numeric forecast horizon adjusted for the users intention } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Makes sure that a forecast is returned for the user specified time period beyond the target date. } diff --git a/man/update_list.Rd b/man/update_list.Rd index 8bc39794d..17bc2b948 100644 --- a/man/update_list.Rd +++ b/man/update_list.Rd @@ -15,7 +15,7 @@ update_list(defaults = list(), optional = list()) A list } \description{ -\lifecycle{stable} +\ifelse{html}{\out{Stable lifecycle}}{\strong{Stable}} Used to handle updating settings in a list. For example when making changes to \code{opts_list} output. }