update 2025-01-16 13:47:43.595942

DESCRIPTION

@@ -69,6 +69,6 @@ Suggests:
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyData: true
 Roxygen: list(markdown = TRUE)

R/mixture-pseudo_class.R

@@ -86,7 +86,7 @@ pseudo_class_pool <- function(fits, df_complete = NULL, ...) {
   cls <- unique(cls)
 
   if ( length(cls) > 1 ) {
-    stop(paste0("'fits' consists of objects with different classes: ", paste(cl, collapse = ', ')))
+    stop(paste0("'fits' consists of objects with different classes: ", paste(cls, collapse = ', ')))
   }
 
   UseMethod("pseudo_class_pool", fits[[1]])

R/mx_mixture.R

@@ -27,7 +27,7 @@
 #'   \item A list of \code{mxModel} objects, specified by the user.
 #' }
 #'
-#' @return Returns an \code{\link[OpenMx]{mxModel}}.
+#' @return Returns an \code{\link[OpenMx:mxModel]{OpenMx::mxModel()}}.
 #' @export
 #' @keywords mixture models openmx
 #' @references Van Lissa, C. J., Garnier-Villarreal, M., & Anadria, D. (2023).
@@ -88,7 +88,7 @@ mx_mixture <- function(model,
 #' the function calls \code{\link{mixture_starts}} and \code{\link{run_mx}}.
 #' @param expand_grid Logical, whether or not to estimate all possible combinations of the `variances` and `covariances` arguments. Defaults to `FALSE`.
 #' @param ... Additional arguments, passed to functions.
-#' @return Returns an \code{\link[OpenMx]{mxModel}}.
+#' @return Returns an \code{\link[OpenMx:mxModel]{OpenMx::mxModel()}}.
 #' @export
 #' @keywords mixture models openmx
 #' @references Van Lissa, C. J., Garnier-Villarreal, M., & Anadria, D. (2023).
@@ -160,7 +160,7 @@ mx_profiles <- function(data = NULL,
 #' Estimate growth mixture models using OpenMx
 #'
 #' This function is a wrapper around \code{\link{mx_mixture}}, adding the
-#' default arguments of \code{\link[lavaan]{growth}} to simplify the
+#' default arguments of \code{\link[lavaan:growth]{lavaan::growth()}} to simplify the
 #' specification of growth mixture models. This function is only
 #' useful if all the latent variables in the model are growth factors.
 #' @param model Syntax for the model; either a character string, or a list of
@@ -172,7 +172,7 @@ mx_profiles <- function(data = NULL,
 #' @param run Logical, whether or not to run the model. If \code{run = TRUE},
 #' the function calls \code{\link{mixture_starts}} and \code{\link{run_mx}}.
 #' @param ... Additional arguments, passed to functions.
-#' @return Returns an \code{\link[OpenMx]{mxModel}}.
+#' @return Returns an \code{\link[OpenMx:mxModel]{OpenMx::mxModel()}}.
 #' @export
 #' @keywords mixture models openmx
 #' @references Van Lissa, C. J., Garnier-Villarreal, M., & Anadria, D. (2023).
@@ -224,9 +224,9 @@ mx_growth_mixture <- function(model,
 #' @param classes A vector of integers, indicating which class solutions to
 #' generate. Defaults to 1L. E.g., \code{classes = 1:6},
 #' @param run Logical, whether or not to run the model. If \code{run = TRUE},
-#' the function calls \code{\link[OpenMx]{mxTryHardOrdinal}}.
+#' the function calls \code{\link[OpenMx:mxTryHardOrdinal]{OpenMx::mxTryHardOrdinal()}}.
 #' @param ... Additional arguments, passed to functions.
-#' @return Returns an \code{\link[OpenMx]{mxModel}}.
+#' @return Returns an \code{\link[OpenMx:mxModel]{OpenMx::mxModel()}}.
 #' @export
 #' @keywords mixture models openmx
 #' @references Van Lissa, C. J., Garnier-Villarreal, M., & Anadria, D. (2023).
@@ -449,7 +449,7 @@ as_mx_mixture <- function(model,
 #' \code{mxModel}s.
 #' @param model A mixture model of class \code{mxModel}.
 #' @param splits Optional. A numeric vector of length equal to the number of
-#' rows in the \code{\link{mxData}} used in the \code{model} object. The data
+#' rows in the \code{\link[OpenMx:mxData]{OpenMx::mxData()}} used in the \code{model} object. The data
 #' will be split by this vector. See Details for the default setting and
 #' possible alternatives.
 #' @param ... Additional arguments, passed to functions.
@@ -466,22 +466,22 @@ as_mx_mixture <- function(model,
 #' }
 #'
 #' If the argument \code{splits} is not provided, the function will call
-#' \code{\link[stats]{kmeans}}\code{(x = data, centers = classes)$cluster},
+#' \code{stats::kmeans(x = data, centers = classes)$cluster},
 #' where \code{data} is extracted from the \code{model} argument.
 #'
 #' Sensible ways to split the data include:
 #' \itemize{
 #'   \item Using Hierarchical clustering:
 #'    \code{cutree(hclust(dist(data)), k = classes))}
 #'   \item Using K-means clustering:
-#'   \code{\link[stats]{kmeans}}\code{(x = data, centers = classes)$cluster}
+#'   \code{stats::kmeans(x = data, centers = classes)$cluster}
 #'   \item Using agglomerative hierarchical clustering:
-#'   \code{hclass(}\code{\link[mclust]{hc}}\code{(data = data), G = classes)[, 1]}
+#'   \code{mclust::hclass(data = data), G = classes)[, 1]}
 #'   \item Using a random split:
-#'   \code{\link{sample.int}}\code{(n = classes,
+#'   \code{sample.int(n = classes,
 #'   size = nrow(data), replace = TRUE)}
 #' }
-#' @return Returns an \code{\link[OpenMx]{mxModel}} with starting values.
+#' @return Returns an \code{\link[OpenMx:mxModel]{OpenMx::mxModel()}} with starting values.
 #' @export
 #' @keywords mixture models openmx
 #' @examples

R/syntax-add_paths.R

@@ -1,28 +1,25 @@
 #' @title Add paths to an object of class 'tidy_sem'
 #' @description Add paths to an object of class \code{tidy_sem}, or replace
 #' existing paths. The paths must be specified as
-#' \code{\link[lavaan]{model.syntax}}, and separated by commas.
+#' \code{\link[lavaan:model.syntax]{lavaan::model.syntax}}, and separated by commas.
 #' @param model An object of class \code{tidy_sem}.
 #' @param ... Paths to add or substitute, specified in
-#' \code{\link{lavaan}{model.syntax}}, and separated by commas.
-# @param strict_check Logical, indicating whether or not to throw an error if
-# the variable names referenced in the new paths do not exist in the
-# \code{data}, or in the \code{dictionary}, or in the existing \code{syntax}
-# element. If \code{strict_check = FALSE}, the check is still performed, but
-# throws a \code{warning} instead of an \code{error}.
-# @param use_cols Character. Which columns to retain from the \code{lavaan}
-# parameter table. Defaults to \code{c("lhs", "op", "rhs", "free", "label")}.
+#' \code{\link[lavaan:model.syntax]{lavaan::model.syntax}},
+#' and separated by commas.
 #' @return An object of class \code{tidy_sem}.
-#' @details Currently, only the \code{\link{lavaan}{lavaan}} commands \code{~,
+#' @details Currently, only the
+#' \code{\link[lavaan:lavaan]{lavaan::lavaan()}}
+#' commands \code{~,
 #' ~~, =~,} and \code{~1} are parsed.
-#' @details  This function
-#' relies on \code{lavaan \link[lavaan]{model.syntax}} to convert syntax strings
+#' @details  This function relies on
+#' \code{\link[lavaan:model.syntax]{lavaan::model.syntax}}
+#' to convert syntax strings
 #' to \code{lavaan} parameter tables. By default, is uses the arguments
 #' \code{int.ov.free = TRUE, int.lv.free = FALSE, auto.fix.first = TRUE,
 #' auto.fix.single = TRUE, auto.var = TRUE, auto.cov.lv.x = TRUE,
 #' auto.efa = TRUE, auto.th = TRUE, auto.delta = TRUE, auto.cov.y = TRUE,
 #' meanstructure = TRUE}, in a similar way
-#' to \code{\link[lavaan]{sem}} and \code{\link[lavaan]{cfa}}.
+#' to \code{\link[lavaan:sem]{lavaan::sem()}} and \code{\link[lavaan:cfa]{lavaan::cfa()}}.
 #' @examples
 #' library(lavaan)
 #' df <- iris[, 1:4]
@@ -33,7 +30,7 @@
 #' res <- estimate_lavaan(model)
 #' summary(res)
 #' @seealso
-#'  \code{\link[lavaan]{model.syntax}}
+#'  \code{\link[lavaan:model.syntax]{lavaan::model.syntax}}
 #' @rdname add_paths
 #' @export
 #' @importFrom lavaan lavParseModelString

cran-comments.md

@@ -1,9 +1,8 @@
-# tidySEM 0.2.7
+# tidySEM 0.2.8
 
-* Stop calling tidySEM functions as default arguments of prepare_graph.lavaan().
-  This ensures that tidySEM works when its namespace is not attached.
-* Frank Gootjes contributed pseudo class functionality, new functions are
-  append_class_draws() and pseudo_class()
+* Fix CRAN check NOTES:
+    + "Rd file(s) with Rd \link{} targets missing package
+      anchors"
 
 ## Test environments