Replies: 3 comments
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We understand the difficulty of the lack of backward compatibility. While it's not an answer to your question, the rationale for the changes to make rxode2 are described here: https://blog.nlmixr2.org/blog/2022-10-12-rxode-and-rxode2/ Can you share a reproducible example of something that is not working so that we can help? |
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Thanks @billdenney I also agree, we need to understand what you are struggling with to help a little more.
This shouldn't have changed from Here is a little example that shows the classic way to create events (which is still supported), and the classic way to solve (which is also still supported), and the different types of outputs. library(rxode2)
#> rxode2 2.0.11.9000 using 4 threads (see ?getRxThreads)
#> no cache: create with `rxCreateCache()`
mod1 <- rxode2({
C2 <- centr/V2;
C3 <- peri/V3;
d/dt(depot) <- -KA*depot;
d/dt(centr) <- KA*depot - CL*C2 - Q*C2 + Q*C3;
d/dt(peri) <- Q*C2 - Q*C3;
d/dt(eff) <- Kin - Kout*(1-C2/(EC50+C2))*eff;
})
theta <-
c(KA=2.94E-01, CL=1.86E+01, V2=4.02E+01, # central
Q=1.05E+01, V3=2.97E+02, # peripheral
Kin=1, Kout=1, EC50=200) # effects
inits <- c(eff=1)
ev <- eventTable(amount.units='mg', time.units='hours')
ev$add.dosing(dose=10000, nbr.doses=10, dosing.interval=12)
ev$add.dosing(dose=20000, nbr.doses=5, start.time=120,
dosing.interval=24)
ev$add.sampling(0:240)
# Gives a matrix (as it has since the beginning)
mod1$solve(theta, ev, inits)
#> time C2 C3 depot centr peri eff
#> [1,] 0 0.000000 0.0000000 10000.00000 0.0000 0.0000 1.000000
#> [2,] 1 44.375548 0.9198298 7452.76491 1783.8970 273.1895 1.084664
#> [3,] 2 54.882956 2.6729825 5554.37049 2206.2948 793.8758 1.180825
#> [4,] 3 51.903426 4.4564927 4139.54175 2086.5177 1323.5783 1.228914
#> [5,] 4 44.497381 5.9807076 3085.10315 1788.7947 1776.2702 1.234610
#> [6,] 5 36.484341 7.1774981 2299.25485 1466.6705 2131.7169 1.214742
#> [7,] 6 29.307381 8.0667719 1713.58058 1178.1567 2395.8313 1.183976
#> [8,] 7 23.370351 8.6971746 1277.09132 939.4881 2583.0608 1.151680
#> [9,] 8 18.652833 9.1211226 951.78613 749.8439 2708.9734 1.122561
#> [10,] 9 14.985806 9.3854005 709.34382 602.4294 2787.4640 1.098295
#> [11,] 10 12.169691 9.5285551 528.65731 489.2216 2829.9809 1.078950
#> [12,] 11 10.020528 9.5810604 393.99590 402.8252 2845.5749 1.063912
#> [13,] 12 8.384345 9.5664499 10293.63592 337.0507 2841.2356 1.052381
#> [14,] 13 51.513863 10.4224722 7671.60489 2070.8573 3095.4743 1.126998
#> [15,] 14 61.069985 12.0761428 5717.46679 2455.0134 3586.6144 1.216409
#> [16,] 15 57.360958 13.7346412 4261.09361 2305.9105 4079.1884 1.260152
#> [17,] 16 49.391978 15.1158931 3175.69289 1985.5575 4489.4202 1.262736
#> [18,] 17 40.940884 16.1574186 2366.76925 1645.8235 4798.7533 1.240381
#> [19,] 18 33.419540 16.8833187 1763.89748 1343.4655 5014.3457 1.207499
#> [20,] 19 27.208411 17.3453462 1314.59132 1093.7781 5151.5678 1.173381
#> [21,] 20 22.269602 17.5982127 979.73400 895.2380 5226.6692 1.142711
#> [22,] 21 18.421030 17.6903920 730.17273 740.5254 5254.0464 1.117142
#> [23,] 22 15.453372 17.6616681 544.18061 621.2256 5245.5154 1.096712
#> [24,] 23 13.175382 17.5434164 405.56506 529.6504 5210.3947 1.080771
#> [25,] 24 11.427655 17.3598208 10302.25814 459.3917 5155.8668 1.068485
#> [26,] 25 54.458848 18.0490943 7678.03085 2189.2457 5360.5810 1.141756
#> [27,] 26 63.926840 19.5385782 5722.25590 2569.8590 5802.9577 1.230339
#> [28,] 27 60.137589 21.0356763 4264.66283 2417.5311 6247.5959 1.273843
#> [29,] 28 52.094616 22.2584603 3178.35294 2094.2036 6610.7627 1.276414
#> [30,] 29 43.574475 23.1445418 2368.75173 1751.6939 6873.9289 1.254030
#> [31,] 30 35.988078 23.7180712 1765.37497 1446.7207 7044.2672 1.221014
#> [32,] 31 29.715170 24.0308200 1315.69246 1194.5498 7137.1535 1.186654
#> [33,] 32 24.717313 24.1374963 980.55465 993.6360 7168.8364 1.155671
#> [34,] 33 20.812017 24.0865539 730.78434 836.6431 7153.7065 1.129758
#> [35,] 34 17.789641 23.9177453 544.63644 715.1436 7103.5704 1.108979
#> [36,] 35 15.458706 23.6624056 405.90478 621.4400 7027.7345 1.092701
#> [37,] 36 13.659619 23.3446732 10302.51132 549.1167 6933.3679 1.080095
#> [38,] 37 56.640896 23.9027107 7678.21955 2276.9640 7099.1051 1.152542
#> [39,] 38 66.060305 25.2638069 5722.39653 2655.6243 7503.3507 1.240622
#> [40,] 39 62.223711 26.6353114 4264.76764 2501.3932 7910.6875 1.284033
#> [41,] 40 54.134566 27.7352404 3178.43106 2176.2095 8237.3664 1.286660
#> [42,] 41 45.569365 28.5011502 2368.80994 1831.8885 8464.8416 1.264310
#> [43,] 42 37.938968 28.9571356 1765.41836 1525.1465 8600.2693 1.231236
#> [44,] 43 31.623081 29.1549129 1315.72479 1271.2479 8659.0091 1.196726
#> [45,] 44 26.583230 29.1491358 980.57875 1068.6458 8657.2933 1.165531
#> [46,] 45 22.636891 28.9882041 730.80229 910.0030 8609.4966 1.139374
#> [47,] 46 19.574394 28.7118174 544.64983 786.8906 8527.4098 1.118343
#> [48,] 47 17.204236 28.3512586 405.91476 691.6103 8420.3238 1.101818
#> [49,] 48 15.366800 27.9306147 10302.51876 617.7454 8295.3926 1.088974
#> [50,] 49 58.310578 28.3879984 7678.22510 2344.0852 8431.2355 1.160799
#> [51,] 50 67.693318 29.6506490 5722.40067 2721.2714 8806.2428 1.248497
#> [52,] 51 63.820866 30.9258680 4264.77072 2565.5988 9184.9828 1.291835
#> [53,] 52 55.696651 31.9316245 3178.43336 2239.0054 9483.6925 1.294505
#> [54,] 53 47.097157 32.6054283 2368.81166 1893.3057 9683.8122 1.272182
#> [55,] 54 39.433221 32.9713290 1765.41964 1585.2155 9792.4847 1.239064
#> [56,] 55 33.084532 33.0809988 1315.72575 1329.9982 9825.0566 1.204441
#> [57,] 56 28.012600 32.9890478 980.57946 1126.1065 9797.7472 1.173085
#> [58,] 57 24.034885 32.7438336 730.80282 966.2024 9724.9186 1.146742
#> [59,] 58 20.941701 32.3850143 544.65022 841.8564 9618.3492 1.125519
#> [60,] 59 18.541531 31.9438320 405.91506 745.3695 9487.3181 1.108805
#> [61,] 60 16.674741 31.4443342 10302.51898 670.3246 9338.9673 1.095780
#> [62,] 61 59.589810 31.8245949 7678.22527 2395.5103 9451.9047 1.167130
#> [63,] 62 68.944471 33.0118152 5722.40080 2771.5677 9804.5091 1.254535
#> [64,] 63 65.044556 34.2132595 4264.77082 2614.7912 10161.3381 1.297815
#> [65,] 64 56.893482 35.1468606 3178.43344 2287.1180 10438.6176 1.300516
#> [66,] 65 48.267719 35.7500925 2368.81171 1940.3623 10617.7775 1.278214
#> [67,] 66 40.578090 36.0469705 1765.41968 1631.2392 10705.9503 1.245063
#> [68,] 67 34.204272 36.0891326 1315.72578 1375.0117 10718.4724 1.210354
#> [69,] 68 29.107762 35.9311556 980.57949 1170.1320 10671.5532 1.178874
#> [70,] 69 25.106009 35.6213646 730.80283 1009.2616 10579.5453 1.152390
#> [71,] 70 21.989315 35.1993858 544.65023 883.9705 10454.2176 1.131019
#> [72,] 71 19.566151 34.6964304 405.91507 786.5593 10304.8398 1.114160
#> [73,] 72 17.676872 34.1365154 10302.51900 710.6103 10138.5451 1.100995
#> [74,] 73 60.569944 34.4576850 7678.22529 2434.9117 10233.9324 1.171984
#> [75,] 74 69.903092 35.5871111 5722.40081 2810.1043 10569.3720 1.259164
#> [76,] 75 65.982135 36.7320299 4264.77083 2652.4818 10909.4129 1.302398
#> [77,] 76 57.810450 37.6103476 3178.43348 2323.9801 11170.2732 1.305123
#> [78,] 77 49.164562 38.1595080 2368.81180 1976.4154 11333.3739 1.282835
#> [79,] 78 41.455272 38.4035002 1765.41973 1666.5019 11405.8396 1.249659
#> [80,] 79 35.062201 38.3939383 1315.72582 1409.5005 11402.9997 1.214884
#> [81,] 80 29.946863 38.1853726 980.57952 1203.8639 11341.0557 1.183311
#> [82,] 81 25.926693 37.8261035 730.80288 1042.2530 11234.3527 1.156718
#> [83,] 82 22.791988 37.3557324 544.65026 916.2379 11094.6525 1.135234
#> [84,] 83 20.351205 36.8054470 405.91508 818.1184 10931.2178 1.118263
#> [85,] 84 18.444695 36.1992409 10302.51901 741.4767 10751.1745 1.104993
#> [86,] 85 61.320914 36.4751353 7678.22530 2465.1007 10833.1152 1.175705
#> [87,] 86 70.637579 37.5602801 5722.40082 2839.6307 11155.4032 1.262712
#> [88,] 87 66.700500 38.6618895 4264.77084 2681.3601 11482.5812 1.305911
#> [89,] 88 58.513080 39.4978468 3178.43345 2352.2258 11730.8605 1.308653
#> [90,] 89 49.851769 40.0055782 2368.81173 2004.0411 11881.6567 1.286376
#> [91,] 90 42.127372 40.2090519 1765.41969 1693.5203 11942.0884 1.253181
#> [92,] 91 35.719548 40.1598597 1315.72578 1435.9258 11927.4783 1.218356
#> [93,] 92 30.589780 39.9125336 980.57949 1229.7092 11854.0225 1.186710
#> [94,] 93 26.555494 39.5153548 730.80290 1067.5309 11736.0604 1.160034
#> [95,] 94 23.406989 39.0079061 544.65026 940.9610 11585.3481 1.138465
#> [96,] 95 20.952707 38.4213568 405.91511 842.2988 11411.1430 1.121408
#> [97,] 96 19.032995 37.7796828 10302.51903 765.1264 11220.5658 1.108056
#> [98,] 97 61.896300 38.0208879 7678.22533 2488.2313 11292.2037 1.178557
#> [99,] 98 71.200337 39.0721047 5722.40084 2862.2535 11604.4151 1.265432
#> [100,] 99 67.250904 40.1405309 4264.77085 2703.4863 11921.7377 1.308603
#> [101,] 100 59.051404 40.9440332 3178.43346 2373.8665 12160.3779 1.311358
#> [102,] 101 50.378278 41.4200220 2368.81173 2025.2068 12301.7465 1.289089
#> [103,] 102 42.642324 41.5924498 1765.41969 1714.2214 12352.9576 1.255880
#> [104,] 103 36.223198 41.5128932 1315.72579 1456.1726 12329.3293 1.221016
#> [105,] 104 31.082375 41.2358692 980.57949 1249.5115 12247.0531 1.189315
#> [106,] 105 27.037277 40.8096443 730.80289 1086.8985 12120.4644 1.162576
#> [107,] 106 23.878197 40.2737870 544.65026 959.9035 11961.3147 1.140940
#> [108,] 107 21.413573 39.6594527 405.91511 860.8256 11778.8575 1.123818
#> [109,] 108 19.483745 38.9906035 10302.51903 783.2465 11580.2092 1.110403
#> [110,] 109 62.337156 39.2052299 7678.22533 2505.9537 11643.9533 1.180743
#> [111,] 110 71.631516 40.2304514 5722.40084 2879.5870 11948.4441 1.267516
#> [112,] 111 67.672619 41.2734528 4264.77085 2720.4393 12258.2155 1.310666
#> [113,] 112 59.463863 42.0520885 3178.43346 2390.4473 12489.4703 1.313430
#> [114,] 113 50.781684 42.5037564 2368.81173 2041.4237 12623.6156 1.291168
#> [115,] 114 43.036876 42.6523971 1765.41969 1730.0824 12667.7619 1.257947
#> [116,] 115 36.609090 42.5495755 1315.72579 1471.6854 12637.2239 1.223054
#> [117,] 116 31.459797 42.2497972 980.57949 1264.6838 12548.1898 1.191312
#> [118,] 117 27.406414 41.8013174 730.80289 1101.7379 12414.9913 1.164523
#> [119,] 118 24.239232 41.2436937 544.65026 974.4171 12249.3770 1.142837
#> [120,] 119 21.766684 40.6080708 405.91511 875.0207 12060.5970 1.125665
#> [121,] 120 19.829105 39.9184002 20302.51903 797.1300 11855.7649 1.112202
#> [122,] 121 107.050477 41.0324924 15130.99026 4303.4292 12186.6502 1.249043
#> [123,] 122 126.844825 43.7909495 11276.77134 5099.1620 13005.9120 1.414973
#> [124,] 123 119.899134 46.5979816 8404.31263 4819.9452 13839.6005 1.509811
#> [125,] 124 104.277203 48.8817813 6263.53670 4191.9435 14517.8890 1.532337
#> [126,] 125 87.575101 50.5116025 4668.06663 3520.5191 15001.9460 1.503759
#> [127,] 126 72.646547 51.5312919 3479.00032 2920.3912 15304.7937 1.448132
#> [128,] 127 60.275102 52.0410471 2592.81714 2423.0591 15456.1910 1.384224
#> [129,] 128 50.401804 52.1477826 1932.36565 2026.1525 15487.8914 1.323446
#> [130,] 129 42.675052 51.9465291 1440.14670 1715.5371 15428.1191 1.271055
#> [131,] 130 36.685545 51.5153828 1073.30759 1474.7589 15300.0687 1.228368
#> [132,] 131 32.057762 50.9159540 799.91100 1288.7220 15122.0383 1.194685
#> [133,] 132 28.478062 50.1957198 596.15493 1144.8181 14908.1288 1.168547
#> [134,] 133 25.696523 49.3907409 444.30031 1033.0002 14669.0500 1.148393
#> [135,] 134 23.519113 48.5281486 331.12664 945.4684 14412.8601 1.132843
#> [136,] 135 21.797486 47.6282200 246.78095 876.2589 14145.5814 1.120778
#> [137,] 136 20.419265 46.7060297 183.92009 820.8544 13871.6908 1.111328
#> [138,] 137 19.299808 45.7727308 137.07125 775.8523 13594.5011 1.103835
#> [139,] 138 18.375583 44.8365348 102.15597 738.6984 13316.4508 1.097806
#> [140,] 139 17.599006 43.9034525 76.13443 707.4800 13039.3254 1.092872
#> [141,] 140 16.934475 42.9778527 56.74120 680.7659 12764.4223 1.088762
#> [142,] 141 16.355370 42.0628801 42.28785 657.4859 12492.6754 1.085273
#> [143,] 142 15.841789 41.1607685 31.51613 636.8399 12224.7482 1.082255
#> [144,] 143 15.378854 40.2730746 23.48822 618.2299 11961.1032 1.079596
#> [145,] 144 14.955423 39.4008531 20017.50522 601.2080 11702.0534 1.077213
#> [146,] 145 103.314240 40.3844462 14918.57614 4153.2325 11994.1805 1.222925
#> [147,] 146 123.961694 43.0512466 11118.46410 4983.2601 12786.2203 1.394725
#> [148,] 147 117.655451 45.7955294 8286.32996 4729.7491 13601.2722 1.493650
#> [149,] 148 102.512890 48.0380400 6175.60699 4121.0182 14267.2979 1.519280
#> [150,] 149 86.170411 49.6424653 4602.53468 3464.0505 14743.8122 1.493194
#> [151,] 150 71.512013 50.6484940 3430.16089 2874.7829 15042.6027 1.439608
#> [152,] 151 59.343910 51.1532236 2556.41827 2385.6252 15192.5074 1.377355
#> [153,] 152 49.624073 51.2612578 1905.23843 1994.8877 15224.5936 1.317891
#> [154,] 153 42.013548 51.0659065 1419.92943 1688.9446 15166.5742 1.266518
#> [155,] 154 36.112469 50.6439855 1058.24012 1451.7213 15041.2637 1.224604
#> [156,] 155 31.552350 50.0561530 788.68158 1268.4045 14866.6774 1.191503
#> [157,] 156 28.024801 49.3491786 587.78590 1126.5970 14656.7060 1.165800
#> [158,] 157 25.283810 48.5585978 438.06307 1016.4091 14421.9036 1.145973
#> [159,] 158 23.138264 47.7111532 326.47815 930.1582 14170.2125 1.130671
#> [160,] 159 21.441992 46.8268338 243.31653 861.9681 13907.5696 1.118796
#> [161,] 160 20.084241 45.9205017 181.33816 807.3865 13638.3890 1.109495
#> [162,] 161 18.981578 45.0031542 135.14696 763.0594 13365.9368 1.102119
#> [163,] 162 18.071374 44.0828880 100.72185 726.4692 13092.6177 1.096184
#> [164,] 163 17.306718 43.1656309 75.06562 695.7301 12820.1924 1.091328
#> [165,] 164 16.652510 42.2556915 55.94462 669.4309 12549.9404 1.087283
#> [166,] 165 16.082506 41.3561716 41.69419 646.5168 12282.7830 1.083849
#> [167,] 166 15.577086 40.4692749 31.07369 626.1989 12019.3746 1.080879
#> [168,] 167 15.121578 39.5965376 23.15848 607.8874 11760.1717 1.078263
#> [169,] 168 14.705000 38.7390007 20017.25947 591.1410 11505.4832 1.075919
#> [170,] 169 103.070213 39.7369981 14918.39299 4143.4225 11801.8884 1.221761
#> [171,] 170 123.723692 42.4179179 11118.32760 4973.6924 12598.1216 1.393638
#> [172,] 171 117.423172 45.1760335 8286.22823 4720.4115 13417.2819 1.492574
#> [173,] 172 102.286081 47.4320907 6175.53117 4111.9005 14087.3309 1.518183
#> [174,] 173 85.948858 49.0497782 4602.47818 3455.1441 14567.7841 1.492071
#> [175,] 174 71.295530 50.0687876 3430.11878 2866.0803 14870.4299 1.438469
#> [176,] 175 59.132332 50.5862203 2556.38688 2377.1197 15024.1074 1.376218
#> [177,] 176 49.417254 50.7066840 1905.21504 1986.5736 15059.8851 1.316771
#> [178,] 177 41.811353 50.5234935 1419.91199 1680.8164 15005.4776 1.265424
#> [179,] 178 35.914777 50.1134693 1058.22713 1443.7740 14883.7004 1.223541
#> [180,] 179 31.359045 49.5372747 788.67190 1260.6336 14712.5706 1.190471
#> [181,] 180 27.835774 48.8416844 587.77869 1118.9981 14505.9803 1.164799
#> [182,] 181 25.098958 48.0622391 438.05770 1008.9781 14274.4850 1.145002
#> [183,] 182 22.957489 47.2256864 326.47414 922.8911 14026.0289 1.129727
#> [184,] 183 21.265199 46.3520206 243.31354 854.8610 13766.5501 1.117877
#> [185,] 184 19.911340 45.4561087 181.33593 800.4359 13500.4643 1.108598
#> [186,] 185 18.812480 44.5489532 135.14530 756.2617 13231.0391 1.101245
#> [187,] 186 17.905993 43.6386555 100.72061 719.8209 12960.6807 1.095330
#> [188,] 187 17.144972 42.7311483 75.06469 689.2279 12691.1510 1.090494
#> [189,] 188 16.494318 41.8307449 55.94393 663.0716 12423.7312 1.086468
#> [190,] 189 15.927789 40.9405519 41.69367 640.2971 12159.3439 1.083053
#> [191,] 190 15.425766 40.0627775 31.07331 620.1158 11898.6449 1.080101
#> [192,] 191 14.973581 39.1989623 23.15820 601.9380 11642.0918 1.077503
#> [193,] 192 14.560252 38.3501517 20017.25925 585.3221 11389.9950 1.075175
#> [194,] 193 102.928643 39.3566839 14918.39283 4137.7314 11688.9351 1.221090
#> [195,] 194 123.585231 42.0459512 11118.32748 4968.1263 12487.6475 1.393009
#> [196,] 195 117.287750 44.8122311 8286.22814 4714.9675 13309.2326 1.491950
#> [197,] 196 102.153632 47.0762734 6175.53111 4106.5760 13981.6532 1.517545
#> [198,] 197 85.819316 48.7017708 4602.47813 3449.9365 14464.4259 1.491415
#> [199,] 198 71.168831 49.7284186 3430.11875 2860.9870 14769.3403 1.437804
#> [200,] 199 59.008414 50.2533221 2556.38685 2372.1383 14925.2367 1.375554
#> [201,] 200 49.296057 50.3810926 1905.21502 1981.7015 14963.1845 1.316115
#> [202,] 201 41.692816 50.2050486 1419.91198 1676.0512 14910.8994 1.264784
#> [203,] 202 35.798842 49.8020140 1058.22712 1439.1134 14791.1981 1.222918
#> [204,] 203 31.245654 49.2326555 788.67189 1256.0753 14622.0987 1.189867
#> [205,] 204 27.724872 48.5437514 587.77868 1114.5398 14417.4942 1.164213
#> [206,] 205 24.990490 47.7708454 438.05769 1004.6177 14187.9411 1.144432
#> [207,] 206 22.851402 46.9406886 326.47414 918.6264 13941.3845 1.129172
#> [208,] 207 21.161441 46.0732783 243.31353 850.6899 13683.7637 1.117337
#> [209,] 208 19.809859 45.1834846 181.33593 796.3563 13419.4949 1.108072
#> [210,] 209 18.713226 44.2823129 135.14529 752.2717 13151.8469 1.100731
#> [211,] 210 17.808918 43.3778677 100.72061 715.9185 12883.2267 1.094829
#> [212,] 211 17.050028 42.4760846 75.06469 685.4111 12615.3971 1.090005
#> [213,] 212 16.401458 41.5812797 55.94393 659.3386 12349.6401 1.085990
#> [214,] 213 15.836967 40.6965622 41.69367 636.6461 12086.8790 1.082586
#> [215,] 214 15.336938 39.8241432 31.07331 616.5449 11827.7705 1.079645
#> [216,] 215 14.886702 38.9655658 23.15820 598.4454 11572.7730 1.077056
#> [217,] 216 14.475280 38.1218780 20017.25925 581.9063 11322.1978 1.074739
#> [218,] 217 102.845536 39.1334207 14918.39283 4134.3905 11622.6259 1.220696
#> [219,] 218 123.503948 41.8275884 11118.32748 4964.8587 12422.7938 1.392640
#> [220,] 219 117.208251 44.5986612 8286.22814 4711.7717 13245.8024 1.491584
#> [221,] 220 102.075878 46.8673912 6175.53111 4103.4503 13919.6152 1.517170
#> [222,] 221 85.743269 48.4974734 4602.47813 3446.8794 14403.7496 1.491031
#> [223,] 222 71.094453 49.5286054 3430.11875 2857.9970 14709.9958 1.437413
#> [224,] 223 58.935669 50.0578945 2556.38685 2369.2139 14867.1947 1.375163
#> [225,] 224 49.224908 50.1899545 1905.21502 1978.8413 14906.4165 1.315730
#> [226,] 225 41.623229 50.0181058 1419.91198 1673.2538 14855.3774 1.264407
#> [227,] 226 35.730782 49.6191744 1058.22712 1436.3774 14736.8948 1.222553
#> [228,] 227 31.179088 49.0538292 788.67189 1253.3993 14568.9873 1.189512
#> [229,] 228 27.659767 48.3688501 587.77868 1111.9226 14365.5485 1.163868
#> [230,] 229 24.926814 47.5997831 438.05769 1002.0579 14137.1356 1.144097
#> [231,] 230 22.789124 46.7733810 326.47414 916.1228 13891.6941 1.128847
#> [232,] 231 21.100530 45.9096429 243.31353 848.2413 13635.1639 1.117020
#> [233,] 232 19.750285 45.0234408 181.33593 793.9615 13371.9619 1.107763
#> [234,] 233 18.654959 44.1257820 135.14529 749.9294 13105.3573 1.100430
#> [235,] 234 17.751931 43.2247725 100.72061 713.6276 12837.7574 1.094535
#> [236,] 235 16.994291 42.3263497 75.06469 683.1705 12570.9259 1.089718
#> [237,] 236 16.346944 41.4348314 55.94393 657.1472 12306.1449 1.085710
#> [238,] 237 15.783650 40.5533284 41.69367 634.5027 12044.3385 1.082312
#> [239,] 238 15.284791 39.6840532 31.07331 614.4486 11786.1638 1.079377
#> [240,] 239 14.835700 38.8285506 23.15820 596.3951 11532.0795 1.076794
#> [241,] 240 14.425398 37.9878702 17.25925 579.9010 11282.3975 1.074483
# Gives a rxSolve data.frame
mod1 %>% rxSolve(theta, ev, inits)
#> ── Solved rxode2 object ──
#> ── Parameters (x$params): ──
#> V2 V3 KA CL Q Kin Kout EC50
#> 40.200 297.000 0.294 18.600 10.500 1.000 1.000 200.000
#> ── Initial Conditions (x$inits): ──
#> depot centr peri eff
#> 0 0 0 1
#> ── First part of data (object): ──
#> # A tibble: 241 × 7
#> time C2 C3 depot centr peri eff
#> [h] <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0 0 0 10000 0 0 1
#> 2 1 44.4 0.920 7453. 1784. 273. 1.08
#> 3 2 54.9 2.67 5554. 2206. 794. 1.18
#> 4 3 51.9 4.46 4140. 2087. 1324. 1.23
#> 5 4 44.5 5.98 3085. 1789. 1776. 1.23
#> 6 5 36.5 7.18 2299. 1467. 2132. 1.21
#> # … with 235 more rows
# You can change the return type as well
# to give a tibble just like you wanted (faster
# than rxSolve data.frame)
rxSolve(mod1, theta, ev, inits,
returnType = "tibble")
#> # A tibble: 241 × 7
#> time C2 C3 depot centr peri eff
#> [h] <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0 0 0 10000 0 0 1
#> 2 1 44.4 0.920 7453. 1784. 273. 1.08
#> 3 2 54.9 2.67 5554. 2206. 794. 1.18
#> 4 3 51.9 4.46 4140. 2087. 1324. 1.23
#> 5 4 44.5 5.98 3085. 1789. 1776. 1.23
#> 6 5 36.5 7.18 2299. 1467. 2132. 1.21
#> 7 6 29.3 8.07 1714. 1178. 2396. 1.18
#> 8 7 23.4 8.70 1277. 939. 2583. 1.15
#> 9 8 18.7 9.12 952. 750. 2709. 1.12
#> 10 9 15.0 9.39 709. 602. 2787. 1.10
#> # … with 231 more rows
# You can also return "data.frame" or "data.table"
# The example below shows data.table
rxSolve(mod1, theta, ev, inits,
returnType = "data.table")
#> time C2 C3 depot centr peri eff
#> 1: 0 [h] 0.00000 0.0000000 10000.00000 0.0000 0.0000 1.000000
#> 2: 1 [h] 44.37555 0.9198298 7452.76491 1783.8970 273.1895 1.084664
#> 3: 2 [h] 54.88296 2.6729825 5554.37049 2206.2948 793.8758 1.180825
#> 4: 3 [h] 51.90343 4.4564927 4139.54175 2086.5177 1323.5783 1.228914
#> 5: 4 [h] 44.49738 5.9807076 3085.10315 1788.7947 1776.2702 1.234610
#> ---
#> 237: 236 [h] 16.34694 41.4348314 55.94393 657.1472 12306.1449 1.085710
#> 238: 237 [h] 15.78365 40.5533284 41.69367 634.5027 12044.3385 1.082312
#> 239: 238 [h] 15.28479 39.6840532 31.07331 614.4486 11786.1638 1.079377
#> 240: 239 [h] 14.83570 38.8285506 23.15820 596.3951 11532.0795 1.076794
#> 241: 240 [h] 14.42540 37.9878702 17.25925 579.9010 11282.3975 1.074483Created on 2023-01-24 with reprex v2.0.2 Session infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23 ucrt)
#> os Windows 10 x64 (build 19044)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz America/Chicago
#> date 2023-01-24
#> pandoc 2.18 @ C:/R/Rstudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.1)
#> backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
#> cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.1)
#> checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.1)
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
#> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
#> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.1)
#> data.table 1.14.2 2021-09-27 [1] CRAN (R 4.2.1)
#> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.1)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)
#> dparser 1.3.1-9 2022-11-10 [1] CRAN (R 4.2.2)
#> dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.2.1)
#> evaluate 0.17 2022-10-07 [1] CRAN (R 4.2.1)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
#> ggplot2 3.4.0 2022-11-04 [1] CRAN (R 4.2.2)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.1)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
#> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
#> lotri 0.4.2 2022-06-18 [1] CRAN (R 4.2.2)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.1)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
#> nlme 3.1-157 2022-03-25 [1] CRAN (R 4.2.1)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
#> PreciseSums 0.5 2022-04-22 [1] CRAN (R 4.2.1)
#> qs 0.25.4 2022-08-09 [1] CRAN (R 4.2.1)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
#> RApiSerialize 0.1.2 2022-08-25 [1] CRAN (R 4.2.1)
#> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
#> D RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.17 2022-10-07 [1] CRAN (R 4.2.1)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> rxode2 * 2.0.11.9000 2023-01-20 [1] local
#> rxode2et 2.0.9.9000 2023-01-20 [1] local
#> rxode2ll 2.0.9.9000 2023-01-20 [1] local
#> rxode2parse 2.0.13.9000 2023-01-20 [1] local
#> rxode2random 2.0.9.9000 2023-01-20 [1] local
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
#> stringfish 0.15.7 2022-04-13 [1] CRAN (R 4.2.1)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
#> sys 3.4 2020-07-23 [1] CRAN (R 4.2.1)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.1)
#> units 0.8-0 2022-02-05 [1] CRAN (R 4.2.1)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
#> vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.2)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.33 2022-09-12 [1] CRAN (R 4.2.1)
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.1)
#>
#> [1] C:/R/R-4.2.1/library
#>
#> D ── DLL MD5 mismatch, broken installation.
#>
#> ────────────────────────────────────────────────────────────────────────────── |
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I'm also converting this to a discussion. If you find a behavior that is plainly different from a prior version of |
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Scripts originally written with RxODE do not work with newer R systems as RxODE is not available as an install package, and the functionality is slightly different. (e.g. return from a sim is a matrix not a data table with rxode2 and needs coercing to a tibble)
It would be good if a user has rxode2 installed, then scripts originally written for RxODE still work out of the box
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