CRAN v1.3.0.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: multilevelcoda
 Type: Package
 Title: Estimate Bayesian Multilevel Models for Compositional Data
-Version: 1.3.0
-Date: 2024-6-10
+Version: 1.3.0.1
+Date: 2024-6-13
 Authors@R: 
     c(person(given = "Flora",
              family = "Le",

R/brmcoda-methods.R

@@ -172,7 +172,7 @@ neff_ratio.brmcoda <- function(object, ...) {
 #' 
 #' @param x1 A \code{brmcoda} object.
 #' @param x2 Another \code{brmcoda} object based on the same responses.
-#' @param ... Other arguments passed to \code{\link{bayes_factor.brmsfit}}.
+#' @param ... Other arguments passed to \code{\link[brms:bayes_factor.brmsfit]{bayes_factor.brmsfit}}.
 #' 
 #' @importFrom brms bayes_factor
 #' @method bayes_factor brmcoda

R/brmcoda.R

@@ -5,10 +5,10 @@
 #' 
 #' @param formula A object of class \code{formula}, \code{brmsformula}:
 #' A symbolic description of the model to be fitted. 
-#' Details of the model specification can be found in \code{\link{brmsformula}}.
+#' Details of the model specification can be found in \code{\link[brms:brmsformula]{brmsformula}}.
 #' @param complr A \code{\link{complr}} object containing data of composition, 
 #' ILR coordinates, and other variables used in the model.
-#' @param ... Further arguments passed to \code{\link{brm}}.
+#' @param ... Further arguments passed to \code{\link[brms:brm]{brm}}.
 #' 
 #' @return A \code{\link{brmcoda}} with two elements
 #'   \item{\code{complr}}{ An object of class \code{complr} used in the \code{brm} model. }

R/plot.R

@@ -7,7 +7,7 @@
 #' that were reallocated to in the model.
 #' @param ref A character value of ((\code{"grandmean"} or \code{"clustermean"} or \code{"users"}),
 #' @param level A character value of (\code{"between"}, \code{"within"}), or \code{"aggregate"}).
-#' @param ... Further arguments passed to \code{\link{ggplot}}.
+#' @param ... Further components to the plot, followed by a plus sign (+).
 #'
 #' @return A ggplot graph object showing the estimated difference in outcome when
 #' each pair of compositional variables are substituted for a specific time.
@@ -86,7 +86,7 @@ plot.substitution <- function(x, to,
 #' Make a plot of \code{brmcoda} model results.
 #'
 #' @param x A \code{\link{brmcoda}} class object.
-#' @param ... Further arguments passed to \code{\link{plot.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:plot.brmsfit]{plot.brmsfit}}.
 #'
 #' @inherit brms::plot.brmsfit return
 #'
@@ -96,11 +96,11 @@ plot.substitution <- function(x, to,
 #' @export
 #' @examples
 #' \dontrun{
-#' cilr <- compilr(data = mcompd, sbp = sbp,
+#' cilr <- complr(data = mcompd, sbp = sbp,
 #'         parts = c("TST", "WAKE", "MVPA", "LPA", "SB"), idvar = "ID")
 #'
 #' # model with compositional predictor at between and within-person levels
-#' fit <- brmcoda(compilr = cilr,
+#' fit <- brmcoda(complr = cilr,
 #'                formula = Stress ~ bilr1 + bilr2 + bilr3 + bilr4 +
 #'                                  wilr1 + wilr2 + wilr3 + wilr4 + (1 | ID),
 #'                chain = 1, iter = 500)
@@ -110,13 +110,13 @@ plot.brmcoda <- function(x, ...) {
   plot(x$model, ...)
 }
 
-#' Create a matrix of output plots from a \code{\link{brmcoda}}'s \code{\link{brmsfit}} object
+#' Create a matrix of output plots from a \code{\link{brmcoda}}'s \code{\link[brms:brmsfit]{brmsfit}} object
 #'
 #' A \code{\link[graphics:pairs]{pairs}}
 #' method that is customized for MCMC output.
 #'
 #' @param x A \code{brmcoda} class object.
-#' @param ... Further arguments passed to \code{\link{pairs.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:pairs.brmsfit]{pairs.brmsfit}}.
 #'
 #' @inherit brms::pairs.brmsfit return
 #' 
@@ -127,11 +127,11 @@ plot.brmcoda <- function(x, ...) {
 #' @export
 #' @examples
 #' \dontrun{
-#' cilr <- compilr(data = mcompd, sbp = sbp,
+#' cilr <- complr(data = mcompd, sbp = sbp,
 #'         parts = c("TST", "WAKE", "MVPA", "LPA", "SB"), idvar = "ID")
 #'
 #' # model with compositional predictor at between and within-person levels
-#' fit <- brmcoda(compilr = cilr,
+#' fit <- brmcoda(complr = cilr,
 #'                formula = Stress ~ bilr1 + bilr2 + bilr3 + bilr4 +
 #'                                  wilr1 + wilr2 + wilr3 + wilr4 + (1 | ID),
 #'                chain = 1, iter = 500)
@@ -147,7 +147,7 @@ pairs.brmcoda <- function(x, ...) {
 #' implemented in the \pkg{bayesplot} package.
 #'
 #' @param object A \code{brmcoda} class object.
-#' @param ... Further arguments passed to \code{\link{mcmc_plot.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:mcmc_plot.brmsfit]{mcmc_plot.brmsfit}}.
 #' 
 #' @inherit brms::mcmc_plot.brmsfit return
 #' 
@@ -159,11 +159,11 @@ pairs.brmcoda <- function(x, ...) {
 #' @export
 #' @examples
 #' \dontrun{
-#' cilr <- compilr(data = mcompd, sbp = sbp,
+#' cilr <- complr(data = mcompd, sbp = sbp,
 #'         parts = c("TST", "WAKE", "MVPA", "LPA", "SB"), idvar = "ID")
 #'
 #' # model with compositional predictor at between and within-person levels
-#' fit <- brmcoda(compilr = cilr,
+#' fit <- brmcoda(complr = cilr,
 #'                formula = Stress ~ bilr1 + bilr2 + bilr3 + bilr4 +
 #'                                  wilr1 + wilr2 + wilr3 + wilr4 + (1 | ID),
 #'                chain = 1, iter = 500)

R/posterior.R

@@ -18,7 +18,7 @@
 #' results are returned on the log-ratio scale.
 #' If \code{"response"}, results are returned on the compositional scale
 #' of the response variable.
-#' @param ... Further arguments passed to \code{\link{predict.brmsfit}}
+#' @param ... Further arguments passed to \code{\link[brms:predict.brmsfit]{predict.brmsfit}}
 #' that control additional aspects of prediction.
 #' @inheritParams brms::predict.brmsfit
 #' 
@@ -68,19 +68,17 @@ predict.brmcoda <- function(object,
 
   if (inherits(object$model$formula, "mvbrmsformula")) {
     if ((length(grep("ilr", object$model$formula$responses, value = T)) > 0)) {
-      if (scale == "linear") {
-      warning(sprintf(
+      if (isFALSE(scale == "response")) {
+        warning(sprintf(
         "This is a mvbrmsformula model, it is recommended to
   set scale = \"response\" to return results on compsitional scale."))
 
       out <- predict(
         object$model,
-        scale = scale,
         summary = summary,
         ...
       )
-    }
-    if (scale == "response") {
+    } else {
       out <- predict(
         object$model,
         summary = FALSE,
@@ -126,7 +124,7 @@ predict.brmcoda <- function(object,
 #' @aliases fitted
 #' 
 #' @inheritParams predict.brmcoda
-#' @param ... Further arguments passed to \code{\link{fitted.brmsfit}}
+#' @param ... Further arguments passed to \code{\link[brms:fitted.brmsfit]{fitted.brmsfit}}
 #' that control additional aspects of prediction.
 #' 
 #' @inherit brms::fitted.brmsfit return
@@ -177,19 +175,17 @@ fitted.brmcoda <- function(object,
 
   if (inherits(object$model$formula, "mvbrmsformula")) {
     if ((length(grep("ilr", object$model$formula$responses, value = T)) > 0)) {
-      if (scale == "linear") {
+      if (isFALSE(scale == "response")) {
         warning(sprintf(
           "This is a mvbrmsformula model, it is recommended to
   set scale = \"response\" to return results on compsitional scale."))
 
         out <- fitted(
           object$model,
-          scale = scale,
           summary = summary,
           ...
         )
-      }
-      if (scale == "response") {
+      } else {
         out <- fitted(
           object$model,
           summary = FALSE,
@@ -227,7 +223,7 @@ fitted.brmcoda <- function(object,
 #' @aliases fixef
 #' 
 #' @param object An object of class \code{brmcoda}.
-#' @param ... Further arguments passed to \code{\link{fixef.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:fixef.brmsfit]{fixef.brmsfit}}.
 #' 
 #' @inherit brms::fixef.brmsfit return
 #' 
@@ -265,7 +261,7 @@ fixef.brmcoda <- function(object, ...) {
 #' of the \code{brmsfit} object in a \code{brmcoda} object.
 #'
 #' @inheritParams fixef.brmcoda
-#' @param ... Further arguments passed to \code{\link{vcov.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:vcov.brmsfit]{vcov.brmsfit}}.
 #' 
 #' @inherit brms::vcov.brmsfit return
 #' 
@@ -301,7 +297,7 @@ vcov.brmcoda <- function(object, ...) {
 #' @aliases ranef
 #' 
 #' @inheritParams fixef.brmcoda
-#' @param ... Further arguments passed to \code{\link{ranef.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:ranef.brmsfit]{ranef.brmsfit}}.
 #' 
 #' @inherit brms::ranef.brmsfit return
 #'
@@ -340,7 +336,7 @@ ranef.brmcoda <- function(object, ...) {
 #' @aliases coef
 #' 
 #' @inheritParams fixef.brmcoda
-#' @param ... Further arguments passed to \code{\link{coef.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:coef.brmsfit]{coef.brmsfit}}.
 #' 
 #' @inherit brms::coef.brmsfit return
 #'
@@ -382,7 +378,7 @@ coef.brmcoda <- function(object, ...) {
 #' @aliases VarCorr
 #' 
 #' @param x An object of class \code{brmcoda}.
-#' @param ... Further arguments passed to \code{\link{VarCorr.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:VarCorr.brmsfit]{VarCorr.brmsfit}}.
 #' 
 #' @inherit brms::VarCorr.brmsfit return
 #' 
@@ -416,7 +412,7 @@ VarCorr.brmcoda <- function(x, ...) {
 #' Compute posterior draws of residuals/predictive errors
 #' 
 #' @inheritParams fixef.brmcoda
-#' @param ... Further arguments passed to \code{\link{residuals.brmsfit}}.
+#' @param ... Further arguments passed to \code{\link[brms:residuals.brmsfit]{residuals.brmsfit}}.
 #' @inherit brms::residuals.brmsfit return
 #'   
 #' @seealso \code{\link[brms:residuals.brmsfit]{residuals.brmsfit}}

R/shiny.R

@@ -6,7 +6,8 @@
 #'
 #' @param object A fitted model object of class \code{brmcoda}.
 #' @param ... Optional arguments to pass to
-#' \code{\link{launch_shinystan.brmsfit}} or \code{\link[shiny:runApp]{runApp}}.
+#' \code{\link[shinystan:launch_shinystan]{launch_shinystan}} or 
+#' \code{\link[shiny:runApp]{runApp}}.
 #'
 #' @seealso \code{\link[shinystan:launch_shinystan]{launch_shinystan}}
 #'

R/substitution-helpers.R

@@ -415,7 +415,7 @@ build.rg <- function(object,
     #                                            factors = factors,
     #                                            length = NA))
     drg <- as.data.table(insight::get_datagrid(model.frame(object),
-                                               at = paste0(resp),
+                                               # at = paste0(resp),
                                                factors = factors,
                                                length = NA))
 

R/substitution.R

@@ -39,7 +39,7 @@
 #' If \code{"response"}, results are returned on the scale of the response variable.
 #' If \code{"linear"}, results are returned on the scale of the linear predictor term,
 #' that is without applying the inverse link function or other transformations.
-#' @param ... Additional arguments passed to \code{\link{describe_posterior}}.
+#' @param ... currently ignored.
 #'
 #' @return A list containing the results of multilevel compositional substitution model.
 #' The first six lists contain the results of the substitution estimation for a compositional part.

R/summary.R

@@ -94,7 +94,7 @@ print.complr <- function(x, ...) {
 #' Create a Summary of a fitted \code{brmsfit} model in a \code{brmcoda} object
 #' 
 #' @param object An object of class \code{brmcoda}.
-#' @param ... Other arguments passed to \code{\link{summary.brmsfit}}.
+#' @param ... Other arguments passed to \code{\link[brms:summary.brmsfit]{summary.brmsfit}}.
 #' 
 #' @method summary brmcoda
 #' 

R/update.R

@@ -60,13 +60,14 @@ update.complr <- function(object, newdata, ...) {
 #' This method allows for updating an existing \code{\link{brmcoda}} object.
 #' 
 #' @param object A fitted \code{\link{brmcoda}} object to be updated.
-#' @param formula. Changes to the formula; for details see \code{\link{update.formula}} and \code{\link{brmsformula}}.
+#' @param formula. Changes to the formula; for details see 
+#' \code{\link[stats:update.formula]{update.formula}} and \code{\link[brms:brmsformula]{brmsformula}}.
 #' @param newcomplr A \code{\link{complr}} object containing data of composition, 
 #' ILR coordinates, and other variables used in the updated model.
 #' @param newdata A \code{data.frame} or \code{data.table}
 #' containing data of all variables used in the analysis. 
 #' It must include a composition and the same ID variable as the existing \code{\link{complr}} object.
-#' @param ... Further arguments passed to \code{\link{brm}}.
+#' @param ... Further arguments passed to \code{\link[brms:brm]{brm}}.
 #' 
 #' @inherit brmcoda return
 #'