adrc.reml.jack: AD model with row and column effects analyzed by MINQUE and...

Description Usage Arguments Details Value Author(s) References Examples

View source: R/qgtools.r

Description

An AD model with row and column effects included is used for controlling field variation. This model will be analyzed by MINQUE approach and tested by jackknife technique. The data set can be irregular or missing but the field layout should be rectangular. It can analyze any genetic mating designs and data including F1, F2, or F3 with parents..

Usage

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adrc.reml.jack(Y, Ped, Row = NULL, Col = NULL, JacNum = NULL, JacRep = NULL)

Arguments

Y

A data matrix for one or more traits

Ped

A pedigree matrix including Environment, Female, Male,Generation is required.

Row

A vector for field rows. It can be default.

Col

A vector for field colums.It can be default.

JacNum

Number of jackknife groups to be used. The default is 10.

JacRep

Repeating times for jackknife process. The default is 1.

Details

A pedigree matrix used for analysis is required in the order of Environment (column 1), Female(column 2), Male(column 3), Generation (column 4). Even though there is only one environment, this first column is needed.If only row or column vector is included, this is equivallent to an AD model with block effects.

Value

Return a list of results: estimated Variance components, estimated proportional variance components, estimated fixed effects, and predicted random effects, and their statistical tests

Author(s)

Jixiang Wu <qgtools@gmail.com>

References

Rao, C.R. 1971. Estimation of variance and covariance components-MINQUE theory. J Multiva Ana 1:19

Wu, J., McCarty Jr., J.C., Jenkins, J.N. 2010. Cotton chromosome substitution lines crossed with cultivars: Genetic model evaluation and seed trait analyses. Theoretical and Applied Genetics 120:1473-1483.

Wu, J., J. N. Jenkins, J. C. McCarty, K. Glover, and W. Berzonsky. 2010. Presentation titled by "Unbalanced Genetic Data Analysis: model evaluation and application" was offered at ASA, CSSA, & SSSA 2010 International Annual Meetings, Long Beach, CA.

Wu, J., J. N. Jenkins, and J.C., McCarty. 2011. A generalized approach and computer tool for quantitative genetics study. Proceedings Applied Statistics in Agriculture, April 25-27, 2010, Manhattan, KS. p.85-106.

Wu, J. 2012. GenMod: An R package for various agricultural data analyses. ASA, CSSA, and SSSA 2012 International Annual Meetings, Cincinnati, OH, p 127

Wu, J., Bondalapati K., Glover K., Berzonsky W., Jenkins J.N., McCarty J.C. 2013. Genetic analysis without replications: model evaluation and application in spring wheat. Euphytica. 190:447-458

Zhu, J. 1989. Estimation of Genetic Variance Components in the General Mixed Model. Ph.D. Dissertation, NC State University, Raleigh, U.S.A

Examples

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  library(qgtools)
  data(adrcdat)
  dat=adrcdat[which(adrcdat$Env==1&adrcdat$Row<=3),]
  Ped=dat[,c(1,4,5,6)]
  Y=as.matrix(dat[,8])
 
  colnames(Y)=colnames(dat)[8]
  
  Row=dat$Row
  Col=dat$Column

  
  ##run AD model with field row and column effects 
  res=adrc.reml.jack(Y,Ped,Row=Row,JacNum=5) 
  res$Var
  res$PVar
  res$FixedEffect
  res$RandomEffect

Example output

$YIELD
        Estimate        SE    PValue     2.5%LL    97.5%UL
V(A)    5218.355  9646.840 0.6695348 -32795.181  43231.891
V(D)   69063.466 33149.080 0.1502018 -61561.040 199687.973
V(Row)   929.278  1596.716 0.6509346  -5362.609   7221.165
V(e)    9359.428  3839.227 0.1032862  -5769.109  24487.965

$YIELD
             Estimate         SE      PValue      2.5%LL    97.5%UL
V(A)/VP   0.072124955 0.11219156 0.623088755 -0.36996777 0.51421768
V(D)/VP   0.780308538 0.13992566 0.007583356  0.22892912 1.33168796
V(Row)/VP 0.008160273 0.01294601 0.628843325 -0.04285369 0.05917424
V(e)/VP   0.139406234 0.10917256 0.353586942 -0.29079008 0.56960255

NULL
$YIELD
                  Pre         SE     PValue      2.5%LL      97.5%UL
A(3)        -2.630909   7.916448 0.75954540   -33.82581   28.5639873
A(4)       -41.939810  57.496910 0.58329922  -268.50735  184.6277310
A(19)      -25.459748  35.124947 0.58540938  -163.87019  112.9506959
A(1)         5.771434  36.053130 0.82465465  -136.29653  147.8393997
A(5)        -4.408206   7.960740 0.66375371   -35.77764   26.9612250
A(13)        8.151241  11.162535 0.58292955   -35.83492   52.1373977
A(14)      -28.905778  56.742950 0.68367615  -252.50233  194.6907699
A(18)        9.685692  16.764211 0.65286055   -56.37397   75.7453485
A(20)       -8.481537  27.461646 0.76900658  -116.69462   99.7315421
A(22)      -16.749267  32.367122 0.68007309  -144.29246  110.7939231
A(23)       24.875303  36.679949 0.60686612  -119.66266  169.4132603
A(24)      -48.845787  69.835111 0.59708164  -324.03222  226.3406431
A(26)      -14.781646  20.242392 0.58292950   -94.54713   64.9838413
A(27)       36.708689  51.766983 0.59263496  -167.27998  240.6973560
A(28)       27.098966  43.452992 0.63191091  -144.12828  198.3262106
A(32)        5.546171  20.038323 0.78165009   -73.41518   84.5075202
A(6)        10.892684  19.121697 0.65654542   -64.45669   86.2420535
A(7)         8.330282  11.593196 0.58829738   -37.35290   54.0134675
A(8)        24.248689  37.686055 0.62282889  -124.25384  172.7512225
A(9)        29.801004  41.928340 0.59187793  -135.41832  195.0203317
A(15)      -31.086105  44.613520 0.59830409  -206.88643  144.7142208
A(25)       -1.084263   8.909560 0.83767903   -36.19253   34.0240085
A(17)       10.573585  21.430867 0.69081290   -73.87511   95.0222762
A(29)       34.661617  62.419615 0.66304946  -211.30393  280.6271618
A(12)      -76.530362 179.049561 0.71967932  -782.07817  629.0174446
A(30)       45.482834  75.171168 0.64041447  -250.73042  341.6960864
A(21)       -2.056214  21.076672 0.84556748   -85.10919   80.9967643
A(11)       13.726349  27.074768 0.68476333   -92.96223  120.4149268
A(10)       21.664211  31.821250 0.60565288  -103.72796  147.0563829
A(31)       -6.359299  14.219826 0.71110924   -62.39276   49.6741624
A(34)      -13.027476  21.374902 0.63839445   -97.25564   71.2006850
A(16)        5.127657   7.043904 0.58397473   -22.62897   32.8842801
D(1*1)     -22.879363  80.244172 0.77839271  -339.08287  293.3241468
D(3*3)     174.394463 110.356458 0.25779221  -260.46702  609.2559433
D(4*4)    -488.202430 123.648970 0.02505101  -975.44328   -0.9615827
D(5*5)       4.100805  91.799875 0.86201619  -357.63815  365.8397578
D(6*6)      36.992940  26.790256 0.31790578   -68.57451  142.5603933
D(7*7)      88.683124  55.246869 0.25103679  -129.01809  306.3843404
D(8*8)     120.782413  26.305494 0.01506646    17.12517  224.4396526
D(9*9)     190.779548  57.125521 0.04264651   -34.32453  415.8836243
D(10*10)   101.844244  67.882912 0.28059022  -165.64951  369.3379995
D(11*11)    26.795941  32.923173 0.54469361  -102.93838  156.5302578
D(12*12)  -450.535310 275.642759 0.24331321 -1536.71024  635.6396157
D(13*13)    58.378209  61.225210 0.48253911  -182.88076  299.6371764
D(14*14)  -328.330221 238.838711 0.31993140 -1269.47818  612.8177352
D(15*15)  -208.023825 106.192170 0.17167088  -626.47586  210.4282071
D(16*16)    50.972415  49.770810 0.45231582  -145.15030  247.0951276
D(17*17)    45.202333  63.103724 0.58932295  -203.45895  293.8636207
D(18*18)   129.854141  80.489046 0.24887759  -187.31430  447.0225822
D(19*19)  -341.399652 119.044195 0.06680610  -810.49530  127.6959990
D(20*20)    25.463462  63.441872 0.73083192  -224.53030  275.4572237
D(21*21)    97.237484 102.317975 0.48391033  -305.94822  500.4231838
D(22*22)   -43.145821  59.575803 0.58569267  -277.90527  191.6136306
D(23*23)   110.609711  86.385328 0.35234083  -229.79313  451.0125469
D(24*24)  -268.246160 190.804885 0.30975853 -1020.11602  483.6236992
D(25*25)    -7.754166  26.806126 0.77676539  -113.38416   97.8758247
D(26*26)  -102.593162  48.661946 0.14626018  -294.34638   89.1600527
D(27*27)   225.920833 143.369773 0.25902685  -339.03017  790.8718340
D(28*28)   129.118561  66.146288 0.17295393  -131.53200  389.7691197
D(29*29)   225.894912 110.970457 0.15809390  -211.38604  663.1758636
D(30*30)   207.148058  94.325328 0.13319054  -164.54248  578.8386009
D(31*31)   -68.999766  52.790732 0.34293968  -277.02254  139.0230026
D(32*32)    50.643701  50.366413 0.46019337  -147.82600  249.1133982
D(34*34)   -31.453284  33.837918 0.49300612  -164.79217  101.8856003
D(1*18)    -45.591461  47.926616 0.48350559  -234.44710  143.2641771
D(3*5)    -348.046030 206.698344 0.23079459 -1162.54433  466.4522690
D(3*6)      73.985881  53.580511 0.31790578  -137.14903  285.1207865
D(3*7)    -166.394813  98.317750 0.22868017  -553.81756  221.0279341
D(3*8)     241.564825  52.610987 0.01506646    34.25035  448.8793051
D(3*9)      67.561130  83.165810 0.54538657  -260.15514  395.2774024
D(3*15)     89.145129 108.344030 0.54065583  -337.78634  516.0766009
D(3*20)   -115.077513 101.982287 0.40966788  -516.94043  286.7854053
D(3*25)   -110.170391  65.057463 0.22843180  -366.53042  146.1896351
D(5*17)   -106.074283  84.954054 0.36383074  -440.83716  228.6885958
D(5*27)    272.315793 175.272280 0.26518476  -418.34757  962.9791589
D(13*29)   153.341984 127.493285 0.38087427  -349.04745  655.7314187
D(1*14)    314.579829 219.300335 0.30066183  -549.57683 1178.7364856
D(12*14) -1125.409465 675.545792 0.23526625 -3787.40902 1536.5900876
D(14*15)   -70.112428  99.595789 0.59500046  -462.57131  322.3464544
D(14*29)    11.763392 106.293025 0.84131206  -407.08606  430.6128448
D(14*30)   362.769751 258.974225 0.31139515  -657.72254 1383.2620379
D(14*32)  -150.251523  94.442780 0.25488828  -522.40489  221.9018417
D(18*21)   324.535388 196.113977 0.23807756  -448.25504 1097.3258142
D(18*25)   -19.235644  35.061804 0.66606878  -157.39727  118.9259834
D(12*20)   224.338844 181.425528 0.36826299  -490.57150  939.2491889
D(20*27)  -356.990821 212.575770 0.23190497 -1194.64922  480.6675770
D(20*29)   298.656414 172.400456 0.21908640  -380.69048  978.0033091
D(1*22)   -191.409890 130.835752 0.29182175  -706.97037  324.1505897
D(11*22)    53.591882  65.846346 0.54469361  -205.87675  313.0605155
D(22*30)    51.526366  87.580869 0.64804895  -293.58752  396.6402522
D(7*23)     90.315224  59.791728 0.27758536  -145.29509  325.9255340
D(10*23)   203.688487 135.765824 0.28059022  -331.29902  738.6759990
D(13*23)   -16.014082  63.152984 0.79058653  -264.86948  232.8413124
D(15*23)   144.135892  89.873935 0.25142760  -210.01386  498.2856430
D(23*31)  -137.999533 105.581465 0.34293968  -554.04507  278.0460052
D(23*34)   -62.906567  67.675836 0.49300612  -329.58434  203.7712007
D(13*24)   -20.571484  88.956047 0.79900925  -371.10429  329.9613165
D(15*24)  -622.957177 392.186321 0.25556905 -2168.37397  922.4596178
D(17*24)   107.036341 146.228058 0.58212575  -469.17778  683.2504612
D(15*26)   -96.337520  93.027064 0.44751526  -462.91223  270.2371904
D(17*26)    21.211617  49.014313 0.71737568  -171.93011  214.3533400
D(21*26)  -130.060421  85.840345 0.27622658  -468.31574  208.1949035
D(1*27)   -123.337204  71.730584 0.22214112  -405.99277  159.3183669
D(7*27)    253.445837 153.742655 0.23969383  -352.37968  859.2713527
D(9*27)    190.565528 149.647553 0.35484285  -399.12317  780.2542260
D(16*27)   101.944831  99.541619 0.45231582  -290.30059  494.1902551
D(25*27)   113.897703  82.425244 0.31757868  -210.90036  438.6957631
D(5*28)    190.006130 116.776936 0.24524548  -270.15535  650.1676110
D(17*28)    68.230992  77.697368 0.51574513  -237.93679  374.3987765
D(9*32)    123.432438  87.950463 0.31054342  -223.13784  470.0027170
D(15*32)   140.078453 105.091431 0.33398885  -274.03610  554.1930046
D(29*32)   -11.971967  36.738202 0.76216535  -156.73947  132.7955379
Row(1)     -18.893618  29.619138 0.62537806  -135.60833   97.8210917
Row(2)      16.657253  16.032480 0.44610132   -46.51900   79.8335085
Row(3)       2.236365  19.737491 0.84044807   -75.53955   80.0122785

qgtools documentation built on Dec. 19, 2019, 1:09 a.m.