S4 class cross-references - what is appropriate syntax?

Question

I'm writing an R package and currently running R CMD check via devtools::check()

I have the following roxygen2 in two of my functions that reference an S4 class (both functions return objects of this class):

#' @return An object of class \code{\link{mod_imputeMulti}}
#' @aliases mod_imputeMulti
#' @seealso \code{\link{multinomial_em}}, \code{\link{multinomial_impute}}

Yet I get the following WARNING:

Rd files with duplicated alias 'mod_imputeMulti':
'multinomial_data_aug.Rd' 'multinomial_em.Rd'

If I don't use second line -- the @aliases tag, I get this WARNING, despite the fact that I do have a link:

checking Rd cross-references ... WARNING
Missing link or links in documentation object 'multinomial_data_aug.Rd': 'mod_imputeMulti'

Missing link or links in documentation object 'multinomial_em.Rd': 'mod_imputeMulti'

See section 'Cross-references' in the 'Writing R Extensions' manual.

Note: adding \code{\link{mod_imputeMulti}} to @seealso doesn't change this (second) WARNING

What is the correct syntax?

I've looked at a lot of references but can't find the solution anywhere:

I hope this is an easy one for someone--thanks in advance for the help!

Edit:

The S4 class documenation is provided below:

#' Class "mod_imputeMulti"
#'  
#' @name mod_imputeMulti-class
#' @description A multivariate multinomial model imputed by EM or Data Augmentation is 
#' represented as a \code{\linkS4class{mod_imputeMulti}} object. A complete 
#' dataset and model is represented as an \code{\linkS4class{imputeMulti}} object.
#' Slots for \code{mod_imputeMulti} objects include: (1) the modeling method; 
#' (2) the call to the estimation function; (3) the number of iterations in estimation;
#' (4) the final log-likelihood; (5) the conjugate prior if any; (6) the MLE estimate of
#' the sufficient statistics and parameters.
#' @docType class
#' @section Objects from the class: Objects are created by calls to
#' \code{\link{multinomial_impute}}, \code{\link{multinomial_em}}, or
#' \code{\link{multinomial_data_aug}}.
#' @seealso \code{\link{multinomial_impute}}, \code{\link{multinomial_em}}, 
#' \code{\link{multinomial_data_aug}}
#' @export
setClass("mod_imputeMulti",
         representation= list(
           method= "character",
           mle_call= "call",
           mle_iter= "numeric",
           mle_log_lik= "numeric",
           mle_cp= "character",
           mle_x_y= "data.frame"),
         validity= function(object) {
           if (!object@method %in% c("EM", "DA", "NULL")) {
             return("Currently only EM and DA methods are defined.")
           } else if (object@mle_iter < 0) {
             return("A negative iteration was given.")
           }
           return(TRUE)
         }
)

@Thomas I only used aliases because of another error I was getting without it. I've updated the post to give a more complete description. — alexwhitworth, Apr 13 '16 at 16:00

score 1 · Accepted Answer · answered Apr 13 '16 at 16:35

Yes, this was a relatively simple fix.

As you can see in the S4 class documenation at the bottom of the OP, note that the name is mod_imputeMulti-class, not mod_imputeMulti.

I needed to add "-class". The @aliases tag is unneeded.

#' @return An object of class \code{\link{mod_imputeMulti-class}}

Also, thanks to @thomas for pointing out the use of @slot for proper translation of the roxygen2 tagging to man/*.Md files.

S4 class cross-references - what is appropriate syntax?

Edit:

1 Answers1