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topepo / caret

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models
http://topepo.github.io/caret/index.html
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Something is wrong; all the Rsquared metric values are missing #703

Closed hmorzaria closed 7 years ago

hmorzaria commented 7 years ago

Hi, I am trying to fit a regression model using boosted GAM ('gamboost'). Two days ago this model worked fine, and I cannot figure out why it stopped working or how to fix it. I am also running other models (GLM, RF, CART, MARS, boosted RT) which are ok (still). I am using R from Rstudio, in a Linux server running Ubuntu Xenial 16.04. I've already updated, upgraded and rebooted the system, updated the R packages, and started a new R session. Thank you, I appreciate any insights.

data subset 50 x 50, original data dims 752 x 260

this.data2 <- structure(list(catch = c(5051.420298, 5012.893249, 5056.85177, 5012.519487, 5059.613807, 5011.747739, 5031.99755, 5047.573712, 5037.963552, 4983.297436, 5060.54549, 5025.482166, 5016.034664, 5040.230693, 4988.462742, 4988.103556, 5008.883962, 5044.235145, 5038.843708, 5008.29056, 5035.390832, 5008.621496, 5069.862575, 5063.075235, 4996.634006, 5063.364755, 5025.543476, 4980.230133, 5052.849329, 4978.945961, 5020.258577, 5004.297958, 5048.92242, 5000.545951, 4992.841933), pPREY1AMB2_DWF = c(0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.234197912524902, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464, 0.400000005960464), pPREY1AMB2_OSH = c(5.52477204942079e-07, 5.46886072905379e-07, 6.35123282111513e-07, 5.31196702247671e-07, 2.47967735065503e-07, 3.62933363309811e-07, 6.32839505801658e-07, 1.1080366207771e-07, 3.42246741717619e-07, 6.04416416722754e-07, 4.25048293463446e-07, 4.75402655671869e-07, 3.10167281339934e-08, 5.16554337085392e-07, 3.50414866041376e-07, 6.43073715975053e-07, 6.1786137100214e-07, 6.45897101645492e-07, 6.94234608168515e-07, 6.93699451840421e-07, 6.92628180869656e-07, 3.45223172818836e-07, 1.71346056907705e-07, 5.33091805810119e-07, 5.41110408532143e-08, 5.51237324316045e-07, 6.56549483254311e-07, 5.00409170682044e-07, 9.30363285088838e-08, 6.32267709639287e-07, 1.67104949464991e-07, 2.1635285090094e-07, 1.61998892392415e-07, 1.16972312124947e-07, 1.89021198041694e-07), pPREY1BEN2_BCR = c(0.000604956249739986, 0.4, 0.4, 0.4, 0.00129943995411521, 0.4, 0.4, 0.4, 0.4, 0.210073792700422, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.00140034841501606, 0.4, 0.4, 0.0004097463571188, 0.4, 0.4, 0.0120867622204455, 0.00414477633662054, 0.4, 0.4, 0.00405467961465001, 0.4, 0.4, 0.010652485799587, 0.0075890926609712, 0.4, 0.4, 0.4, 0.4), pPREY1DSR2_BIV = c(1.2455643712248e-07, 1.48372699423344e-06, 1.21576365402139e-06, 1.49755781365971e-06, 9.88935127599535e-07, 8.86684100729488e-07, 1.45240480846616e-06, 1.72119266396435e-06, 1.44540599051364e-06, 9.7902530605627e-07, 1.63949255333152e-06, 1.48545887103016e-06, 1.75010869863797e-06, 1.8724499302496e-06, 1.44365409970642e-06, 1.93938870105765e-06, 1.82439717613645e-06, 1.3799995997928e-06, 5.92227148034782e-07, 1.10594219154043e-06, 1.57602121842743e-06, 1.79699009979911e-07, 1.65764207853991e-06, 1.16314360652926e-06, 1.0556694366776e-06, 1.58948391832039e-06, 3.73505009873307e-07, 1.81814243868925e-06, 1.51991533680187e-06, 1.31700601092856e-06, 7.67188156571141e-07, 1.35133916262905e-06, 1.51305155727749e-06, 1.19893026982226e-06, 4.19016019361576e-07), pPREY1DSR2_LRF = c(5.63864949863505e-11, 9.4986868282525e-12, 7.46694062575115e-12, 4.83949970781171e-11, 4.57686480337852e-11, 1.61492525299718e-11, 4.80794606311818e-11, 6.3095013952716e-11, 6.26669394471733e-11, 6.05184107837629e-11, 6.3267359256461e-11, 2.40314983853893e-11, 2.03859159471124e-11, 9.99718787394504e-12, 6.27180109348018e-11, 5.64237980040006e-11, 3.89212147447374e-11, 6.19045124919085e-11, 5.72270463772566e-11, 4.99700003931412e-11, 2.71642288034981e-11, 4.01606813351976e-11, 6.55873999434566e-12, 3.07963154343916e-11, 4.03632298298705e-11, 5.54699540263158e-11, 4.21998368547554e-11, 6.44793377161372e-11, 1.55550221183464e-12, 6.31691527897195e-11, 4.30293419729103e-12, 5.12223043434567e-11, 9.62366217731574e-12, 6.26924990871079e-11, 5.1269263531132e-11), pPREY1DSR2_ODF = c(3.41909983993389e-06, 1.73702678675281e-06, 8.57641273660859e-07, 4.96245066258912e-07, 3.39626584958734e-06, 3.73435475142556e-06, 2.07658873709736e-06, 8.92881856871894e-07, 7.31100566330009e-08, 2.11685874168909e-06, 2.08865233282669e-06, 6.80154154640953e-07, 1.24379130774773e-07, 6.73269536020213e-07, 1.7953903256176e-06, 3.25573956480948e-06, 1.18009177235118e-06, 1.98672697867968e-07, 1.64439167450108e-06, 1.17279561980755e-06, 1.77979145219758e-06, 2.08415137670931e-07, 1.20567567480252e-06, 2.41174973457923e-06, 2.78424894854836e-06, 2.88820409993998e-06, 4.12379832575997e-08, 1.65592106280022e-06, 1.18374210241075e-06, 1.00663179773573e-06, 3.21527645802404e-06, 2.06855461470616e-06, 1.78368876229203e-06, 1.72751617030102e-07, 8.54125189531824e-07), pPREY1DSR2_OSH = c(0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.0090370314731729, 0.4, 0.4, 0.4, 0.00258687182248182, 0.4, 0.00946036615169399, 0.0257852229380622, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.000136471680182319, 0.4, 0.4, 0.0269838110740748, 0.4, 1.57724474899807e-05, 0.4, 0.4, 0.126074027657748, 0.4), pPREY1DSR2_SCI = c(1.30932971714527e-07, 1.83253131213745e-07, 1.82136146350968e-07, 8.12315226468109e-08, 1.60512346731881e-07, 1.84026573833412e-07, 1.46525937788075e-07, 1.68859703749098e-07, 1.09931408954585e-07, 1.88106685566063e-07, 1.03672698532224e-07, 1.35652339215334e-07, 1.63907636162454e-08, 6.03701929403688e-08, 1.91993465973107e-07, 1.85336490290084e-07, 1.59809921625354e-07, 1.60372220407148e-07, 1.26965371973606e-07, 1.19266975310874e-07, 1.63141016649885e-07, 2.27915559157952e-08, 1.47626337224147e-07, 1.70527670848933e-07, 1.33225582781147e-07, 1.87158166088036e-07, 1.49644012662525e-07, 1.20227533691307e-07, 1.60931653276262e-07, 1.82248488033212e-07, 1.02819934384222e-07, 1.05995455637305e-07, 1.00885208193216e-07, 5.38394625693983e-08, 1.77522743886761e-07), pPREY1DSR2_SDF = c(2.0601723307363e-10, 3.06242962928374e-10, 2.91943251425302e-10, 3.28178105088757e-10, 6.78906668520335e-10, 2.24163259605715e-10, 7.63138252056021e-10, 7.459124881508e-10, 5.02749212080717e-10, 7.56690277566007e-10, 3.70152508949362e-10, 9.89404925177457e-11, 7.65520770826024e-10, 4.39567853668953e-10, 6.41911110112155e-10, 3.40838621444056e-10, 2.33091202148093e-10, 3.3502274603643e-10, 4.31182511093074e-10, 5.00500296278822e-10, 4.85273898573594e-10, 7.21835619313974e-10, 5.83114772475234e-10, 6.76854258905093e-10, 2.96056334591955e-10, 2.57154513503276e-10, 4.54380786809388e-10, 6.12278507362957e-10, 7.48433152340029e-10, 7.29468188632176e-10, 3.82087088146509e-10, 7.80172618894339e-10, 6.49145689945734e-10, 7.59124507142485e-10, 7.6512501540125e-10), pPREY1DSR2_SRF = c(0.4, 0.000685587211404722, 0.213183771612927, 0.4, 0.00167752933256842, 0.0132457435295103, 0.000355520437393752, 9.66058202485131e-05, 0.042531694862443, 0.4, 0.000586621165457148, 0.000311579979341785, 0.00672653112753811, 0.0967854102438936, 0.00022341120891163, 0.00861842397742279, 0.4, 0.161538749951527, 0.00226362972953092, 0.0302112271119185, 0.0031468854365665, 1.6998240832656e-06, 0.000677477829138668, 0.0549613018599715, 0.0015338896285434, 0.4, 0.4, 0.0382212021500373, 0.00481068582409204, 0.000112232465097271, 0.000430875112635582, 0.158127935961751, 0.0087116771812877, 0.000319997223232189, 0.4), pPREY1DSR2_SSR = c(2.79559587857763e-08, 3.47414911194572e-08, 2.3784113096555e-08, 3.35952889391744e-08, 1.47185577934333e-08, 3.25208243907307e-08, 5.10818149107294e-08, 4.529950924945e-08, 4.40501945439441e-08, 2.74016800346699e-08, 4.5901272725921e-08, 4.12323413991092e-08, 4.84160131099506e-08, 2.143886724025e-08, 3.81990026069941e-08, 4.17703866418719e-08, 5.16482690698443e-08, 3.68781487987087e-08, 5.14076298449848e-08, 4.30520670674749e-08, 5.22233457014621e-08, 5.18069460232542e-08, 2.81999747505469e-08, 3.29004640127171e-08, 4.81008624835898e-08, 4.43125048937744e-08, 1.216486515658e-08, 2.71529844016757e-08, 1.07145562782768e-08, 4.08538158020687e-08, 3.60494337560788e-08, 5.35113331048525e-08, 4.23385030064873e-08, 5.09994645798893e-08, 4.69274170592999e-08 ), pPREY1FLT2_BIV = c(6.29900169523188e-08, 5.64368279814135e-07, 8.58553100238135e-07, 1.69553051979143e-06, 1.74331851918025e-06, 6.55071537278161e-07, 7.4119742527672e-07, 7.0032618485304e-08, 1.91109492899191e-07, 4.76871736114516e-07, 1.20055187217435e-06, 4.11133265947119e-07, 1.21354804435986e-07, 6.68694531542825e-07, 8.94788109838682e-07, 7.94634920713503e-07, 1.23871020716363e-06, 3.92482135704408e-07, 4.93892098911487e-07, 3.64614168542017e-07, 4.03665840060072e-07, 1.48981995061446e-06, 1.72279965691511e-06, 2.0367064906436e-06, 1.31352236563974e-06, 1.94935522925859e-06, 8.06571089102183e-07, 1.80061816754167e-06, 8.00600215811104e-07, 1.80752416516209e-06, 9.51559141481371e-07, 1.54291642844696e-06, 1.18366118008956e-06, 3.60908270001651e-07, 1.70006829901648e-06 ), pPREY1FLT2_OSH = c(0.224000006914139, 0.224000006914139, 0.000887959335751669, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.0135572905869058, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.165866166296597, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139, 0.224000006914139 ), pPREY1FLT2_PIN = c(5.28938915435419e-09, 5.31209054301519e-09, 2.26227969634628e-09, 2.34307312052112e-09, 3.49901687067253e-09, 2.72867432780377e-09, 1.74269439782407e-09, 2.42918948587754e-09, 4.50933895456482e-09, 5.32896240614415e-09, 1.17141639568735e-09, 3.39939932795815e-09, 4.79959609460756e-09, 3.77871878096956e-09, 2.58013982244103e-10, 4.54774813740519e-09, 5.32615955466613e-09, 3.41529236040036e-09, 1.19597662079147e-09, 4.22603676071367e-09, 5.43548114377523e-09, 2.86269758423667e-09, 4.25973336156222e-09, 5.39786313764939e-09, 2.05469827555352e-09, 4.55156168032373e-09, 1.80206910351069e-09, 9.88353017973267e-10, 5.35402486983555e-09, 4.99127305829015e-09, 2.92236231269706e-09, 2.94011109174951e-09, 4.91896964171803e-09, 4.72532248077056e-09, 4.77858144158147e-09 ), pPREY1FLT2_SRF = c(7.85222299409191e-11, 1.40189893059222e-10, 7.89268804912187e-11, 8.44440663439727e-11, 1.34271598733268e-10, 1.41936680941028e-10, 9.57295566183504e-11, 3.5555046916636e-11, 1.12942562742372e-10, 7.62708547308375e-11, 1.49147958809033e-10, 1.23391920270959e-10, 1.48522501935547e-10, 1.18547857552475e-10, 1.30848475192262e-10, 1.25932328027551e-10, 1.39531380983649e-10, 1.41024646331076e-10, 6.31879900281462e-11, 1.50897573015144e-10, 4.26386051451884e-11, 4.99110363778039e-11, 1.44663508159163e-10, 1.17217998518545e-10, 5.87468296709446e-11, 1.1881101534429e-10, 7.41857476205913e-11, 3.38712225141256e-12, 9.50382496302211e-11, 3.9137587560562e-11, 1.19983760603168e-10, 4.23721479297086e-11, 1.06149774805657e-10, 1.52433996871514e-10, 1.43450554608658e-10 ), pPREY1GAG2_BCR = c(8.06143444385521e-11, 1.2106036576933e-10, 1.21961166473202e-10, 1.20234635450889e-10, 1.26374899184995e-10, 1.16883485547894e-10, 1.38926689189424e-10, 1.3193879687424e-10, 1.3596357597025e-10, 1.12011796858124e-10, 7.43113372238125e-11, 2.95324645571885e-11, 9.01927060007391e-11, 2.04099687194489e-11, 1.13614891998044e-10, 8.23527833393081e-12, 1.11027409488132e-10, 1.20141998520257e-10, 1.42946090884835e-11, 1.0631997216463e-10, 1.35208827473377e-10, 1.42124638196553e-10, 1.39374793964775e-10, 2.26751612787175e-11, 1.03010046192951e-10, 1.14139019408653e-10, 9.13879958749076e-11, 1.01095235404306e-10, 6.19645890576696e-11, 8.07832487392111e-11, 1.40731318964196e-10, 5.82081183728718e-11, 1.09120673973292e-10, 4.16932789715726e-12, 1.14864346545535e-10 ), pPREY1GAG2_BIV = c(1.55343823826287e-10, 5.60199016778276e-12, 1.30623945443941e-10, 6.09501761119913e-11, 1.68551850076274e-10, 1.59116693850776e-10, 1.26307418651539e-10, 1.59269894678029e-10, 1.39656497548219e-10, 5.72173571761825e-11, 1.26446316898427e-10, 1.42323800470731e-10, 4.59888854485481e-11, 1.57869920234546e-10, 1.08092904497909e-10, 1.49917285941074e-10, 1.66359756365989e-10, 1.47008961150774e-10, 8.83433178087248e-11, 1.46608519090911e-10, 1.60990524837945e-10, 1.075705944505e-10, 1.08266347866178e-10, 1.11999972681106e-10, 1.06693440178308e-10, 1.30230318364843e-10, 1.56339340399815e-10, 1.48870082072968e-10, 1.40671003786781e-10, 1.65787922232722e-10, 1.68727851880485e-10, 1.52037488250295e-10, 1.24048808780155e-10, 1.17782987752343e-10, 8.91845203762597e-11 ), pPREY1GAG2_FLT = c(2.15712225500073e-11, 2.51283567899448e-11, 2.26829045308078e-11, 2.43985630904886e-11, 1.53554208730842e-11, 2.39667025133868e-11, 2.09034991668017e-11, 1.50296967896749e-12, 2.14026213832414e-11, 1.27649113550165e-11, 1.34286523468345e-11, 2.67565557254691e-11, 1.85327362159628e-12, 2.58839629523634e-11, 2.43044829808793e-11, 1.48590829918305e-11, 2.0428505102942e-11, 9.48319341784003e-12, 2.56761449955974e-11, 7.09666037515637e-12, 1.89113674079959e-11, 2.27204796354868e-11, 2.36663503503471e-11, 2.72987679920866e-11, 3.32633414321821e-12, 2.5461969053214e-11, 2.71028287751655e-11, 2.68560635921076e-11, 9.10260448616104e-13, 6.80594673556023e-12, 2.72273943394169e-11, 9.87303664013021e-12, 2.35123123595368e-11, 2.62692173457403e-11, 2.71133171075519e-11 ), pPREY1GAG2_JCK = c(2.85425037463607e-10, 7.60869075337939e-10, 8.59094125888095e-10, 6.87568132872287e-10, 2.93073209941962e-10, 1.32982352449203e-09, 3.45501315401369e-10, 1.82258990401082e-10, 1.36740481714537e-09, 2.14755154473239e-10, 9.2192916493857e-11, 1.053115193856e-09, 2.46576360418199e-10, 1.16747678973694e-09, 6.36345261966355e-10, 7.53946933178691e-10, 1.29960541164622e-09, 4.82074300972218e-11, 1.09430775845888e-09, 7.72866898828329e-10, 1.3391978816664e-09, 1.00414432649516e-09, 1.28124831511307e-09, 5.90761783060955e-10, 1.09544803405773e-09, 1.28206189980567e-09, 1.19129246770942e-09, 1.25788046991713e-09, 1.11563559299069e-09, 7.9309590393998e-10, 6.74519520593509e-10, 4.85108025500895e-10, 1.40220225530924e-09, 8.24269345432897e-10, 1.36071043677987e-09 ), pPREY1GAG2_LRF = c(6.64570689797335e-09, 6.71296243129982e-09, 1.08409552552268e-09, 4.93629552371221e-09, 6.12721172933824e-09, 2.23166131906101e-10, 4.22615206248936e-09, 5.24690946126876e-09, 5.57258639744265e-09, 7.1286028634442e-09, 9.19340309142895e-10, 4.16127147595716e-09, 3.0508482584358e-09, 6.92307283560857e-09, 2.90832819154961e-09, 5.39980237411057e-09, 7.01803724684709e-09, 2.46642894424001e-09, 2.51955595759381e-09, 3.54337207876928e-09, 1.00959339297955e-10, 3.65925434466831e-10, 5.80309201131924e-09, 6.27467608319316e-09, 5.94820710475387e-09, 7.13297010186757e-09, 2.56270142565156e-10, 4.38239077593373e-09, 3.94087669758327e-09, 3.21554509542911e-09, 3.33140176442487e-10, 6.58243431107794e-09, 4.29758206620309e-09, 2.55480300968223e-09, 8.97850005634141e-11 ), pPREY1GAG2_LUT = c(7.89809699544491e-11, 4.07517746533231e-11, 4.70070066670314e-11, 5.61042753748101e-11, 1.73394611372153e-11, 3.04898108220786e-11, 6.04539662793474e-11, 1.5259907546011e-11, 3.53262698598161e-11, 7.44647597638545e-11, 1.15680524544198e-11, 5.35397756712242e-11, 1.2194727440552e-11, 8.11406709798819e-11, 6.53504502243208e-11, 3.57788960050942e-11, 6.5698821053275e-11, 5.40968348456625e-11, 4.98692479050202e-11, 7.40869856271978e-11, 2.18964851261632e-11, 9.82074681902909e-12, 5.6028827143711e-11, 4.10617189209377e-11, 8.69028808328194e-12, 7.44230928304389e-11, 1.34343382877875e-11, 5.11540556059604e-11, 3.87485991402109e-11, 1.35880118245846e-11, 7.97634299553179e-11, 1.01410722921684e-11, 5.44903685242055e-11, 2.11866489977297e-12, 6.39179008530799e-11 ), pPREY1GAG2_MEN = c(1.9938107089364e-14, 1.47258869122967e-14, 7.0613550722655e-15, 1.89575285935191e-14, 1.55723190023457e-14, 9.3036703203692e-15, 1.13225210245845e-14, 1.58090983589863e-14, 2.09492655117778e-14, 1.93519124620692e-14, 1.1945383282281e-14, 5.99046980852642e-15, 7.40490650715212e-15, 1.67483245017441e-14, 1.94299805746875e-14, 1.78378807614108e-14, 1.21716988730685e-14, 8.3649166939919e-15, 2.10622507343368e-14, 2.01461876317007e-14, 1.47058116488654e-14, 1.81284715980455e-14, 2.09899643687174e-14, 2.13762883695188e-14, 1.96686564515048e-14, 2.06357142390084e-14, 1.53295914862333e-14, 2.1361532848697e-14, 4.29745472459131e-16, 1.32924314693804e-14, 1.9215630833546e-14, 1.367367546836e-14, 7.8749952100114e-15, 2.12566520185451e-14, 1.59519155621113e-14 ), pPREY1GAG2_ODF = c(0.4, 0.0238516684520233, 4.80132205701459e-06, 0.00153743392795605, 0.4, 0.4, 0.4, 1.09841836601582e-05, 0.4, 0.4, 0.4, 0.0326183467714981, 0.4, 0.4, 0.4, 7.33940645555503e-05, 0.4, 0.4, 0.000959372335962498, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.182415301086782, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4 ), pPREY1GAG2_OSH = c(0.4, 6.2668984696218e-05, 0.4, 0.4, 0.00238268362653454, 0.000194760946810003, 0.4, 0.4, 0.4, 0.4, 0.4, 0.327623428727714, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.0918465053246324, 0.4 ), pPREY1GAG2_PIN = c(0.0899160783909561, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.087181920394312, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.00151765985049148, 0.4, 0.4), pPREY1GAG2_SCI = c(3.63318900584437e-07, 2.51644344457358e-07, 3.45282006697783e-07, 2.6708327845709e-07, 3.14708293883566e-07, 3.80482119589335e-07, 1.19881187442304e-08, 2.66683619366912e-07, 1.43693476331287e-07, 2.15167633848321e-07, 8.09565840710338e-08, 4.19576377792973e-07, 2.39082915271354e-07, 1.81094243500256e-07, 6.4373652481274e-08, 2.87384752229241e-07, 3.65511193908308e-07, 1.61723934697272e-07, 3.59715870579722e-08, 2.54062414432584e-09, 1.63692024801987e-07, 3.86701786254633e-07, 4.05512167735474e-07, 8.99249075805541e-08, 2.98306723946749e-07, 3.37273515598613e-07, 1.97949784314955e-07, 2.16946522906172e-07, 1.23499976961637e-07, 3.83458310320458e-07, 1.73428456035954e-07, 3.72313344014924e-07, 3.16490623895199e-07, 2.52882208634793e-07, 3.02744657354113e-07), pPREY1GAG2_SDF = c(0.000204415007089479, 0.038009486837266, 0.0419296637410263, 2.41061994842534e-05, 0.00486552386792801, 0.00557513338626991, 0.00101086548405306, 0.0253500174944888, 4.06271364780216e-05, 1.78364413719033e-05, 0.4, 0.000398676579295216, 0.4, 0.055597274823847, 0.000674897885428781, 0.00017762269308389, 0.0164907101095029, 0.001356946855075, 0.000241439251456917, 0.00113480921212736, 0.00524070656553692, 0.00429838201227256, 0.00120980759761729, 0.4, 0.4, 0.4, 0.4, 0.00224829362729238, 0.0184195164873167, 0.000516867622476772, 0.4, 0.00778188442539108, 0.00403983168439746, 0.349665854636646, 0.171761838951232), pPREY1GAG2_SPL = c(4.18864477395465e-06, 1.12635422561845e-05, 4.76932344519246e-07, 0.000237790009966547, 0.00170114886613919, 0.00799602622129786, 0.00787793957495742, 3.00431487858414e-06, 0.00167601309534071, 0.074477829158719, 1.97175847875115e-05, 0.4, 3.34293365225943e-05, 0.00720514902562459, 9.34010521459565e-07, 0.000109109549282064, 0.0309627121022681, 0.4, 0.4, 0.0259004932231896, 2.91010139197912e-05, 2.65286379842952e-06, 0.000335256038786105, 0.0142845479794619, 7.15603166579436e-05, 0.0244041819337886, 0.4, 2.86548920671891e-05, 7.04770219955127e-06, 0.0144986531551808, 0.000234262362635921, 7.37549673349771e-05, 0.00639660046043385, 0.00374379468117137, 0.271712165331272), pPREY1GAG2_SRF = c(0.4, 0.4, 0.00167186478851698, 0.00395087227808044, 0.4, 0.4, 0.4, 3.75734169694904e-06, 0.4, 0.4, 0.4, 0.0587151374167294, 0.4, 0.4, 0.4, 2.99937356175095e-05, 0.000275364321286205, 0.0245740283374646, 0.0204768219217107, 0.4, 0.0391597909177223, 0.4, 0.4, 0.4, 0.4, 0.00284987727834077, 0.064971272428085, 0.4, 0.4, 1.81989529703315e-05, 0.4, 0.4, 0.4, 0.00742462860007792, 0.4), pPREY1GAG2_SSR = c(5.5526586526424e-09, 4.18072423480687e-09, 2.45179410779806e-09, 4.16667647704223e-09, 5.61079355965253e-09, 1.07044907299223e-09, 5.64464775317736e-09, 4.79587921501978e-09, 4.40372706018748e-09, 2.8419286274345e-09, 5.30832550248972e-09, 4.53197611763848e-09, 3.72343241794421e-09, 1.59678600373014e-09, 3.60531754571092e-09, 4.17136773187111e-09, 4.90559375772161e-09, 4.09042349772175e-09, 5.39343170639435e-09, 4.84467977696993e-09, 2.33209944379243e-09, 4.77100065432464e-09, 5.32883493089332e-09, 4.24070457192871e-09, 4.46670207123113e-09, 4.20858684091094e-09, 5.23410327189348e-09, 4.7348960676813e-09, 4.23614176023662e-09, 5.5695771569098e-09, 2.26689054907178e-09, 2.4201997261887e-09, 4.06124144306859e-09, 4.50365640647997e-09, 5.24224087036345e-09 ), pPREY1JCK2_BCR = c(8.0488902357035e-12, 6.31909717640124e-12, 6.63743048054703e-12, 9.04993439426732e-12, 1.04917943768907e-13, 7.63695764710525e-12, 6.71149281438542e-12, 7.49368197467943e-12, 8.36518901541261e-12, 9.10040743973387e-12, 5.52728153433618e-12, 7.84678031107268e-12, 8.82161886287667e-12, 8.78861489833271e-12, 7.87649397645709e-12, 8.70384544587298e-12, 4.13116324918232e-12, 6.23817353567157e-12, 4.05193890880217e-12, 7.60492602753205e-12, 5.89034909376641e-12, 2.22552952712971e-12, 8.77192123055254e-12, 8.89507031134139e-13, 8.40466733270321e-12, 8.55663580316807e-12, 4.96787242020489e-12, 5.34704437645386e-13, 6.14659773449099e-12, 6.99523125200121e-12, 7.91177470785964e-12, 9.34262857027717e-12, 9.25698294563448e-12, 8.80518044802018e-12, 2.35888571397595e-12 ), pPREY1JCK2_BIV = c(0.000940593797909262, 6.70885801489964e-05, 0.000163652377237978, 4.87494870199563e-07, 6.75372635399578e-05, 4.09132354441179e-06, 0.00175431251150512, 1.07456274420954e-05, 0.000797063593500524, 0.000286699578583313, 0.00144053189341366, 0.000729041212055182, 9.90932380514934e-05, 3.30328297948138e-05, 1.81112311332296e-05, 3.28023239424438e-05, 0.000503574978085011, 4.23845490494021e-05, 4.63424407668453e-06, 0.000361125399005108, 6.79888020877252e-05, 2.19721030491388e-05, 1.74590828465472e-06, 2.63358877772141e-05, 0.00134321368416159, 3.03041887194034e-06, 9.09788222106469e-05, 3.90272510653769e-05, 3.15436923813366e-06, 0.00049087278928355, 0.000211907228930377, 0.000828116835140445, 6.40262385891007e-05, 0.000290403643287681, 0.000605968368161681 ), pPREY1JCK2_JCK = c(8.27349058670153e-12, 5.55335891496599e-12, 8.81820348147032e-12, 1.53787545128129e-11, 4.82904955588077e-12, 8.05608381732136e-13, 7.84538052787272e-12, 1.48780842829274e-11, 3.5805830819992e-12, 1.58746862595077e-11, 2.28290579089157e-12, 6.19207315982387e-12, 1.32261023514236e-11, 1.52946317763267e-11, 1.56248560707633e-11, 6.14406093711899e-12, 7.02527724910154e-13, 1.42342855564162e-11, 1.59017686224936e-11, 7.2690748666285e-12, 1.50644701519174e-11, 2.62509464032703e-12, 1.11875674004698e-11, 1.33610193573123e-11, 1.45884482269617e-11, 8.70392222997281e-12, 1.47662621071018e-11, 1.51542446773567e-11, 1.32783908457847e-11, 1.07761618239975e-12, 2.71717625991269e-12, 1.39053373726845e-11, 1.3130713765825e-11, 7.94887645271064e-12, 1.57066392184444e-11 ), pPREY1JCK2_LPL = c(3.48103114403724e-10, 7.85766880275003e-10, 3.744140279032e-10, 7.66301482063544e-10, 7.91034684677872e-10, 2.63315173684866e-10, 1.56685257544773e-10, 8.6825015145503e-10, 9.28834114693223e-10, 8.90241152418995e-10, 8.43000975229692e-10, 5.17346001762448e-10, 8.23454677495044e-10, 1.3703686468065e-10, 4.70779622166146e-10, 6.90523307685464e-10, 3.22298766920461e-10, 5.99473833681668e-10, 8.00746050517403e-10, 3.83874039171152e-10, 8.96845097547679e-10, 5.32445591340869e-10, 9.10512119465368e-10, 6.98137328424409e-10, 4.98470724509735e-10, 8.15548622467719e-10, 9.26888594359075e-10, 8.13940596412837e-10, 9.02128032443697e-10, 6.53603148574194e-10, 9.27539530641605e-10, 8.23973896300441e-10, 7.86945185286848e-10, 6.72460572977734e-10, 8.97608305716848e-10 ), pPREY1JCK2_ODF = c(2.66692439812465e-11, 5.4974081153872e-11, 6.0885207328224e-11, 5.70000103460421e-11, 6.14076780194913e-11, 5.04191911431212e-12, 2.73191052980449e-11, 5.59301551458601e-11, 5.27167809462141e-11, 3.15141746324971e-11, 1.91468968830005e-11, 4.19630687140154e-11, 5.34805282659324e-11, 3.00726642731754e-11, 1.63981530578078e-11, 3.41826254333242e-11, 4.37970028695828e-11, 2.64514022339033e-11, 5.4092692835191e-11, 5.30045295043801e-11, 5.99037569625108e-11, 4.16130390002848e-11, 6.60679189267249e-12, 5.56135528555542e-11, 6.02333636730448e-11, 1.61513841672726e-11, 2.10351072519345e-11, 1.90672957568866e-11, 2.51314071422902e-11, 1.36451459505859e-11, 5.27648515075074e-11, 2.72471689553349e-11, 4.31157166004957e-11, 3.86795555895585e-11, 2.65240842335984e-11 ), pPREY1JCK2_OSH = c(1.40727046161344e-06, 0.000134940167157054, 0.012237241317824, 3.03387561726096e-07, 0.4, 0.0134520770658714, 0.348984345364128, 0.0260932437365017, 1.75435764622468e-05, 4.09745515237122e-06, 0.000267037076859919, 0.0137091491215156, 5.12040169069667e-05, 0.4, 1.23915272798765e-05, 1.61250212757295e-06, 0.4, 3.01068588410887e-06, 0.4, 0.00706752821624588, 1.14661012702793e-05, 0.000354818584662592, 4.4284305472639e-07, 0.4, 0.020401121214306, 0.369376179299954, 0.00493243208680394, 0.0175341700115511, 0.000154101717018783, 8.89961871818163e-06, 0.0388302451063703, 8.91817064375348e-07, 5.54107199666319e-06, 0.4, 0.000148365530267047 ), pPREY1JCK2_SCI = c(4.63525307408293e-10, 4.83291263096527e-10, 3.14921413563945e-10, 4.39414272292641e-10, 1.26965881003265e-10, 4.71544682029064e-10, 1.95693137812259e-10, 2.26263527605643e-11, 1.01220861230774e-10, 2.5370775731837e-10, 4.64011087411937e-10, 4.13934521946889e-10, 4.91843168536494e-10, 4.38258740303421e-10, 4.20185968629638e-10, 4.98499209461e-10, 2.34927989828701e-10, 3.77968572669118e-10, 4.24654092606959e-10, 8.35910457474738e-11, 2.78016247421229e-10, 9.01582438207175e-11, 4.65457719553414e-10, 4.6473640503986e-10, 4.5831492620057e-10, 1.41429695826193e-10, 1.55446941008909e-10, 3.61314724647612e-10, 4.88345664796356e-10, 1.09743810233632e-12, 2.6303427284843e-10, 4.25909646618744e-10, 4.77128533640527e-10, 4.14269036830565e-10, 4.27466116153794e-10 ), pPREY1JCK2_SDF = c(1.8058666817423e-10, 8.38291729320716e-11, 1.70474388692681e-10, 1.97542174412784e-10, 4.07210601097549e-11, 7.15338440177887e-11, 1.04430967486782e-10, 1.27332002334403e-10, 1.17260676316286e-10, 1.84886743225681e-10, 1.44750740497603e-11, 1.10718468020388e-10, 5.62435964160054e-11, 1.90959831404574e-10, 2.47777370756918e-10, 1.70979817926241e-10, 4.74785991959824e-11, 2.82163611607713e-11, 7.48314799247721e-13, 3.52175110661411e-11, 8.23383797579495e-12, 1.37411079286738e-10, 2.48285773527406e-10, 2.3964558545528e-10, 2.22382149751892e-10, 2.44473229378514e-10, 1.95263298570115e-10, 6.17560439029899e-11, 2.07421862532244e-10, 1.59107369272544e-10, 6.351049365855e-11, 5.23911041343486e-12, 1.24309790952066e-10, 1.30606851874535e-10, 1.36906941262401e-10 ), pPREY1JCK2_SHP = c(7.42078874860071e-11, 1.68166668205724e-10, 1.64970667237302e-11, 1.34553464229258e-10, 1.67448279671485e-10, 1.46865660873204e-10, 8.26087887536135e-11, 1.73410233342246e-10, 1.2382989609172e-11, 1.01322596549246e-10, 1.31769268029758e-10, 1.47184178030861e-10, 1.18529663828799e-10, 1.36365954413249e-10, 1.11939850434895e-10, 1.90574763681255e-10, 8.20441737905276e-11, 1.39020867888331e-10, 1.2495543420035e-10, 1.21686226544858e-10, 1.81317245847897e-10, 9.88372434016413e-11, 1.54330927150722e-10, 1.74276243718773e-10, 7.89001082420466e-11, 1.06626801113238e-10, 1.87398188634839e-10, 1.83072083466673e-10, 1.57462944780225e-10, 8.09084803950022e-11, 1.76073342810952e-10, 1.38144298836708e-10, 1.78414049930659e-10, 1.25357134558127e-10, 6.08666062263607e-11 ), pPREY1KMK2_LPL = c(0.00160976553768009, 0.000664320485357922, 0.0489171772102231, 0.00174788614802462, 0.104968786811571, 0.0230546089221605, 0.00319682027941764, 0.00159770944227096, 0.000103765846773346, 0.00180070514508385, 0.082874309762292, 0.0213941426007022, 0.124264707704302, 0.000582638696879191, 0.0360723553880991, 0.00218102329346568, 0.00376384773296584, 0.00107912925128241, 0.000241990102904142, 0.00448851254525927, 0.00581205897822878, 5.895444979136e-05, 0.000437866568776233, 0.0119023077999817, 0.00104550150608586, 0.0935863148030133, 0.000136670985696882, 0.070948274259399, 0.138433758374898, 0.00224567689444981, 0.10857237382772, 0.0358288333999878, 5.24595838558227e-05, 0.000735878753806347, 0.000168522036537341 ), pPREY1LGS2_BIV = c(7.81860167079312e-11, 3.90998853685087e-11, 1.00970544086104e-10, 8.38410632805016e-11, 1.01186517884458e-10, 7.76680282381322e-11, 9.01675831776306e-11, 8.02981771753642e-11, 8.51281642872638e-12, 1.82162925529063e-11, 1.58165926397747e-11, 3.59594239248739e-11, 4.58883779956573e-11, 1.04581255725943e-10, 9.42794803802114e-11, 7.41931866505255e-11, 9.45958273616006e-11, 2.49799703622991e-11, 1.93986591579914e-11, 3.89592209882751e-11, 3.07600160002838e-11, 7.90397418602542e-11, 1.01078681822689e-10, 4.56258436383043e-11, 8.65078338024823e-11, 5.48673429624319e-11, 7.47401756471057e-11, 7.6795008371027e-11, 1.04923287430331e-10, 6.37339561032537e-11, 2.44980943083277e-11, 6.17989063659079e-11, 1.00480168361898e-10, 9.44695536336038e-11, 8.36847027590776e-11 ), pPREY1LGS2_DWF = c(0.207942648869805, 0.4, 0.4, 0.4, 0.4, 0.4, 0.182438623751744, 0.4, 0.4, 0.382207424683888, 0.00885022078317559, 4.52386054213851e-05, 0.0518601227921124, 0.0280449227008068, 0.4, 0.4, 0.4, 0.00533412387743598, 0.4, 0.000138697662082202, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.226875035531577, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4), pPREY1LGS2_FLT = c(7.16938908202273e-08, 4.94535738477436e-08, 6.26459911384966e-08, 6.78049025614205e-08, 6.72937034517387e-08, 3.80507422899978e-08, 6.1747276967068e-08, 6.84383050556653e-08, 1.90226882692915e-08, 1.3083431261109e-08, 3.23201069705203e-08, 2.30685861394972e-08, 3.18272083545039e-08, 3.70251315518719e-08, 6.61940399875443e-08, 3.60831393847325e-08, 5.17071099208243e-08, 2.61389644660345e-08, 1.08368951496389e-08, 6.28517697919757e-08, 6.31933959722563e-08, 8.07626905786983e-08, 8.26153646438884e-08, 7.09108940684694e-08, 4.83034624376398e-08, 2.84108391009686e-08, 5.04269328864843e-08, 4.6379486412963e-08, 5.5429664585547e-08, 3.37844297102284e-08, 2.78987859187795e-08, 3.58881083445782e-09, 2.93262512864299e-08, 7.40416349034854e-08, 5.03462550358963e-08), pPREY1LGS2_LGS = c(1.62538642474476e-10, 1.52663217911888e-10, 1.56816897418678e-10, 1.01256306616235e-11, 1.02684260583421e-10, 6.0573005462705e-11, 3.18144517112323e-11, 4.73397378698829e-11, 1.47434164487536e-10, 1.75372916692286e-10, 1.82868690006743e-10, 1.45386397397776e-10, 1.50649445652751e-10, 1.79985685250596e-10, 1.14716820594001e-10, 1.35476216369796e-10, 1.71534970485317e-11, 2.83123283495932e-11, 1.4384184025989e-10, 1.39686132986829e-10, 1.89432640212026e-10, 1.40166804825925e-11, 9.14392490105726e-11, 8.06682162082751e-11, 1.50481041517689e-10, 5.20202315416646e-11, 2.76084931214776e-11, 4.03327011091058e-11, 1.73974451079617e-10, 4.93521647690645e-11, 1.89285184992243e-10, 3.75886520269181e-11, 7.96360777715499e-11, 6.59615681445259e-11, 1.23064303056748e-10), pPREY1LGS2_LPL = c(2.55986302855339e-05, 3.61456250341667e-05, 2.33253853265347e-05, 2.1096132341294e-05, 1.70329467421842e-05, 1.02649712016144e-05, 1.13408925232378e-05, 1.84173372875433e-05, 2.89009094875427e-05, 5.01129675000164e-06, 2.01311169303292e-07, 7.60471420063767e-06, 4.7548954500893e-06, 1.64228293788424e-06, 1.00515615848042e-07, 3.52471991695655e-05, 1.9257531390673e-05, 1.99935683661409e-05, 6.76226121295951e-06, 1.28143991071684e-05, 1.37065335246804e-05, 7.66551932774177e-06, 2.20584226724805e-05, 6.1704717006924e-06, 3.04556184857314e-05, 7.15136093761961e-06, 3.31940861316591e-05, 8.55676182951727e-06, 3.22372867020045e-05, 2.13751435555848e-05, 2.0188883818464e-05, 1.06858744608633e-05, 1.93345518763016e-05, 1.52892415496035e-05, 2.6549516000955e-05), pPREY1LGS2_LRF = c(0.0160730088994624, 0.4, 6.86466731182261e-05, 0.4, 0.4, 0.4, 0.4, 7.99197940311093e-06, 0.0117662439705328, 0.0179260345516619, 0.260743214100039, 0.197059334771322, 0.4, 0.000135927705220534, 0.4, 0.000588340269905359, 0.4, 0.0141881723259338, 0.00167942205349509, 1.12684518582743e-06, 0.00975670352338555, 0.000393931142402795, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.00026472697187851, 0.0184935995280552, 0.000304532177664997, 0.0129207400918542, 0.4, 0.4), pPREY1LGS2_MPL = c(1.84452566634874e-09, 2.37859296670197e-09, 4.12452431956226e-09, 3.0406363208552e-09, 4.320911464096e-09, 3.52530106537332e-09, 1.18920226189793e-09, 5.1092079452624e-10, 4.28008777976186e-09, 3.97859658619179e-09, 1.51790206555947e-09, 5.36388745606142e-10, 2.26825891428131e-09, 3.10703187755067e-09, 4.24289361505931e-09, 2.58236728892671e-09, 2.45990582128734e-09, 1.30379770713734e-10, 2.75380545409888e-09, 4.32589171929159e-09, 2.24136938772388e-09, 2.94751630829702e-09, 4.24829340043751e-09, 3.66476936920942e-09, 1.70092502785591e-09, 1.11561136685604e-09, 3.43968891728471e-09, 3.39030050682815e-09, 2.97218080888853e-09, 4.34067237634231e-09, 4.13456677557033e-09, 6.53440254287895e-10, 2.18135493164259e-09, 3.05644180216012e-09, 2.87190668835566e-09), pPREY1LGS2_MUL = c(1.88648177147498e-07, 2.06430740871738e-07, 1.90736994216448e-07, 2.12755606085358e-07, 2.09764615872007e-07, 1.102939890916e-07, 1.15734659696234e-07, 9.17898006520761e-08, 2.02862509307343e-07, 8.70479226940511e-08, 1.50852250357048e-07, 1.53729426937936e-07, 1.45547785876021e-07, 1.65997140654689e-07, 6.85177587153826e-08, 2.08110022641096e-07, 1.31010901966457e-07, 1.44547445120165e-07, 1.18056061996763e-07, 2.03931229912009e-07, 8.13914147186336e-08, 1.9624152902394e-07, 1.92792758343699e-07, 1.74893451984539e-07, 1.21261911762749e-07, 1.8743952313254e-07, 1.72212044535252e-07, 2.17444868348825e-07, 1.63510551823421e-07, 1.21834659400577e-08, 2.13734566198878e-07, 1.79308949243803e-07, 2.10520048030306e-07, 9.56677549882651e-08, 2.59256245985263e-08), pPREY1LGS2_ODF = c(0.4, 0.4, 0.4, 0.00262101653995653, 0.4, 0.4, 0.4, 0.4, 0.4, 0.00189615652295479, 0.4, 0.4, 0.0271470019064709, 0.4, 0.00226978199699353, 0.000403511735872507, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.00313743177317759, 0.4, 0.4, 0.0158286897901533, 0.4, 0.00053819656199386, 0.4, 1.5356547081503e-05, 0.4, 0.0243706288047841, 0.0118712294000335 )), .Names = c("catch", "pPREY1AMB2_DWF", "pPREY1AMB2_OSH", "pPREY1BEN2_BCR", "pPREY1DSR2_BIV", "pPREY1DSR2_LRF", "pPREY1DSR2_ODF", "pPREY1DSR2_OSH", "pPREY1DSR2_SCI", "pPREY1DSR2_SDF", "pPREY1DSR2_SRF", "pPREY1DSR2_SSR", "pPREY1FLT2_BIV", "pPREY1FLT2_OSH", "pPREY1FLT2_PIN", "pPREY1FLT2_SRF", "pPREY1GAG2_BCR", "pPREY1GAG2_BIV", "pPREY1GAG2_FLT", "pPREY1GAG2_JCK", "pPREY1GAG2_LRF", "pPREY1GAG2_LUT", "pPREY1GAG2_MEN", "pPREY1GAG2_ODF", "pPREY1GAG2_OSH", "pPREY1GAG2_PIN", "pPREY1GAG2_SCI", "pPREY1GAG2_SDF", "pPREY1GAG2_SPL", "pPREY1GAG2_SRF", "pPREY1GAG2_SSR", "pPREY1JCK2_BCR", "pPREY1JCK2_BIV", "pPREY1JCK2_JCK", "pPREY1JCK2_LPL", "pPREY1JCK2_ODF", "pPREY1JCK2_OSH", "pPREY1JCK2_SCI", "pPREY1JCK2_SDF", "pPREY1JCK2_SHP", "pPREY1KMK2_LPL", "pPREY1LGS2_BIV", "pPREY1LGS2_DWF", "pPREY1LGS2_FLT", "pPREY1LGS2_LGS", "pPREY1LGS2_LPL", "pPREY1LGS2_LRF", "pPREY1LGS2_MPL", "pPREY1LGS2_MUL", "pPREY1LGS2_ODF"), row.names = c(NA, 35L), class = "data.frame")

fitControl <- trainControl( method = "repeatedcv", number = 10, repeats = 10)

gamboost returns an error

fit.bgam.sel <- caret::train( catch ~ ., data = this.data2, method = 'gamboost', trControl = fitControl, tuneGrid = expand.grid(.mstop = seq(100, 1000, 100), .prune = c(5)), metric = 'Rsquared', maximize = FALSE, type = 'Regression' )

glm works fine

caret::train( catch ~ ., data = this.data2, method = 'glm', trControl = fitControl, tuneGrid = expand.grid(.parameter = sqrt(ncol(this.train.b.sel))) )

sessionInfo()

R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel splines stats graphics grDevices utils datasets methods base

other attached packages: [1] tidyverse_1.1.1 plyr_1.8.4 mboost_2.8-1 stabs_0.6-3 stringr_1.2.0 bindrcpp_0.2
[7] caret_6.0-76 ggthemes_3.4.0 gbm_2.1.3 lattice_0.20-35 survival_2.41-3 dismo_1.1-4
[13] raster_2.5-8 sp_1.2-4 doSNOW_1.0.14 snow_0.4-2 iterators_1.0.8 foreach_1.4.3
[19] future_1.5.0 R.utils_2.5.0 R.oo_1.21.0 R.methodsS3_1.7.1 dplyr_0.7.2 purrr_0.2.3
[25] tidyr_0.6.3 tibble_1.3.3 ggplot2_2.2.1 data.table_1.10.4 stringi_1.1.5 readr_1.1.1

loaded via a namespace (and not attached): [1] httr_1.2.1 jsonlite_1.5 modelr_0.1.0 assertthat_0.2.0 stats4_3.4.0 coin_1.2-1
[7] cellranger_1.1.0 globals_0.10.0 quadprog_1.5-5 quantreg_5.33 glue_1.1.1 digest_0.6.12
[13] rvest_0.3.2 minqa_1.2.4 sandwich_2.4-0 colorspace_1.3-2 Matrix_1.2-10 psych_1.7.5
[19] pkgconfig_2.0.1 broom_0.4.2 SparseM_1.77 listenv_0.6.0 haven_1.0.0 mvtnorm_1.0-6
[25] scales_0.4.1 lme4_1.1-13 MatrixModels_0.4-1 mgcv_1.8-17 car_2.1-5 party_1.2-3
[31] TH.data_1.0-8 nnet_7.3-12 lazyeval_0.2.0 pbkrtest_0.4-7 mnormt_1.5-5 strucchange_1.5-1 [37] magrittr_1.5 readxl_1.0.0 nlme_3.1-131 MASS_7.3-47 forcats_0.2.0 xml2_1.1.1
[43] foreign_0.8-67 tools_3.4.0 hms_0.3 multcomp_1.4-6 munsell_0.4.3 compiler_3.4.0
[49] rlang_0.1.1 grid_3.4.0 nloptr_1.0.4 gtable_0.2.0 ModelMetrics_1.1.0 codetools_0.2-15
[55] reshape2_1.4.2 R6_2.2.1 zoo_1.8-0 nnls_1.4 lubridate_1.6.0 bindr_0.1
[61] modeltools_0.2-21 Rcpp_0.12.12

grayskripko commented 7 years ago

@hmorzaria It would be more informative to include error and warning messages. So we have classic Something is wrong; all the Rsquared metric values are missing: and In addition: There were 50 or more warnings (use warnings() to see the first 50)

warnings() will give us unused argument (type = "Regression") When you run ?caret::train you can make sure there is not any type = 'Regression' argument. If you are interested in how the model determines which kind of task it should solve you can execute caret::getModelInfo()[['gamboost']]$fit and you will see a chunk

if (!any(names(theDots) == "family")) 
        theDots$family <- if (is.factor(y)) 
            Binomial()
        else GaussReg()

You can just omit that argument.

After that, you will get new errors :) And again, warnings(). Degrees of freedom cannot be larger than the rank of the design matrix. It looks like gamboost does not like when ncol(df) > nrow(df)

hmorzaria commented 7 years ago

Thank you for your response. When I run the model I get no warnings except for the missing values message. I am using the latest caret off CRAN.

Something is wrong; all the Rsquared metric values are missing: RMSE Rsquared
Min. : NA Min. : NA
1st Qu.: NA 1st Qu.: NA
Median : NA Median : NA
Mean :NaN Mean :NaN
3rd Qu.: NA 3rd Qu.: NA
Max. : NA Max. : NA
NA's :10 NA's :10
Error: Stopping In addition: Warning message: In nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo, : There were missing values in resampled performance measures.

warnings() only returns Warning message: In nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo, ... : There were missing values in resampled performance measures.

I don't get a warning on the unused "Regression" argument either. Which I got from $gamboost$type [1] "Regression" "Classification" but now I realize it is not an argument.

grayskripko commented 7 years ago

@hmorzaria is this issue solved?

topepo commented 7 years ago

I'm not sure of what the actual issue is (besides the ncol to nrow ratio), but the model doesn;t work when you bypass caret:

> test <- gamboost(catch ~ ., data = this.data2)
Error in solve.default(XtX, crossprod(X, y), LINPACK = FALSE) : 
  Lapack routine dgesv: system is exactly singular: U[2,2] = 0
In addition: Warning message:
In df2lambda(X, df = args$df, lambda = args$lambda, dmat = K, weights = w,  :
  ‘df’ too large:
  Degrees of freedom cannot be larger than the rank of the design matrix.
  Unpenalized base-learner with df = 2 used. Re-consider model specification.