minor code updates and modernised documentation to use more markdown styles

Author: JWiley

DESCRIPTION

@@ -19,7 +19,7 @@ Description: Calculate Bayesian marginal effects, average marginal effects, and
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
     R (>= 4.0.0)
 Imports: 

NAMESPACE

@@ -5,6 +5,7 @@ export(bsummary)
 export(integratemvn)
 export(integratere)
 export(lmcpp)
+export(lmcpp_alt)
 export(marginalcoef)
 export(prediction)
 export(rowBootMeans)

R/RcppExports.R

@@ -77,6 +77,22 @@ lmcpp <- function(X, y) {
     .Call(`_brmsmargins_lmcpp`, X, y)
 }
 
+#' Fast(er?) Linear Regression
+#'
+#' Used to get marginal coefficients off of a generalized linear mixed model.
+#'
+#' @param X A numeric model matrix. If intercept is desired, it must already have been added as a column.
+#' @param y A numeric matrix. A single column if one response variable or multiple columns
+#'   where each column is a different response, such as a for marginal coefficients where
+#'   each column is a different MCMC sample.
+#' @return A numeric matrix with the coefficient.
+#' @export
+#' @examples
+#' lmcpp_alt(cbind(1, mtcars$hp, mtcars$am), as.matrix(mtcars[, c("mpg", "qsec")]))
+lmcpp_alt <- function(X, y) {
+    .Call(`_brmsmargins_lmcpp_alt`, X, y)
+}
+
 #' Bootstrap Row Means
 #'
 #' This takes a numeric matrix, bootstrap resamples each row, and then

R/assert.R

@@ -1,29 +1,27 @@
-#' @title Check Assertions about a \code{brmsfit} Model Object
+#' @title Check Assertions about a [brms::brmsfit-class] class Model Object
 #'
 #' @description
 #' These are a set of internal utility functions.
 #' They are not intended for general use.
 #' Instead, they are intended to be called in circumstances
-#' where the expected result is \code{TRUE}.
+#' where the expected result is `TRUE`.
 #' All of them are designed to try to give informative error
 #' messages if the assertion is not met.
-#' All of them result in a \code{stop()} error if the assertion is not met.
+#' All of them result in a `stop` error if the assertion is not met.
 #'
 #' @details
-#' \itemize{
-#'   \item{\code{.assertbrmsfit}}{asserts that the object should be of class \code{brmsfit}.}
-#'   \item{\code{.assertgaussian}}{asserts that all random effects are Gaussian.}
-#'   \item{\code{.assertfamily}}{asserts that the distribution (family) of the outcome is a currently supported family. Only applies when integrating out random effects.}
-#'   \item{\code{.assertlink}}{asserts that the link function is a currently supported link function. Only applies when integrating out random effects.}
-#' }
+#' - `.assertbrmsfit`: asserts that the object should be [brms::brmsfit-class].
+#' - `.assertgaussian`: asserts that all random effects are Gaussian.
+#' - `.assertfamily`: asserts that the distribution (family) of the outcome is a currently supported family. Only applies when integrating out random effects.
+#' - `.assertlink`: asserts that the link function is a currently supported link function. Only applies when integrating out random effects.
 #'
-#' @param object A \code{brmsfit} model object to be evaluated.
-#' @param dpar Required for \code{.assertdpar} which checks this is valid.
-#'   Optional for \code{.assertlink} which will use \code{NULL} if not
-#'   specified. If specified, this should be \code{NULL} or
+#' @param object A [brms::brmsfit-class] model object to be evaluated.
+#' @param dpar Required for [.assertdpar()] which checks this is valid.
+#'   Optional for [.assertlink()] which will use `NULL` if not
+#'   specified. If specified, this should be `NULL` or
 #'   a character string.
 #'
-#' @return An invisible, logical \code{TRUE} if the assertion is met.
+#' @return An invisible, logical `TRUE` if the assertion is met.
 #'   An (informative) error message if the assertion is not met.
 #' @keywords internal
 #' @name assertall

R/averageposterior.R

@@ -10,12 +10,12 @@
 #'   draws are on different rows.
 #' @param resample An integer indicating the number of
 #'   bootstrap resamples of the posterior predictions to
-#'   use when calculating summaries. Defaults to \code{0L}.
-#'   See the details section for more informations as its implementation
+#'   use when calculating summaries. Defaults to `0L`.
+#'   See the details section for more information as its implementation
 #'   is experimental and it may not operate as one would expect.
-#' @param seed A seed for random number generation. Defaults to \code{FALSE},
+#' @param seed A seed for random number generation. Defaults to `FALSE`,
 #'   which means no seed is set.
-#'   Only used if \code{resample} is a positive, non-zero integer.
+#'   Only used if `resample` is a positive, non-zero integer.
 #' @return A vector of the averaged posterior.
 #' @keywords internal
 .averagePosterior <- function(posterior, resample = 0L, seed = FALSE) {

R/builders.R

@@ -5,26 +5,29 @@
 #' They are not intended for general use.
 #'
 #' @details
-#' \itemize{
-#'   \item{\code{.namesL}}{Generate names of an L matrix from \code{brms}. Create the variable names for the Cholesky decomposition of the random effects correlation matrix in \code{brms}. Note that \code{brms} returns the lower triangular matrix and we want the upper triangular matrix, so the names are transposed. The results can then be passed to the \code{tab2mat} function to convert the row vector into a matrix.}
-#'   \item{\code{.buildL}}{Returns the L matrix object. Rows are posterior draws.}
-#'   \item{\code{.namesSD}}{Create the names of random effect standard deviation estimates.}
-#'   \item{\code{.buildSD}}{Return matrix of random effect standard deviation estimates. Rows are posterior draws.}
-#'   \item{\code{.namesZ}}{Create the names of random effects data for predictions.}
-#'   \item{\code{.buildZ}}{Return matrix of data for random effect predictions.}
-#' }
+#' - `.namesL`: Generate names of an L matrix from \pkg{brms}.
+#'   Create the variable names for the Cholesky decomposition of the random effects
+#'   correlation matrix in [brms::brm()]. Note that [brms::brm()] returns the lower
+#'   triangular matrix and we want the upper triangular matrix, so the names are
+#'   transposed. The results can then be passed to [tab2mat()]
+#'   to convert the row vector into a matrix.
+#' - `.buildL`: Returns the L matrix object. Rows are posterior draws.
+#' - `.namesSD`: Create the names of random effect standard deviation estimates.
+#' - `.buildSD`: Return matrix of random effect standard deviation estimates. Rows are posterior draws.
+#' - `.namesZ`: Create the names of random effects data for predictions.
+#' - `.buildZ`: Return matrix of data for random effect predictions.
 #'
-#' @param data A data object. For example the result of [make_standata()]
+#' @param data A data object. For example the result of [brms::make_standata()]
 #'   for [.buildZ()], which is a list,
-#'   or a dataset of the posterior draws such as from [as_draws_df()]
+#'   or a dataset of the posterior draws such as from [brms::as_draws_df()]
 #'   for [.buildL()] and [.buildSD()].
 #' @param ranef A data set with information about the model object random effects.
-#'   Only used for \code{.namesSD} and \code{.buildSD}.
+#'   Only used for [.namesSD()] and [.buildSD()].
 #' @param block Which random effect block to use. An integer.
 #' @param number The number of elements in that random effect block. An integer.
 #' @param dpar Which dpar to use. Does not apply to the L matrix.
-#' @return A character vector for all \code{.names} functions or a matrix
-#'   for all \code{.build} functions.
+#' @return A character vector for all `.names` functions or a matrix
+#'   for all `.build` functions.
 #' @keywords internal
 #' @name builders
 NULL

R/marginalcoef.R

@@ -1,40 +1,39 @@
 #' Marginal Coefficients from a 'brms' Model
 #'
-#' Calculate marginal coefficients from a \code{brms}
+#' Calculate marginal coefficients from a `brms`
 #' generalized linear mixed model using the method proposed by Hedeker (2018).
 #'
-#' @param object A fitted brms model object that includes random effects. Required.
+#' @param object A fitted `brms` model object that includes random effects. Required.
 #' @param summarize A logical value, whether or not to
 #'   calculate summaries of the posterior predictions.
-#'   Defaults to \code{TRUE}.
+#'   Defaults to `TRUE`.
 #' @param posterior A logical value whether or not to
 #'   save and return the posterior samples. Defaults
-#'   to \code{FALSE} as the assumption is a typical
+#'   to `FALSE` as the assumption is a typical
 #'   use case is to return the summaries only.
 #' @param index An optional integer vector, giving the posterior draws
 #'   to be used in the calculations. If omitted, defaults to all
 #'   posterior draws.
 #' @param backtrans A character string indicating the type of
 #'   back transformation to be applied. Can be one of
-#'   \dQuote{response} meaning to use the response scale,
-#'   \dQuote{linear} or \dQuote{identity} meaning to use the linear predictor scale,
+#'   "response" meaning to use the response scale,
+#'   "linear" or "identity" meaning to use the linear predictor scale,
 #'   or a specific back transformation desired, from a possible list of
-#'   \dQuote{invlogit}, \dQuote{exp}, \dQuote{square}, or \dQuote{inverse}.
+#'   "invlogit", "exp", "square", or "inverse".
 #'   Custom back transformations should only be needed if, for example,
 #'   the outcome variable was transformed prior to fitting the model.
 #' @param k An integer providing the number of random draws to use for
-#'   integrating out the random effects. Only relevant when \code{effects}
-#'   is \dQuote{integrateoutRE}.
+#'   integrating out the random effects. Only relevant when `effects = "integrateoutRE"`.
 #' @param seed An \emph{optional} argument that controls whether (and if so what) random seed
 #'   to use. This can help with reproducibility of results.
 #'   It is missing by default.
-#' @param ... Additional arguments passed to \code{bsummary()}, 
-#'   and only relevant if \code{summarize} is \code{TRUE}.
-#' @return A list with \code{Summary} and \code{Posterior}.
-#'   Some of these may be \code{NULL} depending on the arguments used.
+#' @param ... Additional arguments passed to [bsummary()], 
+#'   and only relevant if `summarize` is `TRUE`.
+#' @return A list with `Summary` and `Posterior`.
+#'   Some of these may be `NULL` depending on the arguments used.
 #' @references
 #' Hedeker, D., du Toit, S. H., Demirtas, H. & Gibbons, R. D. (2018)
-#' \doi{10.1111/biom.12707}
+#' [DOI: 10.1111/biom.12707](https://doi.org/10.1111/biom.12707).
 #' \dQuote{A note on marginalization of regression parameters from mixed models of binary outcomes}
 #' @importFrom data.table as.data.table
 #' @importFrom stats formula