From c2c43e60fb83e362d77b1dd6513dd6ff7133d680 Mon Sep 17 00:00:00 2001
From: Thierry Gosselin <thierrygosselin@me.com>
Date: Tue, 25 Feb 2020 10:54:46 -0500
Subject: [PATCH] updated doc and example

---
 R/write_dadi.R                 | 4 ++--
 docs/reference/write_dadi.html | 4 ++--
 man/write_dadi.Rd              | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/write_dadi.R b/R/write_dadi.R
index 7c9eeea3..f31a5e57 100644
--- a/R/write_dadi.R
+++ b/R/write_dadi.R
@@ -52,11 +52,11 @@
 #' @examples
 #' \dontrun{
 #' # without outgroup:
-#' dadi.data <- radiator::write_dadi(data = "my_new.vcf")
+#' dadi.data <- radiator::write_dadi(data = "my_tidy_dataset.rad")
 #'
 #' # with outgroup and fasta generated by stacks:
 #' dadi.data <- radiator::write_dadi(
-#'    data = "my_new.vcf",
+#'    data = "my_tidy_dataset.rad",
 #'    fasta.ingroup = "batch_1.ingroup.fa",
 #'    fasta.outgroup = "batch_1.outgroup.fa",
 #'    sumstats.ingroup = "batch_1.sumstats.ingroup.tsv",
diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html
index d36f7022..51dbb329 100644
--- a/docs/reference/write_dadi.html
+++ b/docs/reference/write_dadi.html
@@ -212,11 +212,11 @@ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>R
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='co'># without outgroup:</span>
-<span class='no'>dadi.data</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>radiator</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/radiator/man/write_dadi.html'>write_dadi</a></span>(<span class='kw'>data</span> <span class='kw'>=</span> <span class='st'>"my_new.vcf"</span>)
+<span class='no'>dadi.data</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>radiator</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/radiator/man/write_dadi.html'>write_dadi</a></span>(<span class='kw'>data</span> <span class='kw'>=</span> <span class='st'>"my_tidy_dataset.rad"</span>)
 
 <span class='co'># with outgroup and fasta generated by stacks:</span>
 <span class='no'>dadi.data</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>radiator</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/pkg/radiator/man/write_dadi.html'>write_dadi</a></span>(
-   <span class='kw'>data</span> <span class='kw'>=</span> <span class='st'>"my_new.vcf"</span>,
+   <span class='kw'>data</span> <span class='kw'>=</span> <span class='st'>"my_tidy_dataset.rad"</span>,
    <span class='kw'>fasta.ingroup</span> <span class='kw'>=</span> <span class='st'>"batch_1.ingroup.fa"</span>,
    <span class='kw'>fasta.outgroup</span> <span class='kw'>=</span> <span class='st'>"batch_1.outgroup.fa"</span>,
    <span class='kw'>sumstats.ingroup</span> <span class='kw'>=</span> <span class='st'>"batch_1.sumstats.ingroup.tsv"</span>,
diff --git a/man/write_dadi.Rd b/man/write_dadi.Rd
index db745a80..b47fe656 100644
--- a/man/write_dadi.Rd
+++ b/man/write_dadi.Rd
@@ -59,11 +59,11 @@ of missingness, and one with imputed genotypes
 \examples{
 \dontrun{
 # without outgroup:
-dadi.data <- radiator::write_dadi(data = "my_new.vcf")
+dadi.data <- radiator::write_dadi(data = "my_tidy_dataset.rad")
 
 # with outgroup and fasta generated by stacks:
 dadi.data <- radiator::write_dadi(
-   data = "my_new.vcf",
+   data = "my_tidy_dataset.rad",
    fasta.ingroup = "batch_1.ingroup.fa",
    fasta.outgroup = "batch_1.outgroup.fa",
    sumstats.ingroup = "batch_1.sumstats.ingroup.tsv",