From 2150931d20ab12209439eaad977d9f2cbee44eac Mon Sep 17 00:00:00 2001
From: richelbilderbeek <rjcbilderbeek@gmail.com>
Date: Mon, 24 Jun 2024 11:16:51 +0200
Subject: [PATCH] Documentation links to other packages' documentation

---
 NEWS.md                   |  1 +
 R/default_params_doc.R    | 10 +++++-----
 man/bbt_run.Rd            |  8 ++++----
 man/default_params_doc.Rd | 10 +++++-----
 4 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index ea78b8f..fb9351f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,7 @@ Newest versions at top.
 
   * Deprecate 'upgrade_babette', as this is against CRAN guidelines
   * All functions have their return value documented
+  * Documentation links to other packages' documentation
 
 ### BUG FIXES
 
diff --git a/R/default_params_doc.R b/R/default_params_doc.R
index 58a1f77..3037ce8 100644
--- a/R/default_params_doc.R
+++ b/R/default_params_doc.R
@@ -52,9 +52,9 @@
 #' @param mcmc the MCMC options,
 #'   see \link[beautier]{create_mcmc}
 #' @param mrca_prior one Most Recent Common Ancestor prior,
-#'   as returned by \code{\link{create_mrca_prior}}
+#'   as returned by \code{\link[beautier]{create_mrca_prior}}
 #' @param mrca_priors a list of one or more Most Recent Common Ancestor priors,
-#'   as returned by \code{\link{create_mrca_prior}}
+#'   as returned by \code{\link[beautier]{create_mrca_prior}}
 #' @param overwrite will 'BEAST2'  overwrite files? Like 'BEAST2',
 #'  this is set to \link{TRUE} by default.
 #'  If \link{TRUE}, 'BEAST2'  will overwrite the
@@ -63,9 +63,9 @@
 #'  \code{beast2_options$output_state_filename} if its present
 #'  and \link{babette} will give an error message.
 #'  Note that if \code{overwrite} is set to \link{FALSE} when
-#'  a \code{tracelog} (see \link{create_tracelog}),
-#'  \code{screenlog} (see \link{create_screenlog})
-#'  or \code{treelog} (see \link{create_treelog})
+#'  a \code{tracelog} (see \link[beautier]{create_tracelog}),
+#'  \code{screenlog} (see \link[beautier]{create_screenlog})
+#'  or \code{treelog} (see \link[beautier]{create_treelog})
 #'  file already exists,
 #'  'BEAST2'  (and thus \link{babette}) will freeze.
 #' @param rng_seed the random number generator seed. Must be either
diff --git a/man/bbt_run.Rd b/man/bbt_run.Rd
index 41e6f63..2ec4a3b 100644
--- a/man/bbt_run.Rd
+++ b/man/bbt_run.Rd
@@ -35,7 +35,7 @@ see \link[beautier]{create_clock_model}}
 as created by \link[beautier]{create_tree_prior}}
 
 \item{mrca_prior}{one Most Recent Common Ancestor prior,
-as returned by \code{\link{create_mrca_prior}}}
+as returned by \code{\link[beautier]{create_mrca_prior}}}
 
 \item{mcmc}{the MCMC options,
 see \link[beautier]{create_mcmc}}
@@ -75,9 +75,9 @@ If \link{FALSE}, 'BEAST2'  will not overwrite the
 \code{beast2_options$output_state_filename} if its present
 and \link{babette} will give an error message.
 Note that if \code{overwrite} is set to \link{FALSE} when
-a \code{tracelog} (see \link{create_tracelog}),
-\code{screenlog} (see \link{create_screenlog})
-or \code{treelog} (see \link{create_treelog})
+a \code{tracelog} (see \link[beautier]{create_tracelog}),
+\code{screenlog} (see \link[beautier]{create_screenlog})
+or \code{treelog} (see \link[beautier]{create_treelog})
 file already exists,
 'BEAST2'  (and thus \link{babette}) will freeze.}
 
diff --git a/man/default_params_doc.Rd b/man/default_params_doc.Rd
index 7f7eddd..3a4c585 100644
--- a/man/default_params_doc.Rd
+++ b/man/default_params_doc.Rd
@@ -99,10 +99,10 @@ as returned by \link[beautier]{create_inference_model}}
 see \link[beautier]{create_mcmc}}
 
 \item{mrca_prior}{one Most Recent Common Ancestor prior,
-as returned by \code{\link{create_mrca_prior}}}
+as returned by \code{\link[beautier]{create_mrca_prior}}}
 
 \item{mrca_priors}{a list of one or more Most Recent Common Ancestor priors,
-as returned by \code{\link{create_mrca_prior}}}
+as returned by \code{\link[beautier]{create_mrca_prior}}}
 
 \item{overwrite}{will 'BEAST2'  overwrite files? Like 'BEAST2',
 this is set to \link{TRUE} by default.
@@ -112,9 +112,9 @@ If \link{FALSE}, 'BEAST2'  will not overwrite the
 \code{beast2_options$output_state_filename} if its present
 and \link{babette} will give an error message.
 Note that if \code{overwrite} is set to \link{FALSE} when
-a \code{tracelog} (see \link{create_tracelog}),
-\code{screenlog} (see \link{create_screenlog})
-or \code{treelog} (see \link{create_treelog})
+a \code{tracelog} (see \link[beautier]{create_tracelog}),
+\code{screenlog} (see \link[beautier]{create_screenlog})
+or \code{treelog} (see \link[beautier]{create_treelog})
 file already exists,
 'BEAST2'  (and thus \link{babette}) will freeze.}