From b7df46b5388de7f8e515361799f564f8fc75bab7 Mon Sep 17 00:00:00 2001 From: Nils Kehrein Date: Wed, 23 Oct 2024 10:12:43 +0200 Subject: [PATCH] add missing lifecycle badge images --- R/plotting.r | 5 +++++ R/survival.R | 6 ++++-- man/figures/lifecycle-deprecated.svg | 21 +++++++++++++++++++ man/figures/lifecycle-experimental.svg | 21 +++++++++++++++++++ man/figures/lifecycle-stable.svg | 29 ++++++++++++++++++++++++++ man/figures/lifecycle-superseded.svg | 21 +++++++++++++++++++ man/plot_epx.Rd | 2 +- man/plot_ppc.Rd | 1 + man/plot_ppc_combi.Rd | 1 + man/plot_scenario.Rd | 1 + man/plot_sd.Rd | 1 + man/survival.Rd | 6 ++++-- 12 files changed, 110 insertions(+), 5 deletions(-) create mode 100644 man/figures/lifecycle-deprecated.svg create mode 100644 man/figures/lifecycle-experimental.svg create mode 100644 man/figures/lifecycle-stable.svg create mode 100644 man/figures/lifecycle-superseded.svg diff --git a/R/plotting.r b/R/plotting.r index b664dfb..1cb5d6d 100644 --- a/R/plotting.r +++ b/R/plotting.r @@ -1,5 +1,6 @@ #' Creates plot of model results (uncertainties optional) #' +#' `r lifecycle::badge("experimental")` #' All parameter combinations and exposure patterns are simulated and the mean #' of predictions is derived for a single study. The uncertainty is #' passed to the function due to computation time. Results are displayed by @@ -250,6 +251,7 @@ plot_sd <- function(model_base, #' Creates a PPC plot for a single dataset #' +#' `r lifecycle::badge("experimental")` #' A sample of parameters representing the uncertainty within the dataset #' is passed to the function. All parameter combinations and exposure patterns #' are simulated and the range of predicted frond numbers is derived for a @@ -355,6 +357,7 @@ plot_ppc <- function(rs_mean, #' Create PPC plot for one or more datasets #' +#' `r lifecycle::badge("experimental")` #' The function expects a data.frame with five mandatory and one optional #' column. The mandatory columns are as follows: #' - `pred`: mean of predictions e.g. frond number for lemna @@ -459,6 +462,7 @@ plot_ppc_combi <- function(table, xy_lim = NULL) { #' Plot EPx values #' +#' `r lifecycle::badge("experimental")` #' @param EPx_ts the result of `epx_mtw`, ie. a tibble with window.start, #' window.end, endpoint, level and EPx #' @param exposure_ts an exposure time series with columns for time 't' and @@ -550,6 +554,7 @@ plot_epx <- function(EPx_ts, exposure_ts, draw = TRUE, time_col = "time", conc_c #' Creates a prediction plot for one effect scenario #' +#' `r lifecycle::badge("experimental")` #' Sometimes it is helpful if the user can plot results of one effect #' scenario. This is for instance the case for test simulations or predictions #' for one profile. This function runs the simulation for one effect scenario diff --git a/R/survival.R b/R/survival.R index d0a9aba..afe778a 100644 --- a/R/survival.R +++ b/R/survival.R @@ -1,7 +1,9 @@ #' Survival rate #' -#' *Deprecated function*. Derives the survival rate of individuals for -#' *Reduced GUTS* models. Was replaced by [simulate()]. +#' `r lifecycle::badge("deprecated")` +#' Derives the survival rate of individuals for +#' *Reduced GUTS* models. Function was replaced by output of [simulate()] and +#' will be removed in a later version. #' #' The survival rate describes the survival probability at each #' time point. The function simulates the *GUTS* scenario and appends a column diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg new file mode 100644 index 0000000..b61c57c --- /dev/null +++ b/man/figures/lifecycle-deprecated.svg @@ -0,0 +1,21 @@ + + lifecycle: deprecated + + + + + + + + + + + + + + + lifecycle + + deprecated + + diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg new file mode 100644 index 0000000..5d88fc2 --- /dev/null +++ b/man/figures/lifecycle-experimental.svg @@ -0,0 +1,21 @@ + + lifecycle: experimental + + + + + + + + + + + + + + + lifecycle + + experimental + + diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg new file mode 100644 index 0000000..9bf21e7 --- /dev/null +++ b/man/figures/lifecycle-stable.svg @@ -0,0 +1,29 @@ + + lifecycle: stable + + + + + + + + + + + + + + + + lifecycle + + + + stable + + + diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg new file mode 100644 index 0000000..db8d757 --- /dev/null +++ b/man/figures/lifecycle-superseded.svg @@ -0,0 +1,21 @@ + + lifecycle: superseded + + + + + + + + + + + + + + + lifecycle + + superseded + + diff --git a/man/plot_epx.Rd b/man/plot_epx.Rd index bc26edb..008b2a8 100644 --- a/man/plot_epx.Rd +++ b/man/plot_epx.Rd @@ -36,7 +36,7 @@ the EPx plot are returned as a list for later modification} a grid of ggplots } \description{ -Plot EPx values +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} } \examples{ ti <- 0:21 diff --git a/man/plot_ppc.Rd b/man/plot_ppc.Rd index 18bde65..39ffde6 100644 --- a/man/plot_ppc.Rd +++ b/man/plot_ppc.Rd @@ -33,6 +33,7 @@ plot_ppc( a ggplot2 plot object } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} A sample of parameters representing the uncertainty within the dataset is passed to the function. All parameter combinations and exposure patterns are simulated and the range of predicted frond numbers is derived for a diff --git a/man/plot_ppc_combi.Rd b/man/plot_ppc_combi.Rd index 2205eb7..6ec9e60 100644 --- a/man/plot_ppc_combi.Rd +++ b/man/plot_ppc_combi.Rd @@ -15,6 +15,7 @@ plot_ppc_combi(table, xy_lim = NULL) a ggplot2 plot object } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} The function expects a data.frame with five mandatory and one optional column. The mandatory columns are as follows: \itemize{ diff --git a/man/plot_scenario.Rd b/man/plot_scenario.Rd index 5ea9368..07c669c 100644 --- a/man/plot_scenario.Rd +++ b/man/plot_scenario.Rd @@ -17,6 +17,7 @@ plot_scenario(model_base, plot_col = 2, trial_number = NULL) plot of the results for one \verb{effect scenario} } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} Sometimes it is helpful if the user can plot results of one effect scenario. This is for instance the case for test simulations or predictions for one profile. This function runs the simulation for one effect scenario diff --git a/man/plot_sd.Rd b/man/plot_sd.Rd index 68d5b49..b3b9409 100644 --- a/man/plot_sd.Rd +++ b/man/plot_sd.Rd @@ -51,6 +51,7 @@ plot_sd( a ggplot2 plot object } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} All parameter combinations and exposure patterns are simulated and the mean of predictions is derived for a single study. The uncertainty is passed to the function due to computation time. Results are displayed by diff --git a/man/survival.Rd b/man/survival.Rd index db9122c..2736795 100644 --- a/man/survival.Rd +++ b/man/survival.Rd @@ -15,8 +15,10 @@ survival(scenario, ...) a \code{data.frame} containing simulation results } \description{ -\emph{Deprecated function}. Derives the survival rate of individuals for -\emph{Reduced GUTS} models. Was replaced by \code{\link[=simulate]{simulate()}}. +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} +Derives the survival rate of individuals for +\emph{Reduced GUTS} models. Function was replaced by output of \code{\link[=simulate]{simulate()}} and +will be removed in a later version. } \details{ The survival rate describes the survival probability at each