debugging error messages in from package

R/add-functions.R

@@ -73,13 +73,15 @@ add_term <- function(
 
 #' Create model matrix from model object
 #' @param object a model object
+#' @keywords internal
 make_X <- function(object, ...) {
 
   UseMethod("make_X", object)
 
 }
 
 #' @inherit make_X
+#' @keywords internal
 make_X.default <- function(object, newdata, ...) {
 
   X <- model.matrix(object$formula[-2], data = newdata, ...)
@@ -940,7 +942,7 @@ get_sim_cumu <- function(newdata, ...) {
 }
 
 #' Add transition probabilities confidence intervals
-#' @export
+#' @keywords internal
 add_trans_ci <- function(newdata, object, n_sim=100L, alpha=0.05, ...) {
 
   X             <- predict.gam(object, newdata = newdata, type = "lpmatrix")

R/ggplot-extensions.R

@@ -11,8 +11,8 @@
 #' @seealso
 #'   \code{\link[ggplot2]{geom_ribbon}} \code{geom_stepribbon}
 #'   inherits from \code{geom_ribbon}.
-#' @inheritParams ggplot2:::geom_ribbon
-#' @inheritParams ggplot2:::geom_step
+#' @inheritParams ggplot2::geom_ribbon
+#' @inheritParams ggplot2::geom_step
 #' @examples
 #' library(ggplot2)
 #' huron <- data.frame(year = 1875:1972, level = as.vector(LakeHuron))

R/warnings.R

@@ -8,6 +8,7 @@ warn_about_new_time_points <- function(object, newdata, ...) {
 }
 
 #' @inherit warn_about_new_time_points
+#' @keywords internal
 warn_about_new_time_points.glm <- function(object, newdata, time_var, ...) {
 
   is_pam <- (inherits(object, "gam" ) | inherits( object, "scam"))

_pkgdown.yml

@@ -19,6 +19,7 @@ reference:
       - ped_info
       - make_newdata
       - get_intervals
+      - add_counterfactual_transitions
   - title: "Extract information from PAMMs"
     desc: "Functions that help extract information from fitted model objects,
     e.g., smooth effects for plotting"