R/boxcoxTransformation.R
boxcoxTransformation.RdboxcoxTransformation Box-Cox transforms summary values from a single simulation, while
boxcoxTransformationMatrix Box-Cox transforms summary values from multiple simulations. The
output of boxcoxTransformationMatrix needs to be provided as input for boxcoxTransformation.
boxcoxTransformation(summaryValuesVector, boxcoxAddition, boxcoxLambda) boxcoxTransformationMatrix(summaryValuesMatrix)
| summaryValuesVector | Vector of summary statistics from a single simulation |
|---|---|
| boxcoxAddition | Vector of boxcox additions from |
| boxcoxLambda | Vector of boxcox lambda values from |
| summaryValuesMatrix | Matrix of summary statistics from simulations |
boxcoxTransformation returns a vector of Box-Cox transformed summary statistics from a
single observation. boxcoxTransformationMatrix returns a matrix of Box-Cox transformed summary statistics with the
same dimensions as summaryValuesMatrix.
Brian O'Meara and Barb Banbury
# \donttest{ set.seed(1) data(simRunExample) # example simulation simDataParallel <- parallelSimulateWithPriors( nrepSim = 5, multicore = FALSE, coreLimit = 1, phy = simPhyExample, intrinsicFn = brownianIntrinsic, extrinsicFn = nullExtrinsic, startingPriorsFns = "normal", startingPriorsValues = list(c( mean(simCharExample[, 1]), sd(simCharExample[, 1]))), intrinsicPriorsFns = c("exponential"), intrinsicPriorsValues = list(10), extrinsicPriorsFns = c("fixed"), extrinsicPriorsValues = list(0), generation.time = 100000, checkpointFile = NULL, checkpointFreq = 24, verbose = FALSE, freevector = NULL, taxonDF = NULL)#> #> #>nParFree <- sum(attr(simDataParallel, "freevector")) # separate the simulation results: # 'true' generating parameter values from the summary values summaryValuesMat <- simDataParallel[, -1:-nParFree] boxTranMat <- boxcoxTransformationMatrix( summaryValuesMatrix = summaryValuesMat ) boxTranMat#> $boxcoxAddition #> [1] 820.3567514 173.2757586 1058.5052246 822.1376445 173.3177377 #> [6] 0.0000000 1054.0670108 817.0842612 86.4910552 15.2940079 #> [11] 1056.3217822 816.0956687 214.1616240 0.3225309 1044.3126219 #> [16] 806.2257106 698.8452487 76.5643983 299.6079455 126.5457849 #> [21] 2513.3034468 76.0895956 126.9176477 150.3826149 240.0795927 #> [26] 587.4282023 278.3068619 169.6408380 218.4550809 153.1170977 #> [31] 117.2190723 82.9188048 5.6530314 40.0833362 15.1508767 #> [36] 67.3700311 34.0335196 3.5583108 24.5686553 44.1398616 #> [41] 24.7986628 7.5101863 76.8317995 83.0127865 101.0390482 #> [46] 52.6028684 14.0180076 96.8229831 141.9021552 158.4403693 #> [51] 286.8401361 131.4034344 92.4112963 52.3340218 279.7332816 #> [56] 130.4185258 83.6438120 115.6177488 54.9420112 133.9111507 #> [61] 115.6375060 143.1654979 75.1565064 57.9603437 36.5585596 #> [66] 78.6457458 129.5121814 74.0648895 94.7469529 248.7138617 #> [71] 84.7296322 146.4685054 18.6056868 242.0663317 95.1650606 #> [76] 108.6389147 137.8635953 38.8566572 114.1178671 126.8350002 #> [81] 268.0231667 239.5687915 238.5356445 166.5259375 124.2996721 #> [86] 173.9458305 211.2021522 222.7254744 344.0735043 180.2100347 #> [91] 69.3458312 99.1123440 321.9640215 167.1934481 65.9415223 #> [96] 97.0765537 73.5254988 154.0555378 105.7927183 #> #> $boxcoxLambda #> [1] 8.4966 -20.0000 -5.2986 9.0427 -20.0000 20.0000 -5.6862 8.0432 #> [9] -20.0000 2.7490 -4.9472 8.5867 -20.0000 -1.1314 -5.3238 16.9577 #> [17] -8.8730 -20.0000 -18.8671 12.3515 -20.0000 -15.7266 -16.5515 -7.5757 #> [25] -5.5634 20.0000 -17.7518 19.2176 -19.3321 18.7493 20.0000 4.0495 #> [33] -6.4966 14.4366 3.6926 -20.0000 18.1385 -7.7390 -20.0000 -18.2116 #> [41] 2.5506 -12.8399 -20.0000 -18.8832 -20.0000 -11.3672 -4.6105 -7.3300 #> [49] -13.4826 -12.7981 -20.0000 -16.1207 20.0000 -6.3432 -20.0000 -17.3385 #> [57] 19.8030 19.6383 -7.2234 -16.2093 20.0000 10.7878 8.2401 14.3699 #> [65] 3.1293 8.4990 20.0000 -11.0649 -10.6338 -20.0000 -15.6198 14.3642 #> [73] -8.4748 -20.0000 -17.3171 15.2878 16.3352 -7.6976 -16.0705 19.8496 #> [81] -17.2908 -16.5299 -17.4494 -14.3970 -12.6367 -20.0000 -14.4161 -13.7614 #> [89] -20.0000 -16.2764 4.5174 -8.4032 -20.0000 -17.1941 20.0000 20.0000 #> [97] -7.5339 -16.2952 20.0000 #> #> $boxcoxSummaryValuesMatrix #> #> result.1 5.165735e+24 1.670898e-45 8.338559e-17 2.042379e+26 1.662825e-45 #> result.2 4.731359e+24 1.659462e-45 7.690344e-17 1.886231e+26 1.659214e-45 #> result.3 5.889470e+24 1.677232e-45 9.446629e-17 2.347516e+26 1.669126e-45 #> result.4 2.595072e+24 1.126652e-46 4.651298e-17 9.832503e+25 1.121893e-46 #> result.5 3.000516e+24 7.678348e-46 5.213361e-17 1.148226e+26 8.049019e-46 #> #> result.1 1.0000000 5.629414e-18 2.400174e+23 1.803423e-39 2159.551 9.723032e-16 #> result.2 0.7289452 5.226008e-18 2.214790e+23 1.794611e-39 2460.232 9.040382e-16 #> result.3 1.0000000 6.437920e-18 2.744715e+23 1.810754e-39 1922.359 1.102423e-15 #> result.4 1.0000000 3.004830e-18 1.255196e+23 1.213965e-40 2711.581 5.663695e-16 #> result.5 0.9691235 3.399690e-18 1.443989e+23 9.198680e-40 2928.814 6.311943e-16 #> #> result.1 9.026753e+24 2.417191e-47 3.597513 7.426805e-17 9.746046e+48 #> result.2 8.276643e+24 2.400041e-47 3.337236 6.856015e-17 1.029562e+49 #> result.3 1.031291e+25 2.424602e-47 3.597513 8.430883e-17 1.125822e+49 #> result.4 4.499616e+24 1.632074e-48 3.232712 4.115853e-17 2.801968e+48 #> result.5 5.232207e+24 1.056664e-47 3.093494 4.633872e-17 3.776749e+48 #> #> result.1 2.536779e-26 2.609602e-39 1.014434e-47 1.748127e+26 9.769964e-69 #> result.2 2.688936e-26 2.278334e-39 8.971017e-48 1.917247e+26 9.795990e-69 #> result.3 2.960307e-26 1.759793e-39 9.484195e-48 2.107144e+26 9.826814e-69 #> result.4 7.741382e-27 7.981787e-41 6.018459e-49 7.510587e+25 6.600693e-70 #> result.5 1.006539e-26 1.987502e-39 4.232555e-48 5.270489e+25 4.479260e-69 #> #> result.1 5.145195e-31 6.360233e-36 3.691772e-17 5.616538e-14 2.349707e+55 #> result.2 4.590632e-31 4.745385e-36 2.851478e-17 5.369136e-14 2.552190e+55 #> result.3 3.374582e-31 3.928060e-36 2.808528e-17 5.534469e-14 2.374593e+55 #> result.4 3.069154e-32 4.111401e-37 1.962455e-17 3.470062e-14 3.808101e+54 #> result.5 2.508402e-31 3.212603e-36 1.265370e-17 7.474462e-14 2.811041e+55 #> #> result.1 4.649182e-44 6.035438e+42 5.941826e-46 8.725696e+40 2.639240e+41 #> result.2 4.861615e-44 6.649021e+42 6.229711e-46 9.108093e+40 2.493237e+41 #> result.3 4.028681e-44 6.674740e+42 5.957551e-46 9.177626e+40 2.485142e+41 #> result.4 4.543456e-45 2.303638e+42 4.590507e-47 3.079563e+40 3.873397e+40 #> result.5 1.879459e-44 1.128208e+42 2.481586e-46 1.643154e+40 2.739869e+41 #> #> result.1 59047694 1.218781e-05 1.278809e+23 24424.85 2.819525e-37 6.438344e+27 #> result.2 59290468 1.004214e-05 1.245412e+23 22428.81 2.830803e-37 4.644059e+27 #> result.3 58963388 1.069863e-05 1.498571e+23 24211.46 2.733566e-37 6.352371e+27 #> result.4 73913047 1.552229e-05 5.479368e+22 29188.82 2.067234e-38 2.800907e+27 #> result.5 43977888 6.088611e-06 3.724118e+22 18058.98 2.698988e-37 1.070019e+27 #> #> result.1 6.205760e-05 1.559278e-28 1.166416e-30 3642.386 6.178864e-12 #> result.2 7.621785e-05 1.698866e-28 1.285215e-30 3704.002 4.913139e-12 #> result.3 6.187123e-05 1.504137e-28 1.124574e-30 3608.857 5.288954e-12 #> result.4 2.965687e-05 1.168491e-29 1.711285e-31 3043.797 2.273396e-12 #> result.5 3.801414e-05 1.335250e-28 1.993377e-30 4251.292 1.078089e-12 #> 21 22 23 24 25 #> result.1 2.245135e-39 9.212482e-38 1.644718e-41 5.210733e-21 5.830426e-07 #> result.2 2.164848e-39 7.960180e-38 1.337151e-41 3.643763e-21 3.809290e-07 #> result.3 1.714955e-39 6.443351e-38 1.131948e-41 3.358865e-21 3.785644e-07 #> result.4 7.090698e-41 3.360325e-39 5.531424e-43 5.245613e-22 1.425381e-07 #> result.5 1.840763e-39 4.735024e-38 9.293037e-42 2.527101e-21 3.561803e-07 #> 26 27 28 29 30 #> result.1 1.377961e-15 4.939139e-30 3.948156e-29 3.904951e-50 3.056964e-35 #> result.2 1.535184e-15 4.097234e-30 3.377665e-29 3.732658e-50 2.364588e-35 #> result.3 1.441834e-15 3.611544e-30 3.020324e-29 3.331999e-50 1.980135e-35 #> result.4 6.363156e-16 5.561525e-31 5.229261e-30 2.189190e-51 2.154686e-36 #> result.5 2.210569e-15 1.981576e-30 1.504120e-29 3.712446e-50 1.447167e-35 #> 31 32 33 34 35 #> result.1 1.553810e+40 5.178160e-12 6.363909e-50 8.637197e-38 1.080871e+39 #> result.2 1.137914e+40 4.972787e-12 6.096722e-50 6.556671e-38 7.760086e+38 #> result.3 1.294647e+40 4.183893e-12 5.400815e-50 5.377390e-38 8.488854e+38 #> result.4 8.184668e+39 2.126886e-12 3.454492e-51 5.026186e-39 4.715878e+38 #> result.5 1.137784e+39 1.748878e-12 5.301294e-50 4.380764e-38 7.485780e+37 #> 36 37 38 39 #> result.1 1.599019e+41 1.054565e-13 1.505625e-35 9.197340e+41 3.129375e+23 #> result.2 1.239828e+41 9.887686e-14 1.133155e-35 7.040313e+41 3.018171e+23 #> result.3 1.417123e+41 8.324402e-14 9.743338e-36 8.174911e+41 3.546591e+23 #> result.4 6.313592e+40 4.233298e-14 1.052689e-36 4.484758e+41 1.230603e+23 #> result.5 1.418335e+40 2.949554e-14 7.200594e-36 7.720780e+40 1.129676e+23 #> #> result.1 6.244746e+15 1.242606e+26 139656.1 2.873898e+16 6.664392e+42 #> result.2 6.356017e+15 1.436800e+26 155710.7 3.424421e+16 5.008525e+42 #> result.3 7.778439e+15 2.126142e+26 168740.1 3.679712e+16 6.389986e+42 #> result.4 3.506761e+15 1.158398e+26 110997.7 1.223863e+16 2.880001e+42 #> result.5 2.588100e+15 2.333567e+25 100179.0 1.612839e+16 6.210628e+41 #> #> result.1 7.772165e-22 4.558067e-22 6.394847e-49 2.361777e-31 3.160444e+31 #> result.2 6.051756e-22 3.774308e-22 6.172920e-49 1.669116e-31 2.684288e+31 #> result.3 4.729004e-22 3.116346e-22 5.250112e-49 1.223213e-31 2.945370e+31 #> result.4 1.035912e-22 7.317081e-23 4.474858e-50 1.545122e-32 1.089332e+31 #> result.5 3.812740e-22 1.977954e-22 8.691996e-49 1.454353e-31 6.327198e+30 #> #> result.1 9.922307e-13 1.072381e-48 1.707668e-35 4.969993e+31 2.663765e+35 #> result.2 9.262688e-13 1.033402e-48 1.204943e-35 4.015467e+31 2.207025e+35 #> result.3 4.977759e-13 8.780235e-49 8.874417e-36 4.334133e+31 2.464289e+35 #> result.4 6.017054e-13 6.138804e-50 8.985581e-37 1.794612e+31 9.488431e+34 #> result.5 1.177412e-13 1.138121e-48 1.093049e-35 7.567791e+30 3.990254e+34 #> #> result.1 1.494841e-13 3.482702e-34 2.401194e+42 5.480650e-43 2.450553e-40 #> result.2 1.379504e-13 2.532464e-34 1.870521e+42 5.209747e-43 2.256843e-40 #> result.3 1.054366e-13 2.091777e-34 2.168762e+42 5.292160e-43 2.253538e-40 #> result.4 6.597772e-14 2.353592e-35 9.459498e+41 4.148002e-44 2.013455e-41 #> result.5 3.129335e-14 1.811714e-34 2.182416e+41 2.172588e-43 9.357820e-41 #> #> result.1 1.669444e-42 4.874769e-33 1.382059e-27 4.831463e-46 1.830665e-34 #> result.2 1.490798e-42 4.031232e-33 1.087945e-27 5.477817e-46 1.573149e-34 #> result.3 1.488486e-42 4.125065e-33 1.159340e-27 5.399466e-46 1.476078e-34 #> result.4 1.170259e-43 4.902148e-34 1.665431e-28 2.515184e-47 2.004704e-35 #> result.5 6.604396e-43 1.818978e-33 5.192357e-28 3.817565e-46 6.814895e-35 #> #> result.1 3.080090e-33 1.104663e-51 1.008988e-37 384693606 8.668189e-18 #> result.2 2.694972e-33 1.050981e-51 8.209629e-38 355087319 8.298785e-18 #> result.3 2.530931e-33 9.777943e-52 7.387864e-38 361362822 7.479000e-18 #> result.4 3.839140e-34 6.099666e-53 7.726699e-39 498503901 2.599394e-18 #> result.5 1.114853e-33 8.151067e-52 4.239654e-38 230356791 2.887105e-18 #> #> result.1 4.058995e-51 2.898176e-39 4.165843e+37 3.838744e+40 4.062654e-15 #> result.2 3.873648e-51 2.306839e-39 2.822930e+37 2.872851e+40 3.831305e-15 #> result.3 3.547647e-51 2.022206e-39 3.019458e+37 3.281197e+40 3.378204e-15 #> result.4 2.197287e-52 1.877317e-40 4.117454e+37 2.365848e+40 1.480030e-15 #> result.5 2.827530e-51 1.301586e-39 2.567098e+36 2.926545e+39 1.256812e-15 #> #> result.1 1.097079e-36 1.817454e+41 #> result.2 8.484423e-37 1.370079e+41 #> result.3 7.526967e-37 1.588740e+41 #> result.4 7.940714e-38 1.155720e+41 #> result.5 4.935015e-37 1.463428e+40 #>boxcoxTransformation( summaryValuesVector = summaryValuesMat[, 1], boxcoxAddition = boxTranMat$boxcoxAddition, boxcoxLambda = boxTranMat$boxcoxLambda )#> result.1 result.2 result.3 result.4 result.5 #> 5.165735e+24 1.605049e-44 9.291003e-17 9.832503e+25 8.714451e-42# }