Update documentation tags to roxygen2 7.3.1 requirements

amices · Apr 17, 2024 · e8a062a · e8a062a
1 parent f20f17d
commit e8a062a
Show file tree

Hide file tree

Showing 31 changed files with 85 additions and 50 deletions.
diff --git a/R/convergence.R b/R/convergence.R
@@ -120,4 +120,5 @@ convergence <- function(data, diagnostic = "all", parameter = "mean", ...) {
 }
 
 # function to extend is.nan() to data.frame objects
+#' @export
 is.nan.data.frame <- function(x) do.call(cbind, lapply(x, is.nan))
diff --git a/R/df.residual.R b/R/df.residual.R
@@ -1,19 +1,22 @@
+#' @export
 df.residual.mira <- function(object, ...) {
   fit <- object$analyses[[1]]
   df.residual(fit)
 }
 
 
+#' @export
 df.residual.lme <- function(object, ...) {
   object$fixDF[["X"]][1]
 }
 
 
+#' @export
 df.residual.mer <- function(object, ...) {
   sum(object@dims[2:4] * c(1, -1, -1)) + 1
 }
 
-
+#' @export
 df.residual.multinom <- function(object, ...) {
   nrow(object$residuals) - object$edf
 }
diff --git a/R/edit.setup.R b/R/edit.setup.R
@@ -1,4 +1,4 @@
-edit.setup <- function(data, setup,
+mice.edit.setup <- function(data, setup,
                        allow.na = FALSE,
                        remove.constant = TRUE,
                        remove.collinear = TRUE,

diff --git a/R/formula.R b/R/formula.R
@@ -127,7 +127,7 @@ name.formulas <- function(formulas, prefix = "F") {
 check.formulas <- function(formulas, data) {
   formulas <- name.formulas(formulas)
   formulas <- handle.oldstyle.formulas(formulas, data)
-  formulas <- lapply(formulas, expand.dots, data)
+  formulas <- lapply(formulas, mice.expand.dots, data)
   # escape if formula is list of two formula's
   if (any(sapply(formulas, is.list))) {
     return(formulas)
@@ -238,7 +238,7 @@ hasdot <- function(f) {
   }
 }
 
-expand.dots <- function(formula, data) {
+mice.expand.dots <- function(formula, data) {
   if (!is.formula(formula)) {
     return(formula)
   }

diff --git a/R/mice-package.R b/R/mice-package.R
@@ -69,7 +69,6 @@
 #' depend on the operating system. See the discussion in the
 #' "R Installation and Administration" guide for further information.
 #'
-#' @docType package
 #' @aliases mice-package
 #'
 #' @name mice
@@ -92,4 +91,5 @@
 #' \href{https://stefvanbuuren.name/fimd/}{\emph{Flexible Imputation of Missing Data. Second Edition.}}
 #' Chapman & Hall/CRC. Boca Raton, FL.
 #' @useDynLib mice, .registration = TRUE
-NULL
+#' @keywords internal
+"_PACKAGE"
diff --git a/R/mice.R b/R/mice.R
@@ -411,7 +411,7 @@ mice <- function(data,
   visitSequence <- check.visitSequence(visitSequence,
     data = data, where = where, blocks = blocks
   )
-  predictorMatrix <- edit.predictorMatrix(
+  predictorMatrix <- mice.edit.predictorMatrix(
     predictorMatrix = predictorMatrix,
     visitSequence = visitSequence,
     user.visitSequence = user.visitSequence,
@@ -436,7 +436,7 @@ mice <- function(data,
     visitSequence = visitSequence,
     post = post
   )
-  setup <- edit.setup(data, setup, ...)
+  setup <- mice.edit.setup(data, setup, ...)
   method <- setup$method
   predictorMatrix <- setup$predictorMatrix
   visitSequence <- setup$visitSequence

diff --git a/R/mipo.R b/R/mipo.R
@@ -151,6 +151,7 @@ process_mipo <- function(z, x, conf.int = FALSE, conf.level = .95,
   z
 }
 
+#' @export
 vcov.mipo <- function(object, ...) {
   so <- diag(object$t)
   dimnames(so) <- list(object$term, object$term)

diff --git a/R/predictorMatrix.R b/R/predictorMatrix.R
@@ -135,7 +135,7 @@ check.predictorMatrix <- function(predictorMatrix,
   )
 }
 
-edit.predictorMatrix <- function(predictorMatrix,
+mice.edit.predictorMatrix <- function(predictorMatrix,
                                  visitSequence,
                                  user.visitSequence,
                                  maxit) {

diff --git a/man/mice.Rd b/man/mice.Rd
diff --git a/man/mice.impute.cart.Rd b/man/mice.impute.cart.Rd
diff --git a/man/mice.impute.lasso.logreg.Rd b/man/mice.impute.lasso.logreg.Rd
diff --git a/man/mice.impute.lasso.norm.Rd b/man/mice.impute.lasso.norm.Rd
diff --git a/man/mice.impute.lasso.select.logreg.Rd b/man/mice.impute.lasso.select.logreg.Rd
diff --git a/man/mice.impute.lasso.select.norm.Rd b/man/mice.impute.lasso.select.norm.Rd
diff --git a/man/mice.impute.lda.Rd b/man/mice.impute.lda.Rd
diff --git a/man/mice.impute.logreg.Rd b/man/mice.impute.logreg.Rd
diff --git a/man/mice.impute.logreg.boot.Rd b/man/mice.impute.logreg.boot.Rd
diff --git a/man/mice.impute.mean.Rd b/man/mice.impute.mean.Rd
diff --git a/man/mice.impute.midastouch.Rd b/man/mice.impute.midastouch.Rd
diff --git a/man/mice.impute.mnar.Rd b/man/mice.impute.mnar.Rd
diff --git a/man/mice.impute.mpmm.Rd b/man/mice.impute.mpmm.Rd
diff --git a/man/mice.impute.norm.Rd b/man/mice.impute.norm.Rd
diff --git a/man/mice.impute.norm.boot.Rd b/man/mice.impute.norm.boot.Rd