Cross-validation error: check.data.partitions.arg()

[sbreitbart]

Hi again,

I'm having trouble getting a cross-validation started. I've tried both the regular and parallelized options, and the error message continues to be:

Error in check.data.partitions.arg(args <- as.list(environment())) : 
there must be more loci in each partition than there are samples

However, I'm not sure what the issue is. I have almost 1000 loci and 256 samples. I've pasted my xval code, as well as the the heads of my allele frequency and geoDist data, below. Thanks so much!

x.validation(train.prop = 0.9,
                         n.reps = 10,
                         K = 1:5,
                         freqs = allele_frqs,
                         data.partitions = NULL,
                         geoDist = geoDist,
                         coords = coords,
                         prefix = "pilot",
                         n.iter = 10000,
                         make.figs = TRUE,
                         save.files = TRUE,
                         parallel = FALSE,
                         n.nodes = NULL)

head(allele_frqs)
                [,1] [,2] [,3] [,4] [,5] [,6] [,7]
1.2_1A10_sorted    0    1  1.0  0.0    0    0    0
                [,8] [,9] [,10] [,11] [,12] [,13]
1.2_1A10_sorted  1.0  0.0   0.5   0.5   0.5   0.0
                [,14] [,15] [,16] [,17] [,18] [,19]
1.2_1A10_sorted   0.0   1.0     0     0   0.0   0.0
                [,20] [,21] [,22] [,23] [,24] [,25]
1.2_1A10_sorted     0   0.5   0.0   0.0     0     1
                [,26] [,27] [,28] [,29] [,30] [,31]
1.2_1A10_sorted   0.0   0.5   0.5     1     1     1
                [,32] [,33] [,34] [,35] [,36] [,37]
1.2_1A10_sorted     1     0   0.0   1.0   0.0     0
                [,38] [,39] [,40] [,41] [,42] [,43]
1.2_1A10_sorted   0.5   0.5     0   0.5     0     1
                [,44] [,45] [,46] [,47] [,48] [,49]
1.2_1A10_sorted     0   0.0   1.0     0   0.5   0.5
                [,50] [,51] [,52] [,53] [,54] [,55]
1.2_1A10_sorted   0.5   1.0   1.0   0.0   1.0   0.5
                [,56] [,57] [,58] [,59] [,60] [,61]
1.2_1A10_sorted   0.5   0.5   0.5   1.0   0.0   0.5
                [,62] [,63] [,64] [,65] [,66] [,67]
1.2_1A10_sorted     1     1   0.0   1.0     0     0
                [,68] [,69] [,70] [,71] [,72] [,73]
1.2_1A10_sorted   0.0     0     0     0     0   0.5
                [,74] [,75] [,76] [,77] [,78] [,79]
1.2_1A10_sorted   1.0   0.5   0.5   0.5   0.5   0.5
                [,80] [,81] [,82] [,83] [,84] [,85]
1.2_1A10_sorted     0   0.5   0.5     1   0.5     1
                [,86] [,87] [,88] [,89] [,90] [,91]
1.2_1A10_sorted     1     1     0   0.0   1.0     0
                [,92] [,93] [,94] [,95] [,96] [,97]
1.2_1A10_sorted     0   1.0     0     1   0.0     0
                [,98] [,99] [,100] [,101] [,102]
1.2_1A10_sorted     0     1      1      0    0.0
                [,103] [,104] [,105] [,106] [,107]
1.2_1A10_sorted    0.5    0.5    0.0      0      1
                [,108] [,109] [,110] [,111] [,112]
1.2_1A10_sorted      1      0    0.5    0.0      1
                [,113] [,114] [,115] [,116] [,117]
1.2_1A10_sorted      0      1      0    0.0    0.5
                [,118] [,119] [,120] [,121] [,122]
1.2_1A10_sorted    1.0    0.0    0.0      0    1.0
                [,123] [,124] [,125] [,126] [,127]
1.2_1A10_sorted      1      0      0    0.5    1.0
                [,128] [,129] [,130] [,131] [,132]
1.2_1A10_sorted      0    1.0    1.0    0.0      0
                [,133] [,134] [,135] [,136] [,137]
1.2_1A10_sorted      1      0    0.5      0      0
                [,138] [,139] [,140] [,141] [,142]
1.2_1A10_sorted    1.0      0      1      0    0.5
                [,143] [,144] [,145] [,146] [,147]
1.2_1A10_sorted      1      0      1      1      1
                [,148] [,149] [,150] [,151] [,152]
1.2_1A10_sorted      1      0      1      0      0
                [,153] [,154] [,155] [,156] [,157]
1.2_1A10_sorted      0      0    1.0    0.5      1
                [,158] [,159] [,160] [,161] [,162]
1.2_1A10_sorted      0    0.5    0.5    1.0    1.0
                [,163] [,164] [,165] [,166] [,167]
1.2_1A10_sorted    1.0      0      0      0    0.0
                [,168] [,169] [,170] [,171] [,172]
1.2_1A10_sorted      0      0      1    0.0    0.0
                [,173] [,174] [,175] [,176] [,177]
1.2_1A10_sorted      0      0      0      0    1.0
                [,178] [,179] [,180] [,181] [,182]
1.2_1A10_sorted      0    0.5    0.0      1      0
                [,183] [,184] [,185] [,186] [,187]
1.2_1A10_sorted      0    1.0    0.0      1      0
                [,188] [,189] [,190] [,191] [,192]
1.2_1A10_sorted    1.0    0.5      0    1.0    1.0
                [,193] [,194] [,195] [,196] [,197]
1.2_1A10_sorted    0.0      0      0      0    0.0
                [,198] [,199] [,200] [,201] [,202]
1.2_1A10_sorted    0.0    0.0      0      1      1
                [,203] [,204] [,205] [,206] [,207]
1.2_1A10_sorted      1      0      0      0    0.0
                [,208] [,209] [,210] [,211] [,212]
1.2_1A10_sorted      1      0      0    0.0      1
                [,213] [,214] [,215] [,216] [,217]
1.2_1A10_sorted      0      1      1    0.5      0
                [,218] [,219] [,220] [,221] [,222]
1.2_1A10_sorted      0    0.0    0.0      0    1.0
                [,223] [,224] [,225] [,226] [,227]
1.2_1A10_sorted      0      0      0      0      0
                [,228] [,229] [,230] [,231] [,232]
1.2_1A10_sorted    0.0    0.0      0    0.0    1.0
                [,233] [,234] [,235] [,236] [,237]
1.2_1A10_sorted      1      0      1    0.5      0
                [,238] [,239] [,240] [,241] [,242]
1.2_1A10_sorted      1      0      1    0.5    1.0
                [,243] [,244] [,245] [,246] [,247]
1.2_1A10_sorted      0    0.5      0      0    1.0
                [,248] [,249] [,250] [,251] [,252]
1.2_1A10_sorted      0      1      0      0    1.0
                [,253] [,254] [,255] [,256] [,257]
1.2_1A10_sorted    0.0    0.0      0    0.5    0.0
                [,258] [,259] [,260] [,261] [,262]
1.2_1A10_sorted    0.5    0.5    1.0    0.0      0
                [,263] [,264] [,265] [,266] [,267]
1.2_1A10_sorted    0.5      1      1    0.0    1.0
                [,268] [,269] [,270] [,271] [,272]
1.2_1A10_sorted    0.0    0.0    0.5      0    1.0
                [,273] [,274] [,275] [,276] [,277]
1.2_1A10_sorted    0.0    1.0    0.0    1.0    1.0
                [,278] [,279] [,280] [,281] [,282]
1.2_1A10_sorted    0.5      0      0      0    1.0
                [,283] [,284] [,285] [,286] [,287]
1.2_1A10_sorted    0.0    1.0    1.0      1    0.5
                [,288] [,289] [,290] [,291] [,292]
1.2_1A10_sorted    0.5    0.5    0.5      0    1.0
                [,293] [,294] [,295] [,296] [,297]
1.2_1A10_sorted    0.0      1      0      1      1
                [,298] [,299] [,300] [,301] [,302]
1.2_1A10_sorted      0      0      0    0.0      0
                [,303] [,304] [,305] [,306] [,307]
1.2_1A10_sorted    0.0      0      0    1.0      0
                [,308] [,309] [,310] [,311] [,312]
1.2_1A10_sorted    0.0    1.0    0.5    0.5    1.0
                [,313] [,314] [,315] [,316] [,317]
1.2_1A10_sorted    1.0      0    0.0    0.5    1.0
                [,318] [,319] [,320] [,321] [,322]
1.2_1A10_sorted      0    0.0    1.0    0.5    0.5
                [,323] [,324] [,325] [,326] [,327]
1.2_1A10_sorted      0      0    0.5    0.5    0.0
                [,328] [,329] [,330] [,331] [,332]
1.2_1A10_sorted    0.0    0.5      0    0.5      0
                [,333] [,334] [,335] [,336] [,337]
1.2_1A10_sorted    0.5    0.5      0    0.0      0
                [,338] [,339] [,340] [,341] [,342]
1.2_1A10_sorted    0.5    0.5      0    0.5      1
                [,343] [,344] [,345] [,346] [,347]
1.2_1A10_sorted    0.0    0.5    0.5    1.0    0.0
                [,348] [,349] [,350] [,351] [,352]
1.2_1A10_sorted    1.0    1.0    1.0      0      1
                [,353] [,354] [,355] [,356] [,357]
1.2_1A10_sorted      0      0      0    1.0    1.0
                [,358] [,359] [,360] [,361] [,362]
1.2_1A10_sorted    0.5      0    0.5    1.0      0
                [,363] [,364] [,365] [,366] [,367]
1.2_1A10_sorted      0    0.0    0.5    0.5    0.0
                [,368] [,369] [,370] [,371] [,372]
1.2_1A10_sorted    1.0      0      0      0      0
                [,373] [,374] [,375] [,376] [,377]
1.2_1A10_sorted      0      0    0.0    0.0    0.5
                [,378] [,379] [,380] [,381] [,382]
1.2_1A10_sorted      0    1.0    0.0    0.5    0.5
                [,383] [,384] [,385] [,386] [,387]
1.2_1A10_sorted    0.0    1.0      0    0.5    0.5
                [,388] [,389] [,390] [,391] [,392]
1.2_1A10_sorted    0.5    1.0    0.0      0    0.5
                [,393] [,394] [,395] [,396] [,397]
1.2_1A10_sorted    1.0      1    1.0    1.0      1
                [,398] [,399] [,400] [,401] [,402]
1.2_1A10_sorted      0    1.0    1.0      0      0
                [,403] [,404] [,405] [,406] [,407]
1.2_1A10_sorted    1.0    1.0      0    1.0    1.0
                [,408] [,409] [,410] [,411] [,412]
1.2_1A10_sorted    1.0      1      1      0    0.0
                [,413] [,414] [,415] [,416] [,417]
1.2_1A10_sorted      1      1    0.0    0.0      0
                [,418] [,419] [,420] [,421] [,422]
1.2_1A10_sorted    1.0      1    1.0    0.0      0
                [,423] [,424] [,425] [,426] [,427]
1.2_1A10_sorted      1      1    0.0    0.0    0.5
                [,428] [,429] [,430] [,431] [,432]
1.2_1A10_sorted    0.5      1      1      0    1.0
                [,433] [,434] [,435] [,436] [,437]
1.2_1A10_sorted    0.0      0      0    0.0      1
                [,438] [,439] [,440] [,441] [,442]
1.2_1A10_sorted    1.0      1      0      0    1.0
                [,443] [,444] [,445] [,446] [,447]
1.2_1A10_sorted      0      0    0.0      1      0
                [,448] [,449] [,450] [,451] [,452]
1.2_1A10_sorted      0      0    0.5    0.5      0
                [,453] [,454] [,455] [,456] [,457]
1.2_1A10_sorted      0      1      0      0    0.0
                [,458] [,459] [,460] [,461] [,462]
1.2_1A10_sorted    0.0      0      1      0    0.5
                [,463] [,464] [,465] [,466] [,467]
1.2_1A10_sorted    0.5      0      0    1.0    0.5
                [,468] [,469] [,470] [,471] [,472]
1.2_1A10_sorted    1.0    0.0    0.0    1.0    1.0
                [,473] [,474] [,475] [,476] [,477]
1.2_1A10_sorted    0.0    1.0    0.0    1.0    0.0
                [,478] [,479] [,480] [,481] [,482]
1.2_1A10_sorted    0.0    1.0    1.0      0      0
                [,483] [,484] [,485] [,486] [,487]
1.2_1A10_sorted      1    0.0    0.0    0.0      0
                [,488] [,489] [,490] [,491] [,492]
1.2_1A10_sorted      1      1    0.0    1.0    1.0
                [,493] [,494] [,495] [,496] [,497]
1.2_1A10_sorted      0    1.0      0      1      1
                [,498] [,499] [,500] [,501] [,502]
1.2_1A10_sorted      0    0.5      1    1.0    1.0
                [,503] [,504] [,505] [,506] [,507]
1.2_1A10_sorted      0      1      1      0      1
                [,508] [,509] [,510] [,511] [,512]
1.2_1A10_sorted    0.0      0      0      0      1
                [,513] [,514] [,515] [,516] [,517]
1.2_1A10_sorted      0      1      0    0.5      0
                [,518] [,519] [,520] [,521] [,522]
1.2_1A10_sorted      0    0.0      0    0.5    0.5
                [,523] [,524] [,525] [,526] [,527]
1.2_1A10_sorted    0.5    0.0    0.0      0      1
                [,528] [,529] [,530] [,531] [,532]
1.2_1A10_sorted      0    0.0      0    0.0    1.0
                [,533] [,534] [,535] [,536] [,537]
1.2_1A10_sorted      0      1      1    1.0    1.0
                [,538] [,539] [,540] [,541] [,542]
1.2_1A10_sorted    0.0    0.0      1      1      1
                [,543] [,544] [,545] [,546] [,547]
1.2_1A10_sorted      0      0      1      0      0
                [,548] [,549] [,550] [,551] [,552]
1.2_1A10_sorted    1.0      0      0      1    0.0
                [,553] [,554] [,555] [,556] [,557]
1.2_1A10_sorted      0      1    0.0      0      0
                [,558] [,559] [,560] [,561] [,562]
1.2_1A10_sorted      0      0    0.5    0.0    1.0
                [,563] [,564] [,565] [,566] [,567]
1.2_1A10_sorted      1      0      1    0.5      0
                [,568] [,569] [,570] [,571] [,572]
1.2_1A10_sorted    0.5    1.0    0.0    1.0      0
                [,573] [,574] [,575] [,576] [,577]
1.2_1A10_sorted      0    0.0      0      1      0
                [,578] [,579] [,580] [,581] [,582]
1.2_1A10_sorted    0.5    0.5    0.0    0.0    0.0
                [,583] [,584] [,585] [,586] [,587]
1.2_1A10_sorted    0.0      0    1.0    1.0    1.0
                [,588] [,589] [,590] [,591] [,592]
1.2_1A10_sorted    0.0    0.0      0      0      1
                [,593] [,594] [,595] [,596] [,597]
1.2_1A10_sorted      0    0.0    0.0      0      0
                [,598] [,599] [,600] [,601] [,602]
1.2_1A10_sorted    0.0    0.5    0.0    1.0    1.0
                [,603] [,604] [,605] [,606] [,607]
1.2_1A10_sorted    0.0      0      0      0    0.0
                [,608] [,609] [,610] [,611] [,612]
1.2_1A10_sorted    1.0      0    1.0    1.0    0.0
                [,613] [,614] [,615] [,616] [,617]
1.2_1A10_sorted      0    0.5    0.0    1.0    1.0
                [,618] [,619] [,620] [,621] [,622]
1.2_1A10_sorted    1.0      0      0      0    0.0
                [,623] [,624] [,625] [,626] [,627]
1.2_1A10_sorted    1.0    0.0      0    0.5      0
                [,628] [,629] [,630] [,631] [,632]
1.2_1A10_sorted      0      0      1      0      0
                [,633] [,634] [,635] [,636] [,637]
1.2_1A10_sorted    0.5    0.0    0.0    1.0    0.0
                [,638] [,639] [,640] [,641] [,642]
1.2_1A10_sorted      0    0.5    0.5    1.0    1.0
                [,643] [,644] [,645] [,646] [,647]
1.2_1A10_sorted      0    0.0    0.0    1.0    0.0
                [,648] [,649] [,650] [,651] [,652]
1.2_1A10_sorted    0.0    0.5    0.5      0      0
                [,653] [,654] [,655] [,656] [,657]
1.2_1A10_sorted    0.5    0.5      1      0      1
                [,658] [,659] [,660] [,661] [,662]
1.2_1A10_sorted    0.0    0.0    1.0      0      0
                [,663] [,664] [,665] [,666] [,667]
1.2_1A10_sorted    1.0      0      1      0      0
                [,668] [,669] [,670] [,671] [,672]
1.2_1A10_sorted      0      1      0      1      0
                [,673] [,674] [,675] [,676] [,677]
1.2_1A10_sorted      0      0      0      0      0
                [,678] [,679] [,680] [,681] [,682]
1.2_1A10_sorted      0      1      0      1      1
                [,683] [,684] [,685] [,686] [,687]
1.2_1A10_sorted    1.0    0.5      1    1.0      0
                [,688] [,689] [,690] [,691] [,692]
1.2_1A10_sorted      1    0.5      0    0.5      0
                [,693] [,694] [,695] [,696] [,697]
1.2_1A10_sorted      0      1      0      0      0
                [,698] [,699] [,700] [,701] [,702]
1.2_1A10_sorted    1.0      0      1      0      0
                [,703] [,704] [,705] [,706] [,707]
1.2_1A10_sorted    0.5      0      1    0.5    0.5
                [,708] [,709] [,710] [,711] [,712]
1.2_1A10_sorted    1.0    1.0      1    0.5      1
                [,713] [,714] [,715] [,716] [,717]
1.2_1A10_sorted      0      0    0.5    0.5    0.0
                [,718] [,719] [,720] [,721] [,722]
1.2_1A10_sorted    0.0      0    1.0      0      0
                [,723] [,724] [,725] [,726] [,727]
1.2_1A10_sorted    0.5    0.5    0.0    1.0      0
                [,728] [,729] [,730] [,731] [,732]
1.2_1A10_sorted      0      0      0    0.0    1.0
                [,733] [,734] [,735] [,736] [,737]
1.2_1A10_sorted    1.0      0      1    1.0      0
                [,738] [,739] [,740] [,741] [,742]
1.2_1A10_sorted    0.0    1.0    0.5    1.0    0.0
                [,743] [,744] [,745] [,746] [,747]
1.2_1A10_sorted    0.0      0      0      1      0
                [,748] [,749] [,750] [,751] [,752]
1.2_1A10_sorted    1.0    0.0      0    1.0    1.0
                [,753] [,754] [,755] [,756] [,757]
1.2_1A10_sorted    1.0      0    0.5    1.0    0.5
                [,758] [,759] [,760] [,761] [,762]
1.2_1A10_sorted      0    0.5    0.5      0      0
                [,763] [,764] [,765] [,766] [,767]
1.2_1A10_sorted      0    1.0    0.5      0      0
                [,768] [,769] [,770] [,771] [,772]
1.2_1A10_sorted      1    1.0      1      0    0.0
                [,773] [,774] [,775] [,776] [,777]
1.2_1A10_sorted    0.0      0      0      1      0
                [,778] [,779] [,780] [,781] [,782]
1.2_1A10_sorted      0      0      1      0      0
                [,783] [,784] [,785] [,786] [,787]
1.2_1A10_sorted    0.5    0.5      1    0.5    0.5
                [,788] [,789] [,790] [,791] [,792]
1.2_1A10_sorted      0    0.0      0      0      0
                [,793] [,794] [,795] [,796] [,797]
1.2_1A10_sorted      0      1      0      1      1
                [,798] [,799] [,800] [,801] [,802]
1.2_1A10_sorted      1      0      0      0    0.5
                [,803] [,804] [,805] [,806] [,807]
1.2_1A10_sorted      0      0      0      0      0
                [,808] [,809] [,810] [,811] [,812]
1.2_1A10_sorted    1.0    1.0      0      0      0
                [,813] [,814] [,815] [,816] [,817]
1.2_1A10_sorted      1    0.5    0.5      1      1
                [,818] [,819] [,820] [,821] [,822]
1.2_1A10_sorted    0.5      1      0    0.0    1.0
                [,823] [,824] [,825] [,826] [,827]
1.2_1A10_sorted      0      0    0.0    1.0    1.0
                [,828] [,829] [,830] [,831] [,832]
1.2_1A10_sorted    0.0      0      1      0      0
                [,833] [,834] [,835] [,836] [,837]
1.2_1A10_sorted      1    0.5      0      1    1.0
                [,838] [,839] [,840] [,841] [,842]
1.2_1A10_sorted      0      0      0      0      0
                [,843] [,844] [,845] [,846] [,847]
1.2_1A10_sorted      0      0      0      0      0
                [,848] [,849] [,850] [,851] [,852]
1.2_1A10_sorted    0.5    1.0    1.0      1      0
                [,853] [,854] [,855] [,856] [,857]
1.2_1A10_sorted      0      0      1    0.0      1
                [,858] [,859] [,860] [,861] [,862]
1.2_1A10_sorted      0    0.0    0.5    0.5    0.5
                [,863] [,864] [,865] [,866] [,867]
1.2_1A10_sorted      1      0      0      0      0
                [,868] [,869] [,870] [,871] [,872]
1.2_1A10_sorted      0    0.0      0      1    1.0
                [,873] [,874] [,875] [,876] [,877]
1.2_1A10_sorted    1.0    1.0    0.0      0      0
                [,878] [,879] [,880] [,881] [,882]
1.2_1A10_sorted      0      0      1      0      0
                [,883] [,884] [,885] [,886] [,887]
1.2_1A10_sorted      1    0.0    0.0    0.0      0
                [,888] [,889] [,890] [,891] [,892]
1.2_1A10_sorted      1    0.5    0.0    0.0      1
                [,893] [,894] [,895] [,896] [,897]
1.2_1A10_sorted      0      0      0      0    0.5
                [,898] [,899] [,900] [,901] [,902]
1.2_1A10_sorted    0.5      0      1      0      0
                [,903] [,904] [,905] [,906] [,907]
1.2_1A10_sorted    1.0    1.0      0    1.0    0.0
                [,908] [,909] [,910] [,911] [,912]
1.2_1A10_sorted      0    0.5      0      1      0
                [,913] [,914] [,915] [,916] [,917]
1.2_1A10_sorted      0    0.0      0    1.0      0
                [,918] [,919] [,920] [,921] [,922]
1.2_1A10_sorted      1    0.0      0      0    0.5
                [,923] [,924] [,925] [,926] [,927]
1.2_1A10_sorted    0.5    1.0    1.0      0      0
                [,928] [,929] [,930] [,931] [,932]
1.2_1A10_sorted    1.0      0    1.0    0.0      0
                [,933] [,934] [,935] [,936] [,937]
1.2_1A10_sorted    0.0    0.0    1.0    0.0    1.0
                [,938] [,939] [,940] [,941] [,942]
1.2_1A10_sorted    0.0    0.0      0      0    1.0
                [,943] [,944] [,945] [,946] [,947]
1.2_1A10_sorted    1.0    0.0      0      0      0
                [,948] [,949] [,950] [,951] [,952]
1.2_1A10_sorted      0    0.0    1.0    0.0    0.0
                [,953] [,954] [,955] [,956] [,957]
1.2_1A10_sorted    0.5    1.0    1.0      0    0.0
                [,958] [,959] [,960] [,961] [,962]
1.2_1A10_sorted      0      0    1.0    0.0    1.0
                [,963] [,964] [,965] [,966] [,967]
1.2_1A10_sorted    0.5      0    1.0    0.0      0
                [,968] [,969] [,970] [,971] [,972]
1.2_1A10_sorted      0      1      0      0      0

head(geoDist)
          [,1]      [,2]      [,3]         [,4]
[1,]  0.000000 13.727390  9.892015 2.381399e+01
[2,] 13.727390  0.000000  9.937058 1.106926e+01
[3,]  9.892015  9.937058  0.000000 1.626971e+01
          [,5]         [,6]      [,7]      [,8]
[1,] 16.905986 1.828637e+01  8.317481 31.363702
[2,]  8.187294 1.004428e+01 10.916122 17.903873
[3,]  8.058421 8.970985e+00  1.867842 24.315685
          [,9]    [,10]    [,11]     [,12]
[1,]  5.964326 45.92081 43.45138  9.154768
[2,] 19.600855 32.41610 29.85356 22.485798
[3,] 13.978948 38.56634 36.40676 15.783890
         [,13]     [,14]     [,15]    [,16]
[1,]  8.317481 16.468504  5.964326 43.40656
[2,] 10.916122  5.371396 19.600855 29.96805
[3,]  1.867842  9.118442 13.978948 35.94834
         [,17]    [,18]    [,19]     [,20]
[1,] 30.406730 12.24447 39.08124  9.883878
[2,] 16.787384 23.64079 25.57166 21.401822
[3,] 23.839923 15.00909 31.88374 13.101854
         [,21]     [,22]    [,23]    [,24]
[1,]  9.142378  5.964326 10.97315 39.08124
[2,] 20.627234 19.600855 24.44317 25.57166
[3,] 12.420918 13.978948 17.80078 31.88374
         [,25]     [,26]     [,27]    [,28]
[1,] 21.583312 11.745072 30.406730  1.48979
[2,]  9.010918  7.528755 16.787384 15.13899
[3,] 14.141029  3.077151 23.839923 11.24280
          [,29]    [,30]        [,31]        [,32]
[1,] 17.1660898 39.08124 1.828637e+01 2.381399e+01
[2,]  7.8109772 25.57166 1.004428e+01 1.106926e+01
[3,]  8.5568906 31.88374 8.970985e+00 1.626971e+01
         [,33]      [,34]     [,35]     [,36]
[1,] 32.655466 17.1660898  9.892015 11.745072
[2,] 20.380216  7.8109772  9.937058  7.528755
[3,] 24.133420  8.5568906  0.000000  3.077151
         [,37]    [,38]    [,39]     [,40]
[1,] 16.804830 48.49421 56.31489  5.650492
[2,]  3.896618 34.97805 42.77823  8.256005
[3,] 10.760120 41.12646 48.90084  6.197529
         [,41]     [,42]     [,43]     [,44]
[1,]  5.650492  9.142378 32.655466 21.583312
[2,]  8.256005 20.627234 20.380216  9.010918
[3,]  6.197529 12.420918 24.133420 14.141029
         [,45]    [,46]     [,47]     [,48]
[1,] 21.583312 50.52262  9.892015  9.883878
[2,]  9.010918 37.26605  9.937058 21.401822
[3,] 14.141029 42.61930  0.000000 13.101854
        [,49]    [,50]      [,51]    [,52]
[1,] 39.08124 56.31489 17.1660898 43.45138
[2,] 25.57166 42.77823  7.8109772 29.85356
[3,] 31.88374 48.90084  8.5568906 36.40676
         [,53]    [,54]    [,55]        [,56]
[1,]  3.810523 49.70464  1.48979 1.828637e+01
[2,] 17.537094 36.42498 15.13899 1.004428e+01
[3,] 12.872313 41.84917 11.24280 8.970985e+00
        [,57]     [,58]     [,59]     [,60]
[1,] 49.70464 16.468504  4.861119 15.837669
[2,] 36.42498  5.371396  9.151953  2.255406
[3,] 41.84917  9.118442  6.204685 10.972246
         [,61]     [,62]     [,63]     [,64]
[1,]  8.199477 11.745072 32.655466 11.745072
[2,] 21.623524  7.528755 20.380216  7.528755
[3,] 15.196454  3.077151 24.133420  3.077151
         [,65]    [,66]     [,67]     [,68]
[1,]  6.174407 43.40656 16.905986  2.923925
[2,] 15.363908 29.96805  8.187294 11.791398
[3,]  7.244576 35.94834  8.058421  6.972162
        [,69]     [,70]    [,71]     [,72]
[1,] 39.08124 13.727390 10.97315  5.234699
[2,] 25.57166  0.000000 24.44317 18.914828
[3,] 31.88374  9.937058 17.80078 13.568196
         [,73]     [,74]     [,75]     [,76]
[1,] 16.025114  6.626549  0.000000 25.546411
[2,]  6.074307 17.386262 13.727390 12.333971
[3,]  8.129785  9.435412  9.892015 18.414704
            [,77]     [,78]     [,79]     [,80]
[1,] 1.828637e+01 30.406730 13.727390 12.391455
[2,] 1.004428e+01 16.787384  0.000000  6.048940
[3,] 8.970985e+00 23.839923  9.937058  4.614962
         [,81]     [,82]     [,83]     [,84]
[1,]  9.366031 11.745072 16.025114 31.363702
[2,]  4.663915  7.528755  6.074307 17.903873
[3,]  6.284298  3.077151  8.129785 24.315685
         [,85]    [,86]     [,87]    [,88]
[1,] 18.332730 56.92666 16.468504 35.14007
[2,]  6.684932 43.22762  5.371396 21.68886
[3,] 10.769003 50.16342  9.118442 27.92420
         [,89]    [,90]     [,91]     [,92]
[1,]  5.650492 43.40656 26.064500  5.234699
[2,]  8.256005 29.96805 13.791249 18.914828
[3,]  6.197529 35.94834 17.891471 13.568196
        [,93]     [,94]     [,95]     [,96]
[1,] 56.92666 18.332730  6.174407 16.804830
[2,] 43.22762  6.684932 15.363908  3.896618
[3,] 50.16342 10.769003  7.244576 10.760120
         [,97]     [,98]     [,99]    [,100]
[1,]  9.366031 15.837669 32.655466 21.583312
[2,]  4.663915  2.255406 20.380216  9.010918
[3,]  6.284298 10.972246 24.133420 14.141029
        [,101]   [,102]    [,103]    [,104]
[1,] 14.952789  1.48979  0.000000  6.626549
[2,]  6.618463 15.13899 13.727390 17.386262
[3,]  6.603231 11.24280  9.892015  9.435412
        [,105]       [,106]    [,107]    [,108]
[1,] 12.391455 1.828637e+01 16.905986  5.234699
[2,]  6.048940 1.004428e+01  8.187294 18.914828
[3,]  4.614962 8.970985e+00  8.058421 13.568196
        [,109]     [,110]    [,111]    [,112]
[1,]  6.174407 17.1660898  8.199477  1.665943
[2,] 15.363908  7.8109772 21.623524 12.812012
[3,]  7.244576  8.5568906 15.196454  8.242690
        [,113]    [,114]    [,115]    [,116]
[1,] 16.025114  9.142378 21.583312 14.952789
[2,]  6.074307 20.627234  9.010918  6.618463
[3,]  8.129785 12.420918 14.141029  6.603231
        [,117]       [,118]    [,119]    [,120]
[1,] 16.804830 2.381399e+01  9.154768 32.655466
[2,]  3.896618 1.106926e+01 22.485798 20.380216
[3,] 10.760120 1.626971e+01 15.783890 24.133420
        [,121]    [,122]    [,123]    [,124]
[1,]  8.317481  5.234699  8.199477  5.650492
[2,] 10.916122 18.914828 21.623524  8.256005
[3,]  1.867842 13.568196 15.196454  6.197529
        [,125]       [,126]    [,127]    [,128]
[1,] 26.064500 2.381399e+01  5.964326  4.861119
[2,] 13.791249 1.106926e+01 19.600855  9.151953
[3,] 17.891471 1.626971e+01 13.978948  6.204685
        [,129]   [,130]   [,131]   [,132]    [,133]
[1,] 16.804830 43.40656 10.97315 56.92666 15.837669
[2,]  3.896618 29.96805 24.44317 43.22762  2.255406
[3,] 10.760120 35.94834 17.80078 50.16342 10.972246
       [,134]    [,135]   [,136]    [,137]
[1,]  1.48979  9.892015  1.48979 26.064500
[2,] 15.13899  9.937058 15.13899 13.791249
[3,] 11.24280  0.000000 11.24280 17.891471
        [,138]    [,139]       [,140]    [,141]
[1,]  5.234699 15.837669 2.381399e+01  2.923925
[2,] 18.914828  2.255406 1.106926e+01 11.791398
[3,] 13.568196 10.972246 1.626971e+01  6.972162
       [,142]   [,143]    [,144]    [,145]
[1,] 43.45138 49.70464 30.406730 16.905986
[2,] 29.85356 36.42498 16.787384  8.187294
[3,] 36.40676 41.84917 23.839923  8.058421
        [,146]    [,147]    [,148]    [,149]
[1,]  9.883878  9.366031 26.064500 14.952789
[2,] 21.401822  4.663915 13.791249  6.618463
[3,] 13.101854  6.284298 17.891471  6.603231
        [,150]    [,151]    [,152]    [,153]
[1,]  1.665943  6.174407  9.142378  0.000000
[2,] 12.812012 15.363908 20.627234 13.727390
[3,]  8.242690  7.244576 12.420918  9.892015
         [,154]    [,155]    [,156]    [,157]
[1,] 17.1660898  9.892015  5.650492 16.025114
[2,]  7.8109772  9.937058  8.256005  6.074307
[3,]  8.5568906  0.000000  6.197529  8.129785
        [,158]    [,159]    [,160]    [,161]
[1,]  9.142378 16.468504 13.727390 16.804830
[2,] 20.627234  5.371396  0.000000  3.896618
[3,] 12.420918  9.118442  9.937058 10.760120
       [,162]   [,163]    [,164]    [,165]   [,166]
[1,] 43.40656 43.45138  6.174407 15.837669 26.61110
[2,] 29.96805 29.85356 15.363908  2.255406 40.33422
[3,] 35.94834 36.40676  7.244576 10.972246 34.36716
       [,167]   [,168]   [,169]   [,170]   [,171]
[1,] 31.96628 56.31489 35.14007 28.31295 26.01825
[2,] 38.31249 42.77823 21.68886 41.83503 37.81521
[3,] 41.05036 48.90084 27.92420 34.53871 35.83058
       [,172]   [,173]   [,174]   [,175]   [,176]
[1,] 67.64837 19.10550 60.65089 45.59188 10.74314
[2,] 54.01648 23.04208 74.37614 33.90323 24.08198
[3,] 60.44171 26.92198 67.73380 43.75003 17.22092
       [,177]   [,178]   [,179]    [,180]   [,181]
[1,] 36.96603 44.52613 34.13337 12.391455 35.14007
[2,] 31.59103 57.94499 43.49140  6.048940 21.68886
[3,] 40.36560 50.17720 43.93824  4.614962 27.92420
       [,182]   [,183]   [,184]   [,185]   [,186]
[1,] 11.19847 37.75311 62.16315 25.31214 66.14583
[2,] 24.91824 48.11047 48.44166 29.71801 79.76410
[3,] 19.18610 47.64360 56.00100 33.56386 74.15484
       [,187]    [,188]   [,189]   [,190]   [,191]
[1,] 38.59104  4.861119 34.71303 44.45755 14.63601
[2,] 26.81432  9.151953 46.51066 57.68184 25.20191
[3,] 36.67593  6.204685 44.48320 49.58293 24.46573
        [,192]   [,193]   [,194]   [,195]   [,196]
[1,] 31.363702 12.24447 14.05146 37.70531 59.67875
[2,] 17.903873 23.64079 27.69184 46.93784 46.04929
[3,] 24.315685 15.00909 22.72827 47.50656 54.20303
       [,197]   [,198]   [,199]    [,200]   [,201]
[1,] 33.87966 58.61775 27.68830  6.626549 50.03334
[2,] 33.06748 72.00214 14.55139 17.386262 63.37370
[3,] 39.91026 67.20534 24.03137  9.435412 58.73818
       [,202]   [,203]    [,204]    [,205]   [,206]
[1,] 42.85174 18.63858 31.363702 12.391455 12.93478
[2,] 56.37785 31.93623 17.903873  6.048940 25.62269
[3,] 48.87025 27.79568 24.315685  4.614962 22.65471
       [,207]   [,208]    [,209]   [,210]   [,211]
[1,] 16.72664 53.84188 10.205682 51.64401 22.93071
[2,] 30.12551 40.16037  6.952792 65.33436 13.51734
[3,] 22.94684 48.13919 12.329305 59.40656 23.12970
        [,212]   [,213]   [,214]   [,215]    [,216]
[1,]  6.626549 45.50503 39.80516 10.43120 26.064500
[2,] 17.386262 59.18336 53.31059 20.96019 13.791249
[3,]  9.435412 53.38628 45.78558 20.17329 17.891471
       [,217]    [,218]   [,219]   [,220]   [,221]
[1,] 18.76328  9.356426 20.95983 46.33814 46.81335
[2,] 30.93437 22.715832 33.85329 32.62234 60.53615
[3,] 22.34050 18.775875 25.78314 40.43785 54.29847
       [,222]    [,223]   [,224]   [,225]    [,226]
[1,] 32.58176 25.546411 34.64744 38.55904  8.054848
[2,] 23.33911 12.333971 48.33804 51.78508 16.078471
[3,] 33.09390 18.414704 41.55780 43.75400 16.749428
       [,227]   [,228]   [,229]   [,230]   [,231]
[1,] 56.31489 19.75452 16.54676 18.97530 53.60073
[2,] 42.77823 31.34020 28.44776 32.62860 40.88777
[3,] 48.90084 22.36143 19.78772 26.03506 45.02233
        [,232]   [,233]   [,234]   [,235]   [,236]
[1,]  9.996153 57.55152 41.80524 49.70464 34.58300
[2,] 10.860142 71.22565 32.05643 36.42498 48.18354
[3,] 15.002789 64.12424 41.94031 41.84917 41.00031
       [,237]   [,238]    [,239]   [,240]   [,241]
[1,] 43.67069 32.48324 16.905986 12.55566 27.93393
[2,] 43.10997 45.65015  8.187294 23.81914 40.82077
[3,] 49.99539 37.62373  8.058421 15.09442 37.30109
       [,242]   [,243]    [,244]   [,245]   [,246]
[1,] 23.73464 35.21033 10.410578 51.51119 42.19076
[2,] 37.34514 24.37808 13.710858 64.86173 35.59032
[3,] 32.19555 25.84186  3.785468 56.90540 44.82119
       [,247]   [,248]   [,249]   [,250]   [,251]
[1,] 49.70464 32.98215 38.58851 56.92666 31.44390
[2,] 36.42498 46.65220 41.32337 43.22762 44.29246
[3,] 41.84917 41.04709 46.40958 50.16342 35.90875
       [,252]   [,253]   [,254]   [,255]   [,256]
[1,] 61.99722 29.32784 66.46809 40.01624 45.81092
[2,] 48.64336 28.32399 80.05419 26.34009 41.82967
[3,] 54.13418 35.14166 72.54891 34.55246 50.21709

[gbradburd]

Hello!

So, if you have 256 samples and ~1000 loci, and you're doing k-fold cross-validation with a "training" proportion of 90% (train.prop=0.9), then the testing partition for each cross-validation replicate will contain the remaining 10% of your data, which will be ~100 loci, which will be less than the number of samples that you have. To get around this issue, you could try to increase the number of loci (if possible), you could try to change the training proportion to be something like 60%, or you could try to decrease the number of samples, either by subsampling, or by collapsing multiple samples (e.g., co-located samples) into a single, multi-individual sample.

Hope that helps, -Gideon

[sbreitbart]

Hi Gideon,

Thanks so much. That makes total sense. Looks like it's running!

-Sophie