diff --git a/man/est.incidence.by.Rd b/man/est.incidence.by.Rd index 5b1fc006..92c08bca 100644 --- a/man/est.incidence.by.Rd +++ b/man/est.incidence.by.Rd @@ -21,7 +21,7 @@ est.incidence.by( ) } \arguments{ -\item{pop_data}{\code{\link[=data.frame]{data.frame()}} with cross-sectional serology data per antibody and age, and additional columns to identify possible \code{strata}.} +\item{pop_data}{\link{data.frame} with cross-sectional serology data per antibody and age, and additional columns to identify possible \code{strata}.} \item{curve_params}{a \code{\link[=data.frame]{data.frame()}} containing MCMC samples of parameters from the Bayesian posterior distribution of a longitudinal decay curve model. The parameter columns must be named: \itemize{ diff --git a/man/plot_curve_params_one_ab.Rd b/man/plot_curve_params_one_ab.Rd index 868cb5f3..e5739f2d 100644 --- a/man/plot_curve_params_one_ab.Rd +++ b/man/plot_curve_params_one_ab.Rd @@ -48,14 +48,30 @@ plot_curve_params_one_ab( at the top level of the plot. You must supply \code{mapping} if there is no plot mapping.} \item{\code{data}}{Ignored by \code{stat_function()}, do not use.} - \item{\code{stat}}{The statistical transformation to use on the data for this -layer, either as a \code{ggproto} \code{Geom} subclass or as a string naming the -stat stripped of the \code{stat_} prefix (e.g. \code{"count"} rather than -\code{"stat_count"})} - \item{\code{position}}{Position adjustment, either as a string naming the adjustment -(e.g. \code{"jitter"} to use \code{position_jitter}), or the result of a call to a -position adjustment function. Use the latter if you need to change the -settings of the adjustment.} + \item{\code{stat}}{The statistical transformation to use on the data for this layer. +When using a \verb{geom_*()} function to construct a layer, the \code{stat} +argument can be used the override the default coupling between geoms and +stats. The \code{stat} argument accepts the following: +\itemize{ +\item A \code{Stat} ggproto subclass, for example \code{StatCount}. +\item A string naming the stat. To give the stat as a string, strip the +function name of the \code{stat_} prefix. For example, to use \code{stat_count()}, +give the stat as \code{"count"}. +\item For more information and other ways to specify the stat, see the +\link[ggplot2:layer_stats]{layer stat} documentation. +}} + \item{\code{position}}{A position adjustment to use on the data for this layer. This +can be used in various ways, including to prevent overplotting and +improving the display. The \code{position} argument accepts the following: +\itemize{ +\item The result of calling a position function, such as \code{position_jitter()}. +This method allows for passing extra arguments to the position. +\item A string naming the position adjustment. To give the position as a +string, strip the function name of the \code{position_} prefix. For example, +to use \code{position_jitter()}, give the position as \code{"jitter"}. +\item For more information and other ways to specify the position, see the +\link[ggplot2:layer_positions]{layer position} documentation. +}} \item{\code{na.rm}}{If \code{FALSE}, the default, missing values are removed with a warning. If \code{TRUE}, missing values are silently removed.} \item{\code{show.legend}}{logical. Should this layer be included in the legends?