<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'><div dir='ltr'>
<font class="Apple-style-span" face="Tahoma" size="2">Hi,</font><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">I'm trying to run an sPCA on microsattelite data stored as a GENIND object in adegenet. I've got the data in and it recognizes the xy data as spatial coordinates. However, I am hoping to use a Gabriel Graph as the connection network (Type = 2) and keep getting an error message telling me:</div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; "><div>Error in chooseCN(xy = xy, ask = ask, type = type, plot.nb = plot.nb, : </div><div> Duplicate locations detected and incompatible with graph type 1-4.</div><div>Please choose another graph (5-7) or add random noise to locations (see ?jitter).</div></div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">However, I have checked the data and there are no duplicate coordinates. I even checked using the duplicated() function and R did not find any duplicates.</div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div><div><font class="Apple-style-span" face="Tahoma" size="2">> duplicated(Datum2@other$xy)</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"> [97] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">[109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">[121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">[133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">[145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">[157] FALSE FALSE</font></div></div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">I have tried the jitter() function to add additional noise but this didn't help. The spatial data are in Lambert which are metric units similar to UTMS.</div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">My code is as follows:</div><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div><font class="Apple-style-span" face="Tahoma" size="2">mySpca<-spca(Datum2, type=2, ask=FALSE, scannf=FALSE)</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">Any help would be much appreciated!</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">Thanks,</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">John Benson</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">PhD Candidate, Trent University</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">The spatial data look like this:</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><div> [,1] [,2]</div><div> [1,] 1358690 12086700</div><div> [2,] 1346840 12099300</div><div> [3,] 1343380 12100000</div><div> [4,] 1337699 12111573</div><div> [5,] 1343380 12100001</div><div> [6,] 1359610 12097200</div><div> [7,] 1358690 12086701</div><div> [8,] 1335017 12085102</div><div> [9,] 1359610 12097201</div><div> [10,] 1369480 12084800</div><div> [11,] 1386141 12100827</div><div> [12,] 1344620 12090900</div><div> [13,] 1327740 12120600</div><div> [14,] 1338520 12105500</div><div> [15,] 1344030 12120600</div><div> [16,] 1368710 12083800</div><div> [17,] 1366550 12094400</div><div> [18,] 1374040 12103000</div><div> [19,] 1368710 12083801</div><div> [20,] 1374040 12103001</div><div> [21,] 1344620 12090901</div><div> [22,] 1344620 12090902</div><div> [23,] 1361250 12104500</div><div> [24,] 1366550 12094402</div><div> [25,] 1322700 12093301</div><div> [26,] 1322700 12093302</div><div> [27,] 1361250 12104501</div><div> [28,] 1361250 12104502</div><div> [29,] 1375160 12094100</div><div> [30,] 1368240 12084200</div><div> [31,] 1375160 12094101</div><div> [32,] 1366550 12094401</div><div> [33,] 1335017 12085103</div><div> [34,] 1335510 12091900</div><div> [35,] 1335510 12091901</div><div> [36,] 1344030 12120601</div><div> [37,] 1351600 12114500</div><div> [38,] 1351600 12114501</div><div> [39,] 1327740 12120601</div><div> [40,] 1439300 12123800</div><div> [41,] 1395347 12140837</div><div> [42,] 1395471 12140894</div><div> [43,] 1437200 12137800</div><div> [44,] 1451450 12123900</div><div> [45,] 1444700 12154000</div><div> [46,] 1411350 12129200</div><div> [47,] 1411200 12104600</div><div> [48,] 1434570 12121900</div><div> [49,] 1453800 12111500</div><div> [50,] 1391720 12129300</div><div> [51,] 1436910 12170800</div><div> [52,] 1436910 12170801</div><div> [53,] 1410830 12146300</div><div> [54,] 1431050 12153700</div><div> [55,] 1437240 12137800</div><div> [56,] 1411350 12129201</div><div> [57,] 1391720 12129300</div><div> [58,] 1411200 12104601</div><div> [59,] 1439300 12123801</div><div> [60,] 1432480 12108400</div><div> [61,] 1410830 12146301</div><div> [62,] 1447040 12110400</div><div> [63,] 1432480 12108401</div><div> [64,] 1411350 12129202</div><div> [65,] 1411350 12129203</div><div> [66,] 1447040 12110401</div><div> [67,] 1427600 12124500</div><div> [68,] 1407900 12113000</div><div> [69,] 1411200 12104602</div><div> [70,] 1436910 12136700</div><div> [71,] 1437240 12137801</div><div> [72,] 1399090 12126100</div><div> [73,] 1439300 12123800</div><div> [74,] 1431050 12153701</div><div> [75,] 1427600 12124501</div><div> [76,] 1468400 12095100</div><div> [77,] 1461320 12144200</div><div> [78,] 1399090 12126101</div><div> [79,] 1410830 12146301</div><div> [80,] 1459760 12047200</div><div> [81,] 1459760 12047201</div><div> [82,] 1459760 12047202</div><div> [83,] 1480320 12031700</div><div> [84,] 1477090 12029900</div><div> [85,] 1469420 12061300</div><div> [86,] 1468100 12069400</div><div> [87,] 1463578 12025986</div><div> [88,] 1486470 12056700</div><div> [89,] 1486470 12056701</div><div> [90,] 1475832 12054690</div><div> [91,] 1475864 12055208</div><div> [92,] 1459950 12026100</div><div> [93,] 1469420 12061301</div><div> [94,] 1480840 12056600</div><div> [95,] 1468620 12021000</div><div> [96,] 1459950 12026101</div><div> [97,] 1467330 12053900</div><div> [98,] 1469450 12046300</div><div> [99,] 1469020 12029500</div><div>[100,] 1469020 12029501</div><div>[101,] 1298060 12161000</div><div>[102,] 1274250 12146100</div><div>[103,] 1320480 12159600</div><div>[104,] 1315350 12165100</div><div>[105,] 1281280 12155100</div><div>[106,] 1296740 12157600</div><div>[107,] 1266680 12172900</div><div>[108,] 1336180 12158500</div><div>[109,] 1291430 12152600</div><div>[110,] 1286870 12164500</div><div>[111,] 1278650 12150800</div><div>[112,] 1278990 12152200</div><div>[113,] 1283450 12159000</div><div>[114,] 1284180 12150000</div><div>[115,] 1292120 12144100</div><div>[116,] 1302840 12152300</div><div>[117,] 1282470 12160300</div><div>[118,] 1280813 12143228</div><div>[119,] 1212660 12517338</div><div>[120,] 1207823 12519046</div><div>[121,] 1202968 12517038</div><div>[122,] 1202113 12525129</div><div>[123,] 1243157 12494427</div><div>[124,] 1207363 12526526</div><div>[125,] 1236696 12499338</div><div>[126,] 1212576 12524585</div><div>[127,] 1183104 12517301</div><div>[128,] 1248668 12457722</div><div>[129,] 1222785 12507983</div><div>[130,] 1250901 12523857</div><div>[131,] 1037579 12579038</div><div>[132,] 1034475 12573747</div><div>[133,] 1031892 12578378</div><div>[134,] 1026728 12578284</div><div>[135,] 1029287 12574751</div><div>[136,] 1026712 12569199</div><div>[137,] 1031170 12569280</div><div>[138,] 1036705 12569110</div><div>[139,] 1038039 12573816</div><div>[140,] 959564 12587107</div><div>[141,] 1240410 12519266</div><div>[142,] 1281810 12296773</div><div>[143,] 1232201 12518809</div><div>[144,] 1188599 12314074</div><div>[145,] 1164718 12328228</div><div>[146,] 1231657 12527596</div><div>[147,] 1240025 12528250</div><div>[148,] 1218479 12504667</div><div>[149,] 1205978 12523118</div><div>[150,] 1246742 12469679</div><div>[151,] 1259798 12584201</div><div>[152,] 1193215 12521249</div><div>[153,] 1206737 12537081</div><div>[154,] 1053449 12362999</div><div>[155,] 1003255 12572308</div><div>[156,] 1002522 12573407</div><div>[157,] 1003973 12572318</div><div>[158,] 1061455 12643756</div><div><br></div></font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div> </div></body>
</html>