[adegenet-commits] r208 - in pkg/misc: . bug-report.1.2-2.05
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 20 11:38:57 CET 2008
Author: jombart
Date: 2008-11-20 11:38:57 +0100 (Thu, 20 Nov 2008)
New Revision: 208
Added:
pkg/misc/bug-report.1.2-2.05/
pkg/misc/bug-report.1.2-2.05/boot_coord.21.input
pkg/misc/bug-report.1.2-2.05/boot_dist.21.input
pkg/misc/bug-report.1.2-2.05/monmonier-bug-corrected.html
pkg/misc/bug-report.1.2-2.05/monmoniersnippet.r
Log:
New bug report for monmonier (after bug 1.2-2.03).
Added: pkg/misc/bug-report.1.2-2.05/boot_coord.21.input
===================================================================
--- pkg/misc/bug-report.1.2-2.05/boot_coord.21.input (rev 0)
+++ pkg/misc/bug-report.1.2-2.05/boot_coord.21.input 2008-11-20 10:38:57 UTC (rev 208)
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Added: pkg/misc/bug-report.1.2-2.05/boot_dist.21.input
===================================================================
--- pkg/misc/bug-report.1.2-2.05/boot_dist.21.input (rev 0)
+++ pkg/misc/bug-report.1.2-2.05/boot_dist.21.input 2008-11-20 10:38:57 UTC (rev 208)
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+-1 0.000984252 0.000996403 0.00590551 -1 0 0.00449597 0.00162402 -1 -1 -1 0.00166776 -1 0.00214928 -1 -1 0.00185202 -1 0.000984252 -1 0.00590551 -1 0.00232283 -1 -1 -1 0.0019685 -1 0.00140997 0.00551667 -1 -1 -1 0.00153106 0.00109491 -1 -1 0.00130359 -1 0.00123031 0.00408546 0.00688976 0.00247067 0.00101159 0.00148642 -1 0.00498256 0.00259843 -1 0.00165127 0.00474191 -1 -1 0.00540334 0.0019685 -1 -1 -1 -1 0.00261252 0.00100434 -1 -1 0.00480074 0.00184649 -1 -1 -1 0.0019685 0.00679353 0.00344488 -1 0.00279479 -1 0.00480074 -1 -1 -1 0.00732721 -1 -1 0 -1 0.0019685 0.00468915 0.00371829 0.00156665 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 0.000984252 0.000777681 0.00590551 -1 0.0019685 0.00449597 4.92126e-05 -1 -1 -1 2.73403e-05 -1 0.000180781 -1 -1 0.000186367 -1 0.000984252 -1 0.00590551 -1 0.000354331 -1 -1 -1 0 -1 0.000136229 0.00551667 -1 -1 -1 0.000874891 0.000489214 -1 -1 0.000253718 -1 0.000246063 0.00381703 0.00688976 0.000502169 0.000683508 8.03471e-05 -1 0.00498256 0.000629921 -1 0.000219626 0.00474191 -1 -1 0.00540334 0.000656168 -1 -1 -1 -1 0.00261252 0.000723124 -1 -1 0.00480074 0.000235895 -1 -1 -1 0 0.00679353 0.00295276 -1 0.00279479 -1 0.00480074 -1 -1 -1 0.00732721 -1 -1 0.0019685 -1 0 0.00468915 0.00371829 5.24158e-05 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 0.00370489 0.00371705 0.00665765 -1 0.00468915 0.00114445 0.00434466 -1 -1 -1 0.0043884 -1 0.00486993 -1 -1 0.00349107 -1 0.00370489 -1 0.00665765 -1 0.00504348 -1 -1 -1 0.00468915 -1 0.00413061 0.000738251 -1 -1 -1 0.0042517 0.0035127 -1 -1 0.00363053 -1 0.00395096 0.00143745 0.00258003 0.00519132 0.00373223 0.00420706 -1 0.000452273 0.00531907 -1 0.00437191 0.000119717 -1 -1 0.000892746 0.00468915 -1 -1 -1 -1 0.00298971 0.00372498 -1 -1 0.000189708 0.00456713 -1 -1 -1 0.00468915 0.00245255 0.00265034 -1 0.00395313 -1 0.000223186 -1 -1 -1 0.0100479 -1 -1 0.00468915 -1 0.00468915 0 0.00541406 0.00428729 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 0.00273403 0.00274618 0.00148731 -1 0.00371829 0.00445222 0.0033738 -1 -1 -1 0.00341754 -1 0.00389907 -1 -1 0.00346048 -1 0.00273403 -1 0.00148731 -1 0.00407262 -1 -1 -1 0.00371829 -1 0.00315975 0.00621658 -1 -1 -1 0.00328084 0.00280431 -1 -1 0.00297463 -1 0.0029801 0.00485695 0.00772091 0.00422045 0.00276137 0.0032362 -1 0.00575195 0.00434821 -1 0.00340105 0.00548556 -1 -1 0.00617825 0.00131234 -1 -1 -1 -1 0.000848158 0.00275412 -1 -1 0.00554752 0.00359627 -1 -1 -1 0.00371829 0.00761592 0.00473535 -1 0.000330514 -1 0.00555689 -1 -1 -1 0.00330271 -1 -1 0.00371829 -1 0.00371829 0.00541406 0 0.00331643 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 0.000582398 0.000426301 0.00550366 -1 0.00156665 0.00409411 1.07744e-05 -1 -1 -1 4.04443e-06 -1 0.000233197 -1 -1 0.000168895 -1 0.000582398 -1 0.00550366 -1 0.000406746 -1 -1 -1 5.24158e-05 -1 2.83138e-05 0.00511482 -1 -1 -1 0.00062446 0.000227135 -1 -1 9.41413e-05 -1 7.13437e-05 0.00347712 0.00648791 0.000554585 0.000357366 2.97142e-06 -1 0.00458071 0.000682337 -1 0.00014815 0.00434005 -1 -1 0.00500149 0.00055716 -1 -1 -1 -1 0.00221067 0.000386165 -1 -1 0.00439888 0.000205716 -1 -1 -1 5.24158e-05 0.00639167 0.00266447 -1 0.00239294 -1 0.00439888 -1 -1 -1 0.00692535 -1 -1 0.00156665 -1 5.24158e-05 0.00428729 0.00331643 0 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 -1 -1 -1 -1
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+-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 -1 -1 -1
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Added: pkg/misc/bug-report.1.2-2.05/monmonier-bug-corrected.html
===================================================================
--- pkg/misc/bug-report.1.2-2.05/monmonier-bug-corrected.html (rev 0)
+++ pkg/misc/bug-report.1.2-2.05/monmonier-bug-corrected.html 2008-11-20 10:38:57 UTC (rev 208)
@@ -0,0 +1,255 @@
+<html>
+<head>
+<title>Re: monmonier bug corrected</title>
+<link rel="important stylesheet" href="chrome://messenger/skin/messageBody.css">
+</head>
+<body>
+<table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part1"><tr><td><b>Subject: </b>Re: monmonier bug corrected</td></tr><tr><td><b>From: </b>Yi-Hsin Erica Tsai <erica.tsai at duke.edu></td></tr><tr><td><b>Date: </b>Wed, 19 Nov 2008 13:43:15 -0500</td></tr></table><table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part2"><tr><td><b>To: </b>Thibaut Jombart <jombart at biomserv.univ-lyon1.fr></td></tr></table><br>
+<div class="moz-text-flowed">Hi Thibaut,
+<br>
+<br>Thanks so much for taking the time to fix this bug. I tried the patch
+you sent, but unfortunately I still have the problem. I attached the
+code snippet that is causing the problem and two example input files.
+Is it possible that my data is the problem? There are a lot of '-1' in
+the genetic distance matrix in particular.
+<br>
+<br>Best,
+<br>--Erica
+<br>
+<br>Thibaut Jombart wrote:
+<br><blockquote type=cite>Yi-Hsin Erica Tsai wrote:
+<br><blockquote type=cite>Hi Thibaut,
+<br>
+<br>Sorry, I forgot to include that before. I am using v. 1.2-2 and it
+still has the problem.
+<br>
+<br>Best,
+<br>--Erica
+<br>
+<br></blockquote>Dear Erica,
+<br>
+<br>here is a patch for the bug you revealed in monmonier. The information
+you provided in your bug report has been most helpful. So, thanks very
+much. Hopefully this version would fix the problem. Please let me know.
+<br>
+<br>Best,
+<br>
+<br>Thibaut.
+<br>
+<br></blockquote></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR> X Y
+p0 -90.344 36.5335
+p1 -74.1975 40.1195
+p2 -84.481 43.7834
+p3 -76.3179 34.969
+p4 -76.8712 44.2157
+p5 -88.8705 45.1112
+p6 -78.4352 35.6824
+p7 -74.3502 44.6391
+p8 -83.5004 31.6054
+p9 -93.1657 46.4127
+p10 -75.888 38.319
+p11 -75.9765 40.1213
+p12 -66.5238 33.2075
+p13 -69.7984 42.4932
+p14 -82.2384 31.4897
+p15 -72.0661 39.4346
+p16 -82.577 38.5903
+p17 -90.0066 42.56
+p18 -85.0228 42.9751
+p19 -93.5859 45.4816
+p20 -76.5085 33.8483
+p21 -70.4951 33.6796
+p22 -79.9123 39.3928
+p23 -92.1904 44.6224
+p24 -77.3186 32.2079
+p25 -69.7134 34.6623
+p26 -78.1516 38.9149
+p27 -70.6276 39.4889
+p28 -75.3315 41.893
+p29 -85.7151 32.1938
+p30 -73.1039 32.0742
+p31 -76.2046 33.2625
+p32 -77.9082 43.0392
+p33 -68.7914 44.8949
+p34 -78.588 45.2082
+p35 -70.8774 33.5931
+p36 -90.8861 41.3575
+p37 -83.9036 40.4439
+p38 -87.8924 37.4479
+p39 -80.2635 43.605
+p40 -79.6913 36.4895
+p41 -92.281 32.0393
+p42 -69.5303 44.9076
+p43 -76.3818 39.3835
+p44 -77.1981 45.3669
+p45 -76.295 36.3057
+p46 -93.7414 35.0623
+p47 -79.8463 39.9623
+p48 -92.5742 37.2472
+p49 -80.633 40.2381
+p50 -84.8784 35.6219
+p51 -72.3111 37.6343
+p52 -66.7465 32.9605
+p53 -92.6153 33.852
+p54 -78.361 39.2669
+p55 -93.7132 31.9208
+p56 -68.9082 31.8468
+p57 -89.7587 43.0175
+p58 -67.1441 43.0791
+p59 -84.9746 39.6774
+p60 -74.2897 45.8349
+p61 -68.5075 42.0095
+p62 -87.6326 37.4078
+p63 -85.7332 35.1211
+p64 -70.8549 42.9514
+p65 -69.6103 33.2328
+p66 -91.7401 41.047
+p67 -77.5502 31.6751
+p68 -71.9995 40.802
+p69 -86.9889 36.2725
+p70 -89.0967 34.8409
+p71 -82.2763 31.9477
+p72 -84.9376 39.7443
+p73 -70.3067 35.2987
+p74 -84.228 33.4885
+p75 -70.2873 31.6575
+p76 -90.4143 42.8158
+p77 -72.6012 36.343
+p78 -88.8231 31.7612
+p79 -76.495 31.0011
+p80 -70.753 38.6799
+p81 -89.2748 45.1426
+p82 -89.7011 42.6919
+p83 -67.0321 45.591
+p84 -83.0428 34.2016
+p85 -85.9246 39.6852
+p86 -80.7755 41.9134
+p87 -90.3781 45.767
+p88 -90.5544 44.1087
+p89 -90.3846 42.3437
+p90 -89.0507 40.8231
+p91 -89.439 39.5179
+p92 -91.0141 38.3423
+p93 -92.6128 37.4016
+p94 -91.8339 40.9619
+p95 -93.6944 39.4091
+</pre></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR>-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 0 1.21513e-05 0.00492126 -1 0.000984252 0.00351171 0.000639764 -1 -1 -1 0.000683508 -1 0.00116503 -1 -1 0.000867772 -1 0 -1 0.00492126 -1 0.00133858 -1 -1 -1 0.000984252 -1 0.000425715 0.00453242 -1 -1 -1 0.000546807 0.000110656 -1 -1 0.000319335 -1 0.000246063 0.00310121 0.00590551 0.00148642 2.73403e-05 0.000502169 -1 0.00399831 0.00161417 -1 0.000667014 0.00375766 -1 -1 0.00441909 0.000984252 -1 -1 -1 -1 0.00162827 2.00868e-05 -1 -1 0.00381649 0.000862237 -1 -1 -1 0.000984252 0.00580927 0.00246063 -1 0.00181054 -1 0.00381649 -1 -1 -1 0.00634296 -1 -1 0.000984252 -1 0.000984252 0.00370489 0.00273403 0.000582398 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 1.21513e-05 0 0.00493341 -1 0.000996403 0.00352387 0.000476937 -1 -1 -1 0.000513391 -1 0.000958462 -1 -1 0.000694851 -1 1.21513e-05 -1 0.00493341 -1 0.00113201 -1 -1 -1 0.000777681 -1 0.000296339 0.00454457 -1 -1 -1 0.00048605 5.55075e-05 -1 -1 0.000214834 -1 0.000148853 0.00308353 0.00591766 0.00127985 3.03781e-06 0.00035809 -1 0.00401046 0.0014076 -1 0.000520094 0.00376981 -1 -1 0.00443124 0.000850588 -1 -1 -1 -1 0.00164042 9.91939e-07 -1 -1 0.00382864 0.000695434 -1 -1 -1 0.000777681 0.00582143 0.0024181 -1 0.00182269 -1 0.00382864 -1 -1 -1 0.00635511 -1 -1 0.000996403 -1 0.000777681 0.00371705 0.00274618 0.000426301 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 0.00492126 0.00493341 0 -1 0.00590551 0.00515213 0.00556102 -1 -1 -1 0.00560477 -1 0.00608629 -1 -1 0.00548619 -1 0.00492126 -1 0 -1 0.00625984 -1 -1 -1 0.00590551 -1 0.00534697 0.00748518 -1 -1 -1 0.00546807 0.00503192 -1 -1 0.00484689 -1 0.00516732 0.00596449 0.00885827 0.00640768 0.0049486 0.00542343 -1 0.00695107 0.00653543 -1 0.00558827 0.00671041 -1 -1 0.00737185 0.00328084 -1 -1 -1 -1 0.0023938 0.00494135 -1 -1 0.00676924 0.0057835 -1 -1 -1 0.00590551 0.00876203 0.00639764 -1 0.0019199 -1 0.00676924 -1 -1 -1 0.0033902 -1 -1 0.00590551 -1 0.00590551 0.00665765 0.00148731 0.00550366 -1 -1 -1 -1 -1 -1 -1 -1 -1
+-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
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+-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
+-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
+</pre></div><div class="moz-text-plain"><pre wrap><BR><HR WIDTH="90%" SIZE=4><BR>## Input files
+boot_coord_filename <- "boot_coord.21.input"
+boot_dist_filename <- "boot_dist.21.input"
+
+#### Necessary libraries
+
+library(spdep)
+library(ade4)
+library(adegenet)
+library(gplots)
+source("import.R")
+source("monmonier.R")
+
+#### Code snippet
+
+coords <- read.table(boot_coord_filename)
+Da <- read.table(boot_dist_filename)
+Da <- as.dist(Da)
+
+# Calc monmonier barrier
+cn <- chooseCN(coords, ask=FALSE, type=1, plot.nb = FALSE)
+mon <- monmonier(coords, Da, cn, threshold=NULL, scanthres = 0, nrun=1) #threshold is arbitrarily set at 0
+</pre></div></body>
+</html>
Added: pkg/misc/bug-report.1.2-2.05/monmoniersnippet.r
===================================================================
--- pkg/misc/bug-report.1.2-2.05/monmoniersnippet.r (rev 0)
+++ pkg/misc/bug-report.1.2-2.05/monmoniersnippet.r 2008-11-20 10:38:57 UTC (rev 208)
@@ -0,0 +1,22 @@
+## Input files
+boot_coord_filename <- "boot_coord.21.input"
+boot_dist_filename <- "boot_dist.21.input"
+
+#### Necessary libraries
+
+library(spdep)
+library(ade4)
+library(adegenet)
+library(gplots)
+source("import.R")
+source("monmonier.R")
+
+#### Code snippet
+
+coords <- read.table(boot_coord_filename)
+Da <- read.table(boot_dist_filename)
+Da <- as.dist(Da)
+
+# Calc monmonier barrier
+cn <- chooseCN(coords, ask=FALSE, type=1, plot.nb = FALSE)
+mon <- monmonier(coords, Da, cn, threshold=NULL, scanthres = 0, nrun=1) #threshold is arbitrarily set at 0
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