From 12f6e207b591d14b29dd7b55a6833251c1b39084 Mon Sep 17 00:00:00 2001
From: Frederick Boehm <frederick.boehm@gmail.com>
Date: Fri, 9 Mar 2018 15:54:51 -0600
Subject: [PATCH] updated documentation after deprecating calc_lrt()

---
 man/{calc_lrt.Rd => calc_lrt-deprecated.Rd} |  8 ++++++--
 man/qtl2pleio-deprecated.Rd                 | 11 ++++++++++-
 2 files changed, 16 insertions(+), 3 deletions(-)
 rename man/{calc_lrt.Rd => calc_lrt-deprecated.Rd} (70%)

diff --git a/man/calc_lrt.Rd b/man/calc_lrt-deprecated.Rd
similarity index 70%
rename from man/calc_lrt.Rd
rename to man/calc_lrt-deprecated.Rd
index e920b17..e614526 100644
--- a/man/calc_lrt.Rd
+++ b/man/calc_lrt-deprecated.Rd
@@ -1,7 +1,7 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/calc_lrt.R
-\name{calc_lrt}
-\alias{calc_lrt}
+\name{calc_lrt-deprecated}
+\alias{calc_lrt-deprecated}
 \title{Calculate the LRT statistic}
 \usage{
 calc_lrt(loglik_mat)
@@ -12,3 +12,7 @@ calc_lrt(loglik_mat)
 \description{
 Calculate the LRT statistic
 }
+\seealso{
+\code{\link{qtl2pleio-deprecated}}
+}
+\keyword{internal}
diff --git a/man/qtl2pleio-deprecated.Rd b/man/qtl2pleio-deprecated.Rd
index 6f075d6..f69a393 100644
--- a/man/qtl2pleio-deprecated.Rd
+++ b/man/qtl2pleio-deprecated.Rd
@@ -1,11 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/calc_loglik_bvlmm.R, R/qtl2pleio-deprecated.r
+% Please edit documentation in R/calc_loglik_bvlmm.R, R/calc_lrt.R,
+%   R/qtl2pleio-deprecated.r
 \name{calc_loglik_bvlmm}
 \alias{calc_loglik_bvlmm}
+\alias{calc_lrt}
 \alias{qtl2pleio-deprecated}
 \title{Deprecated functions in package \pkg{qtl2pleio}.}
 \usage{
 calc_loglik_bvlmm(X, Bhat, Y, Sigma)
+
+calc_lrt(loglik_mat)
 }
 \description{
 The functions listed below are deprecated and will be defunct in
@@ -18,4 +22,9 @@ The functions listed below are deprecated and will be defunct in
 For \code{calc_loglik_bvlmm}, use \code{\link{mvtnorm::dmvnorm}}.
 }
 
+\section{\code{calc_lrt}}{
+
+For \code{calc_lrt}, use \code{\link{qtl2pleio::calc_lrt_tib}}.
+}
+
 \keyword{internal}