first pass at roxygen2md

DESCRIPTION

@@ -125,3 +125,4 @@ Collate:
     "unspread_draws.R"
     "util.R"
     "x_at_y.R"
+Roxygen: list(markdown = TRUE)

R/compare_levels.R

@@ -72,7 +72,7 @@ comparison_types = within(list(), {
 #' result of this function.
 #' @param comparison One of (a) the comparison types \code{ordered},
 #' \code{control}, \code{pairwise}, or \code{default} (may also be given as
-#' strings, e.g. \code{"ordered"}), see `Details`; (b) a user-specified
+#' strings, e.g. \code{"ordered"}), see *Details*; (b) a user-specified
 #' function that takes a \code{factor} and returns a list of pairs of names of
 #' levels to compare (as strings) and/or unevaluated expressions containing
 #' representing the comparisons to make; or (c) a list of pairs of names of

R/compose_data.R

@@ -10,7 +10,7 @@
 #' input into a Bayesian modeling function. \strong{These functions typically should not be called directly}
 #' (instead use \code{\link{compose_data}}), but are exposed for the rare cases in which
 #' you may need to provide your own conversion routines for a data type not already
-#' supported (see `Details`).
+#' supported (see *Details*).
 #'
 #' \code{data_list} creates a list with class \code{c("data_list", "list")}
 #' instead of \code{c("list")}, but largely otherwise acts like the \code{\link{list}}
@@ -38,7 +38,7 @@
 #' implementations of \code{as_data_list.numeric}, \code{as_data_list.logical},
 #' etc for examples.
 #'
-#' @param object The object to convert (see `Details`).
+#' @param object The object to convert (see *Details*).
 #' @param name The name of the element in the returned list corresponding to
 #' this object.
 #' @param scalar_as_array If \code{TRUE}, returns single scalars as an

R/deprecated.R

@@ -17,7 +17,7 @@
 #' functions use \code{.variable} and \code{.value}; or they set \code{.iteration} even
 #' when iteration information is not available --- new functions always set \code{.draw}
 #' but may not set \code{.iteration}), so be careful when upgrading to new function names.
-#' See `Deprecated Arguments and Column Names`, below, for more information.
+#' See *Deprecated Arguments and Column Names*, below, for more information.
 #'
 #' Deprecated functions are:
 #'

R/geom_slabinterval.R

@@ -253,7 +253,7 @@ get_line_size = function(i_data, size_domain, size_range) {
 #' the x/y axis opposite the \code{orientation} of this geom so that the maximum height at each value of the
 #' opposite axis is \code{1}; if \code{"groups"}, normalize within values of the opposite axis and within
 #' groups so that the maximum height in each group is \code{1}; if \code{"none"}, values are taken as is with no
-#' normalization (this should probably only be used with functions whose values are in [0,1], such as CDFs).
+#' normalization (this should probably only be used with functions whose values are in \[0,1\], such as CDFs).
 #' @param interval_size_domain The minimum and maximum of the values of the size aesthetic that will be translated into actual
 #' sizes for intervals drawn according to \code{interval_size_range} (see the documentation for that argument.)
 #' @param interval_size_range This geom scales the raw size aesthetic values when drawing interval and point sizes, as

R/recover_types.R

@@ -60,7 +60,7 @@ apply_prototypes = function(...) {
 #' for a full list of supported models, see \link{tidybayes-models}.
 #' @param ...  Lists (or data frames) providing data prototypes used to convert
 #' columns returned by \code{\link{spread_draws}} and \code{\link{gather_draws}} back into useful data types.
-#' See `Details`.
+#' See *Details*.
 #' @return A decorated version of \code{model}.
 #' @author Matthew Kay
 #' @aliases apply_prototypes

R/spread_draws.R

@@ -110,8 +110,8 @@ spread_samples = function(...) {
 #'
 #' For variables that do not share the same subscripts (or share
 #' some but not all subscripts), we can supply their specifications separately.
-#' For example, if we have a variable d[i] with the same i subscript
-#' as b[i,v], and a variable x with no subscripts, we could do this:
+#' For example, if we have a variable `d[i]` with the same `i` subscript
+#' as `b[i,v]`, and a variable `x` with no subscripts, we could do this:
 #'
 #' \preformatted{spread_draws(fit, x, d[i], b[i,v])}
 #'
@@ -223,7 +223,7 @@ spread_samples = function(...) {
 #' @param model A supported Bayesian model fit. Tidybayes supports a variety of model objects;
 #' for a full list of supported models, see \link{tidybayes-models}.
 #' @param ... Expressions in the form of
-#' \code{variable_name[dimension_1, dimension_2, ...] | wide_dimension}. See `Details`.
+#' \code{variable_name[dimension_1, dimension_2, ...] | wide_dimension}. See *Details*.
 #' @param regex If \code{TRUE}, variable names are treated as regular expressions and all column matching the
 #' regular expression and number of dimensions are included in the output. Default \code{FALSE}.
 #' @param sep Separator used to separate dimensions in variable names, as a regular expression.

R/tidy_draws.R

@@ -34,7 +34,7 @@ as_sample_data_frame = function(...) {
 #' as columns. While this function can be useful for quick glances at models (especially
 #' combined with \code{\link{gather_variables}} and \code{\link{median_qi}}), it is
 #' generally speaking not as useful as \code{\link{spread_draws}} or
-#' \code{\link{gather_draws}} for most applications, and is mainly used internally (see `Details`).
+#' \code{\link{gather_draws}} for most applications, and is mainly used internally (see *Details*).
 #'
 #' In practice, apart from quick looks at a model you will probably not call this directly;
 #' \code{\link{spread_draws}} or \code{\link{gather_draws}}, which are build on top of this