/
index.html
297 lines (252 loc) · 13.5 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Changelog • admixr</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Changelog" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-news">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">admixr</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.8.6</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/tutorial.html">admixr - Tutorial</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/bodkan/admixr/">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1 data-toc-skip>Changelog <small></small></h1>
<small>Source: <a href='https://github.com/bodkan/admixr/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="admixr-086" class="section level1">
<h1 class="page-header" data-toc-text="0.8.6">
<a href="#admixr-086" class="anchor"></a>admixr 0.8.6</h1>
<ul>
<li>Satisfying further checks on various testing servers.</li>
<li>Cleanup of tests and imports.</li>
<li>Updated license.</li>
<li>Prepared for the first CRAN submission.</li>
</ul>
</div>
<div id="admixr-081" class="section level1">
<h1 class="page-header" data-toc-text="0.8.1">
<a href="#admixr-081" class="anchor"></a>admixr 0.8.1</h1>
<ul>
<li>Fixed a minor bug in single-source qpAdm analyses. The package now detects this and correctly handles missing “subsets/patterns” information.</li>
</ul>
</div>
<div id="admixr-080" class="section level1">
<h1 class="page-header" data-toc-text="0.8.0">
<a href="#admixr-080" class="anchor"></a>admixr 0.8.0</h1>
<p>Finally resumed the development of <em>admixr</em>! Apologies to everyone for having to wait so long. Thank you for your patience and feedback since the last release. I hope that things will start moving a little bit faster and we will reach version 1.0 in the next couple of months.</p>
<p>New features and improvements:</p>
<ul>
<li>New function <code><a href="../reference/loginfo.html">loginfo()</a></code> which operates on any output object from an admixr wrapper and shows the full log output (the “log file” in ADMIXTOOLS jargon) associated with the analysis. It also has options for saving the log file to a permanent location and to only show a log file for a target sample of interest (relevant for <em>qpAdm</em> analyses with multiple targets at once).</li>
<li>
<em>admixr</em> can now (hopefully) detect broken/truncated output files generated by ADMIXTOOLS whenever there is some fatal issue with an analysis. The package should now detect this and inform the user.</li>
<li>Removed <em>qpAdm</em> argument <code>details</code> - the user will always want to see the full analysis summary so this option is redundant. It is still kept in <em>qpWave</em> - for now, until I figure out how useful the full output actually is. Given the implementation of <code><a href="../reference/loginfo.html">loginfo()</a></code> above, we might remove the argument from <em>qpWave</em> too at some point soon.</li>
<li>The function <code><a href="../reference/download_data.html">download_data()</a></code> now fetches data from a more stable location.</li>
</ul>
</div>
<div id="admixr-071" class="section level1">
<h1 class="page-header" data-toc-text="0.7.1">
<a href="#admixr-071" class="anchor"></a>admixr 0.7.1</h1>
<ul>
<li>Parse admixture proportions from the “best coefficients” line of the qpAdm output file.</li>
</ul>
</div>
<div id="admixr-070" class="section level1">
<h1 class="page-header" data-toc-text="0.7.0">
<a href="#admixr-070" class="anchor"></a>admixr 0.7.0</h1>
<ul>
<li>Fixed handling of warnings when dealing with duplicated populations.</li>
<li>9s are now replaced with NAs in <code><a href="../reference/read_ind.html">read_geno()</a></code> and <code><a href="../reference/write_ind.html">write_geno()</a></code>, which makes it more convenient to write custom analytic code working on data.frames.</li>
<li>Renamed <code><a href="../reference/qpAdm.html">qpAdm()</a></code> output elements and changed its function signature.</li>
</ul>
</div>
<div id="admixr-063" class="section level1">
<h1 class="page-header" data-toc-text="0.6.3">
<a href="#admixr-063" class="anchor"></a>admixr 0.6.3</h1>
<ul>
<li>Rename <code>keep_transversions()</code> to <code><a href="../reference/transversions_only.html">transversions_only()</a></code>. The old function is now deprecated.</li>
<li>
<code><a href="../reference/print.EIGENSTRAT.html">print.EIGENSTRAT()</a></code> now uses a pre-calculated numbers of removed/remaining sites, instead of calculating them each and every time.</li>
<li>Printing EIGENSTRAT objects now also shows “group” and “exclude” modifiers only if present.</li>
</ul>
</div>
<div id="admixr-062" class="section level1">
<h1 class="page-header" data-toc-text="0.6.2">
<a href="#admixr-062" class="anchor"></a>admixr 0.6.2</h1>
<ul>
<li>
<code><a href="../reference/read_output.html">read_output()</a></code> made public.</li>
<li>Fixed issues with parsing of mis-formatted ind files (tabs at the ends of lines etc.).</li>
</ul>
</div>
<div id="admixr-061" class="section level1">
<h1 class="page-header" data-toc-text="0.6.1">
<a href="#admixr-061" class="anchor"></a>admixr 0.6.1</h1>
<ul>
<li>
<p>It turned out that dragging along Rcpp and Boost dependencies just for the VCF -> EIGENSTRAT conversion function causes unnecessary complications in the installation process. It’s not worth having it in the package if it would be used only by a small fraction of potential users.</p>
<p>This function has been removed and the <code>vcf2eigenstrat</code> program is maintained in its own repository.</p>
</li>
</ul>
</div>
<div id="admixr-060" class="section level1">
<h1 class="page-header" data-toc-text="0.6.0">
<a href="#admixr-060" class="anchor"></a>admixr 0.6.0</h1>
<ul>
<li>Conversion of VCF to EIGENSTRAT format is now implemented in C++ and should be approximately infinitely faster than the old conversion function written in pure R.</li>
<li>Conversion of EIGENSTRAT <em>into</em> VCF has been removed.</li>
</ul>
</div>
<div id="admixr-050" class="section level1">
<h1 class="page-header" data-toc-text="0.5.0">
<a href="#admixr-050" class="anchor"></a>admixr 0.5.0</h1>
<ul>
<li>Added full implementations of <code><a href="../reference/qpWave.html">qpWave()</a></code> and <code><a href="../reference/qpAdm.html">qpAdm()</a></code> functions.</li>
<li>
<code><a href="../reference/filter_bed.html">filter_bed()</a></code> now implemented simply by calling <code>bedtools</code> in the background. This turned out to be way faster and memory efficient than the previous data.table-based solution.</li>
</ul>
</div>
<div id="admixr-041" class="section level1">
<h1 class="page-header" data-toc-text="0.4.1">
<a href="#admixr-041" class="anchor"></a>admixr 0.4.1</h1>
<ul>
<li>Fixed missing <code>group_labels()</code> update.</li>
<li>Removed the huge built-in data set. Implemented <code><a href="../reference/download_data.html">download_data()</a></code> function that fetches the example data set from the web.</li>
</ul>
</div>
<div id="admixr-040" class="section level1">
<h1 class="page-header" data-toc-text="0.4.0">
<a href="#admixr-040" class="anchor"></a>admixr 0.4.0</h1>
<ul>
<li>The package now has a tutorial vignette describing the main functionality.</li>
<li>Simple SNP dataset is now included with the package.</li>
<li>The API of many utility functions has been simplified and their internals re-written.</li>
<li>
<code>filter_sites</code> is now implemented using <code>data.table</code> and allows overlap with an arbitrary BED file.</li>
</ul>
</div>
<div id="admixr-030" class="section level1">
<h1 class="page-header" data-toc-text="0.3.0">
<a href="#admixr-030" class="anchor"></a>admixr 0.3.0</h1>
<ul>
<li>All wrappers have been given simpler names (<code>qpDstat()</code> -> <code><a href="../reference/f4ratio.html">d()</a></code>, <code>qpF4ratio()</code> -> <code><a href="../reference/f4ratio.html">f4ratio()</a></code>, etc).</li>
<li>F4 statistic can now be calculated using a separate <code><a href="../reference/f4ratio.html">f4()</a></code> function (<code>f4mode</code> parameter remains in the <code><a href="../reference/f4ratio.html">d()</a></code> function though, as <code><a href="../reference/f4ratio.html">f4()</a></code> calls <code><a href="../reference/f4ratio.html">d()</a></code> internally).</li>
<li>All tests are performed on Travis CI using installed and compiled ADMIXTOOLS software.</li>
</ul>
</div>
<div id="admixr-020" class="section level1">
<h1 class="page-header" data-toc-text="0.2.0">
<a href="#admixr-020" class="anchor"></a>admixr 0.2.0</h1>
<ul>
<li><p>The package now includes qpAdm functionality.</p></li>
<li><p>Formal tests for all implemented wrapper functions have been implemented.</p></li>
</ul>
</div>
<div id="admixr-010" class="section level1">
<h1 class="page-header" data-toc-text="0.1.0">
<a href="#admixr-010" class="anchor"></a>admixr 0.1.0</h1>
<p>Implemented:</p>
<ul>
<li>D statistic as qpDstat,</li>
<li>f4 statistic as qpDstat(f4mode = TRUE),</li>
<li>f4-ratio statistic as qpF4Ratio,</li>
<li>f3 statistic as qp3Pop.</li>
</ul>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Martin Petr.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>
</div>
</body>
</html>