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["Accuracy of genomic prediction based on Goddard et al. (2011), with notation after Dekkers (2007)",null,null,null,"and other methods"]
[]
[null,null,null,null,"Goddard, M.E. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136, 245-257 (2009)."]
[null,null,null,null,"Goddard, M.E., Hayes, B.J. & Meuwissen, T.H.E. Using the genomic relationship matrix to predict the accuracy of genomic selection. Journal of Animal Breeding and Genetics 128, 409-421 (2011)."]
[null,null,null,null,"Meuwissen, T., Hayes, B. & Goddard, M. Accelerating Improvement of Livestock with Genomic Selection. Annual Review of Animal Biosciences 1, 221-237 (2013)."]
[null,null,null,null,"Daetwyler, H.D., Villanueva, B. & Woolliams, J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLOS ONE 3, e3395 (2008)."]
[null,null,null,null,"Lee, S.H., Weerasinghe, W.M. S.P. ,  Wray, N. R., Goddard, M.E.,  and van der Werf, J.H.J. Using information of relatives in genomic prediction to apply effective stratified medicine. Scientific Reports. (2017) Also bioRxiv (2016): 054494"]
["# markers","M  =",50000]
["Effective population size","Ne  =",1500]
["Average chromosome size (M)","L  =",1,null,null,null,null,null,null,null,null,null,null,"nchrom","Me Lee et al","Me Goddard"]
["Number of chromosomes","k  =",30,null,null,null,null,null,null,null,null,null,null,50,126.77937619370306]
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["Number of training individuals","T  =",5000,"Alternate derivations of Me",null,null,null,null,null,null,null,null,null,150,363.74522864809734]
[null,null,"Goddard et al. 2011","Meuwissen et al., 2013","Goddard 2009","Goddard 2009","Goddard 2009","Daetwyler et al 2008","Lee et al 2017","doi: http://dx.doi.org/10.1101/054494",null,null,null,200,479.47159149368912]
[null,null,"Me = 2NeLk/ln(NeL)","Me = 2NeLk/ln(2Ne)","Me = 2NeLk/ln(4NeLk)","Me = 2NeLk","Me=4NeLk","Me = 2NeLk","      Eq. (10)  ","           Eq(11)",null,null,null,250,594.08300768378444]
["Effective number of chr. Segments","Me  =",{"$f":"2*C9*C10*C11/LN(C9*C10)","v":12306.479941295485},{"$f":"2*C9*C10*C11/LN(2*C9)","v":11241.052729535588},{"$f":"2*C9*C10*C11/LN(4*C9*C10*C11)","v":7437.5787998312981},{"$f":"2*C9*C10*C11","v":90000},{"$f":"2*F16","v":180000},{"$f":"2*C9*C10*C11","v":90000},{"$f":"    C$11   /  (         1/(8*C9^2*C$10^2/(LN(4*C9*C$10+1)+4*C9*C$10*(LN(4*C9*C$10+1)-1)))  +  (1/(3*C9))  * (C$11-1))","v":3329.0838587423623},{"$f":"    C$11   /  (         1/(4*C9^2*C$10^2/(LN(2*C9*C$10+1)+2*C9*C$10*(LN(2*C9*C$10+1)-1)))  +  (1/(3*C9))  * (C$11-1))","v":3416.5058813405126},null,null,null,300,707.82116541090693]
["Proportion of genetic variance captured by markers = b","q2  =",{"$f":"$C$8/(C16+$C$8)","v":0.80248475033591171},{"$f":"$C$8/(D16+$C$8)","v":0.8164457952873464},0.87051023118939097,0.35714285714285715,0.21739130434782608,1,0.93757470374776331,0.93604025899915766,null,null,null,350,820.84316747913704]
["Varance ratio of resdual and effective QTL variance","Lambda",{"$f":"C16/(C17*$C$12)","v":30670.937824411296},{"$f":"D16/(D17*$C$12)","v":27536.556117799155},{"$f":"E16/(E17*$C$12)","v":17087.860735810595},504000,1656000,180000,7101.4796910262821,7299.9122601703975,null,null,null,400,933.25919235562935]
["Accuracy of genomic prediction as predictor of effects captured by markers","rQhat  =",{"$f":"SQRT($C$13/($C$13+C18))","v":0.37439301572320988},{"$f":"SQRT($C$13/($C$13+D18))","v":0.39201186405459343},{"$f":"SQRT($C$13/($C$13+E18))","v":0.47578218281863244},9.9111970574691066E-2,5.4865606697768944E-2,0.16439898730535729,0.64278504512053869,0.63757898709469796,null,null,null,450,1045.1506967950991]
["Accuracy of genomic prediction as predictor of full breeding value","rGBV  =",{"$f":"SQRT(C17)*C19","v":0.33538692871966619},{"$f":"SQRT(D17)*D19","v":0.35421168939805581},0.44391018994601111,5.9230731379189668E-2,2.5581221026345753E-2,0.16439898730535729,0.6223987398637274,0.61685240098587035,null,null,null,500,1156.5802932410797]
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[null,null,null,null,null,null,null,null,null,null,null,null,null,600,1378.2427551834908]
[null,"Compare methods with the same Me =",1303,null,null,null,null,null,null,null,null,null,null,650,1488.5491024396067]
[null,null,"Me = 2NeLk/ln(NeL)","Me = 2NeLk/ln(2Ne)","Me = 2NeLk/ln(4NeLk)","Me = 2NeLk","Me=4NeLk","Me = 2NeLk","      Eq. (10)  ","           Eq(11)",null,null,null,700,1598.5445624570543]
["Effective number of chr. Segments","Me  =",{"$f":"$C23","v":1303},{"$f":"$C23","v":1303},1303,1303,1303,1303,1303,1303,null,null,null,750,1708.2529406702563]
["Proportion of genetic variance captured by markers = b","q2  =",{"$f":"C8/(C25+C8)","v":0.97460187513400776},{"$f":"$C$8/(D25+$C$8)","v":0.97460187513400776},0.97460187513400776,0.97460187513400776,0.97460187513400776,1,{"$f":"$C$8/(I25+$C$8)","v":0.97460187513400776},0.97460187513400776,null,null,null,800,1817.6947497227889]
["Varance ratio of resdual and effective QTL variance","Lambda",{"$f":"C25/(C26*$C$12)","v":2673.9123599999998},{"$f":"D25/(D26*$C$12)","v":2673.9123599999998},{"$f":"E25/(E26*$C$12)","v":2673.9123599999998},{"$f":"F25/(F26*$C$12)","v":2673.9123599999998},2673.9123599999998,2606,2673.9123599999998,2673.9123599999998,null,null,null,850,1926.8878428360897]
["Accuracy of genomic prediction as predictor of effects captured by markers","rQhat  =",{"$f":"SQRT($C$13/($C$13+C27))","v":0.80719150868026202},{"$f":"SQRT($C$13/($C$13+D27))","v":0.80719150868026202},{"$f":"SQRT($C$13/($C$13+E27))","v":0.80719150868026202},0.80719150868026202,0.80719150868026202,0.81078712124830854,0.80719150868026202,0.80719150868026202,null,null,null,900,2035.8478951397537]
["Accuracy of genomic prediction as predictor of full breeding value","rGBV  =",{"$f":"SQRT(C26)*C28","v":0.79687500707420611},{"$f":"SQRT(D26)*D28","v":0.79687500707420611},0.79687500707420611,0.79687500707420611,0.79687500707420611,0.81078712124830854,0.79687500707420611,0.79687500707420611,null,null,null,950,2144.5887759092388]
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[null,null,null,null,null,null,null,null,null,null,null,null,null,1150,2577.589577135207]
[null,null,null,null,null,null,null,null,null,null,null,null,null,1200,2685.3969327326663]
[null,null,null,null,null,null,null,null,null,null,null,null,null,1250,2793.0433128920608]
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["Accuracy of genomic prediction based on Goddard et al. (2011), with notation after Dekkers (2007)",null,null,null,"and other methods"]
[]
[null,null,null,null,"Goddard, M.E. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136, 245-257 (2009)."]
[null,null,null,null,"Goddard, M.E., Hayes, B.J. & Meuwissen, T.H.E. Using the genomic relationship matrix to predict the accuracy of genomic selection. Journal of Animal Breeding and Genetics 128, 409-421 (2011)."]
[null,null,null,null,"Meuwissen, T., Hayes, B. & Goddard, M. Accelerating Improvement of Livestock with Genomic Selection. Annual Review of Animal Biosciences 1, 221-237 (2013)."]
[null,null,null,null,"Daetwyler, H.D., Villanueva, B. & Woolliams, J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLOS ONE 3, e3395 (2008)."]
[null,null,null,null,"Lee, S.H., Weerasinghe, W.M. S.P. ,  Wray, N. R., Goddard, M.E.,  and van der Werf, J.H.J. Using information of relatives in genomic prediction to apply effective stratified medicine. Scientific Reports. (2017) Also bioRxiv (2016): 054494"]
["# markers","M  =",50000]
["Effective population size","Ne  =",400]
["Average chromosome size (M)","L  =",1,null,null,null,null,null,null,null,null,null,null,"nchrom","Me Goddard","Me Lee et al"]
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["Number of training individuals","T  =",10000,"Alternate derivations of Me",null,null,null,null,null,null,null,null,null,3,400.56984083440091,311.02874751328983]
[null,null,"Goddard et al. 2011","Meuwissen et al., 2013","Goddard 2009","Goddard 2009","Goddard 2009","Daetwyler et al 2008","Lee et al 2017","doi: http://dx.doi.org/10.1101/054494",null,null,null,4,534.0931211125345,381.7251379226069]
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["Varance ratio of resdual and effective QTL variance","Lambda",{"$f":"C16/(C17*$C$12)","v":14422.036010387345},{"$f":"D16/(D17*$C$12)","v":12827.152957115581},{"$f":"E16/(E17*$C$12)","v":7752.3736810942737},118400.00000000001,313600,80000,3168.9288225265168,3257.7820785044587,null,null,null,8,1068.186242225069,579.20324400830441]
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[null,"Compare methods with the same Me =",8000,null,null,null,null,null,null,null,null,null,null,13,1735.8026436157372,723.07609460669585]
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[null,null,2800,0.33591956814729212,0.52285239201567923,null,null,null,null,null,null,null,null,null,null,null," h2=",0.3]
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[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Ne","Acc Goddard","Acc Lee et al"]
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{"sheet":"Sheet1","index":2,"n_rows":29,"n_cols":10,"rows_kept":29,"cut":false,"hidden":false,"merged":[]}
["Accuracy of genomic prediction based on Goddard et al. (2011), with notation after Dekkers (2007)",null,null,null,"and other methods"]
[]
[null,null,null,null,"Goddard, M.E. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136, 245-257 (2009)."]
[null,null,null,null,"Goddard, M.E., Hayes, B.J. & Meuwissen, T.H.E. Using the genomic relationship matrix to predict the accuracy of genomic selection. Journal of Animal Breeding and Genetics 128, 409-421 (2011)."]
[null,null,null,null,"Meuwissen, T., Hayes, B. & Goddard, M. Accelerating Improvement of Livestock with Genomic Selection. Annual Review of Animal Biosciences 1, 221-237 (2013)."]
[null,null,null,null,"Daetwyler, H.D., Villanueva, B. & Woolliams, J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLOS ONE 3, e3395 (2008)."]
[null,null,null,null,"Lee, S.H., Weerasinghe, W.M. S.P. ,  Wray, N. R., Goddard, M.E.,  and van der Werf, J.H.J. Using information of relatives in genomic prediction to apply effective stratified medicine. Scientific Reports. (2017) Also bioRxiv (2016): 054494"]
["# markers","M  =",50000]
["Effective population size","Ne  =",1000]
["Average chromosome size (M)","L  =",1]
["Number of chromosomes","k  =",30]
["Heritability of phenotypes","h2  =",0.3]
["Number of training individuals","T  =",2000,"Alternate derivations of Me"]
[null,null,"Goddard et al. 2011","Meuwissen et al., 2013","Goddard 2009","Goddard 2009","Goddard 2009","Daetwyler et al 2008","Lee et al 2017","doi: http://dx.doi.org/10.1101/054494"]
[null,null,"Me = 2NeLk/ln(NeL)","Me = 2NeLk/ln(2Ne)","Me = 2NeLk/ln(4NeLk)","Me = 2NeLk","Me=4NeLk","Me = 2NeLk","      Eq. (10)  ","           Eq(11)"]
["Effective number of chr. Segments","Me  =",{"$f":"2*C9*C10*C11/LN(C9*C10)","v":8685.8896380650367},{"$f":"2*C9*C10*C11/LN(2*C9)","v":7893.7994954371134},{"$f":"2*C9*C10*C11/LN(4*C9*C10*C11)","v":5130.2892438563667},{"$f":"2*C9*C10*C11","v":60000},{"$f":"2*F16","v":120000},{"$f":"2*C9*C10*C11","v":60000},{"$f":"    C$11   /  (         1/(8*C9^2*C$10^2/(LN(4*C9*C$10+1)+4*C9*C$10*(LN(4*C9*C$10+1)-1)))  +  (1/(3*C9))  * (C$11-1))","v":2253.1228408952934},{"$f":"    C$11   /  (         1/(4*C9^2*C$10^2/(LN(2*C9*C$10+1)+2*C9*C$10*(LN(2*C9*C$10+1)-1)))  +  (1/(3*C9))  * (C$11-1))","v":2313.1605864821595}]
["Proportion of genetic variance captured by markers = b","q2  =",{"$f":"C8/(C16+C8)","v":0.85199355941208788},{"$f":"C8/(D16+C8)","v":0.86365034659611073},{"$f":"C8/(E16+C8)","v":0.90694245732751932},{"$f":"C8/(F16+C8)","v":0.45454545454545453},{"$f":"C8/(G16+C8)","v":0.29411764705882354},1,{"$f":"C8/(C8+I16)","v":0.95688060888234772},{"$f":"C8/(C8+J16)","v":0.95578243484910208}]
["Accuracy of estimating SNP effects","Theta  =",{"$f":"C13*C17*C12/C16","v":5.8853630076876301E-2},{"$f":"C13*D17*C12/D16","v":6.5645220436267498E-2},{"$f":"C13*E17*C12/E16","v":0.10606916072971162},{"$f":"C13*F17*C12/F16","v":4.5454545454545452E-3},{"$f":"C13*G17*C12/G16","v":1.4705882352941176E-3}]
["Accuracy of genomic prediction as predictor of effects captured by markers","rQhat  =",{"$f":"SQRT(C18/(1+C18))","v":0.23575920733314915},{"$f":"SQRT(D18/(1+D18))","v":0.24819626105994583},{"$f":"SQRT(E18/(1+E18))","v":0.30967305922922533},{"$f":"SQRT(F18/(1+F18))","v":6.7267279399631244E-2},3.8320083261967369E-2,{"$f":"SQRT(C12/(C12+(H16/C13)))","v":9.9503719020998915E-2}]
["Accuracy of genomic prediction as predictor of full breeding value","rGBV  =",{"$f":"SQRT(C17)*C19","v":0.21761399332379336},{"$f":"SQRT(C17)*C19","v":0.21761399332379336},{"$f":"SQRT(E17)*E19","v":0.29491257498375256},{"$f":"SQRT(F17)*F19","v":4.5351590519507858E-2},2.078198301416901E-2,{"$f":"H19*H17","v":9.9503719020998915E-2},{"$f":"SQRT(C12/(C12+(I16/C13)))","v":0.45858029559675212},{"$f":"SQRT(C12/(C12+(J16/C13)))","v":0.45383022080147789}]
[]
[]
[null,"Compare methods with the same Me =",1303]
[null,null,"Me = 2NeLk/ln(NeL)","Me = 2NeLk/ln(2Ne)","Me = 2NeLk/ln(4NeLk)","Me = 2NeLk","Me=4NeLk","Me = 2NeLk","      Eq. (10)  ","           Eq(11)"]
["Effective number of chr. Segments","Me  =",{"$f":"$C23","v":1303},{"$f":"$C23","v":1303},1303,1303,1303,1303,1303,1303]
["Proportion of genetic variance captured by markers = b","q2  =",{"$f":"C8/(C25+C8)","v":0.97460187513400776},{"$f":"C8/(C25+C8)","v":0.97460187513400776},{"$f":"C8/(E25+C8)","v":0.97460187513400776},{"$f":"C8/(F25+C8)","v":0.97460187513400776},{"$f":"C8/(G25+C8)","v":0.97460187513400776},1,{"$f":"C8/(C8+I25)","v":0.97460187513400776},{"$f":"C8/(C8+J25)","v":0.97460187513400776}]
[null,"Theta  =",{"$f":"C13*C26*C12/C25","v":0.4487806025175784},{"$f":"C13*D26*C12/D25","v":0.4487806025175784},{"$f":"C13*E26*C12/E25","v":0.4487806025175784},{"$f":"C13*F26*C12/F25","v":0.4487806025175784},{"$f":"C13*G26*C12/G25","v":0.4487806025175784}]
["Accuracy of genomic prediction as predictor of effects captured by markers","rQhat  =",{"$f":"SQRT(C27/(1+C27))","v":0.55656478905545137},{"$f":"SQRT(D27/(1+D27))","v":0.55656478905545137},{"$f":"SQRT(E27/(1+E27))","v":0.55656478905545137},{"$f":"SQRT(F27/(1+F27))","v":0.55656478905545137},0.55656478905545137,{"$f":"SQRT(C12/(C12+(H25/C13)))","v":0.56150836571810181}]
["Accuracy of genomic prediction as predictor of full breeding value","rGBV  =",{"$f":"SQRT(C26)*C28","v":0.54945148139745525},{"$f":"SQRT(C26)*C28","v":0.54945148139745525},{"$f":"SQRT(E26)*E28","v":0.54945148139745525},{"$f":"SQRT(F26)*F28","v":0.54945148139745525},0.54945148139745525,{"$f":"H28*H26","v":0.56150836571810181},{"$f":"SQRT(C12/(C12+(I25/C13)))","v":0.56150836571810181},{"$f":"SQRT(C12/(C12+(J25/C13)))","v":0.56150836571810181}]

{"sheet":"Sheet2","index":3,"n_rows":0,"n_cols":0,"rows_kept":0,"cut":false,"hidden":false,"merged":[]}

{"sheet":"Sheet3","index":4,"n_rows":0,"n_cols":0,"rows_kept":0,"cut":false,"hidden":false,"merged":[]}

{"sheet":"Sheet4","index":5,"n_rows":6,"n_cols":7,"rows_kept":6,"cut":false,"hidden":false,"merged":[]}
[null,null,null,null,"values for \"alpha\""]
[null,null,null,null,null,"Ne = 200","Ne = 1000"]
[null,null,null,null,"Me",{"$f":"2.2*200","v":440.00000000000006},{"$f":"2.2*1000","v":2200}]
[null,null,null,"Nmarkers"]
[null,null,null,50000,null,{"$f":"D5/(D5+F3)","v":0.99127676447264079},{"$f":"D5/(G3+D5)","v":0.95785440613026818}]
[null,null,null,500000,null,{"$f":"D6/(D6+F3)","v":0.99912077371912722},{"$f":"D6/(D6+G3)","v":0.99561927518916771}]