Rank predicted doses of different agents
rank.mbnma.predict.RdRanks predictions at different doses from best to worst.
# S3 method for class 'mbnma.predict'
rank(x, lower_better = TRUE, rank.doses = NULL, ...)Arguments
- x
An object on which to apply the rank method
- lower_better
Indicates whether negative responses are better (
TRUE) or positive responses are better (FALSE)- rank.doses
A list of numeric vectors. Each named element corresponds to an agent (as named/coded in
predict), and each number within the vector for that element corresponds to the dose for that agent. Doses of agents specified inrank.dosesmust be a subset of those for which responses have been predicted inpredict. If left asNULL(the default) then all doses of all agents inpredictwill be ranked.- ...
Arguments to be passed to methods
Value
An object of class("mbnma.rank") which is a list containing a summary data
frame, a matrix of rankings for each MCMC iteration, and a matrix of probabilities
that each agent has a particular rank, for each parameter that has been ranked.
Details
If predict contains multiple predictions at dose=0, then only the first of these
will be included, to avoid duplicating rankings.
Examples
# \donttest{
# Using the triptans data
network <- mbnma.network(triptans)
#> Values for `agent` with dose = 0 have been recoded to `Placebo`
#> agent is being recoded to enforce sequential numbering
# Rank all predictions from a log-linear dose-response MBNMA
loglin <- mbnma.run(network, fun=dloglin())
#> `likelihood` not given by user - set to `binomial` based on data provided
#> `link` not given by user - set to `logit` based on assigned value for `likelihood`
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 182
#> Unobserved stochastic nodes: 77
#> Total graph size: 3644
#>
#> Initializing model
#>
pred <- predict(loglin, E0 = 0.5)
rank <- rank(pred)
summary(rank)
#> $Predictions
#> rank.param mean sd 2.5% 25% 50% 75% 97.5%
#> 1 Placebo_0 184.00000 0.00000000 184.000 184 184 184 184.000
#> 2 eletriptan_0.069 175.89133 1.63638345 172.000 175 176 177 178.000
#> 3 eletriptan_0.14 163.68733 3.46298094 154.000 163 164 166 168.000
#> 4 eletriptan_0.21 151.46900 4.77437297 139.000 149 153 155 158.000
#> 5 eletriptan_0.28 138.50667 5.21072670 128.000 135 139 142 147.000
#> 6 eletriptan_0.34 128.53567 5.12739290 120.000 124 129 132 138.000
#> 7 eletriptan_0.41 118.01900 4.70255360 110.000 114 117 121 128.000
#> 8 eletriptan_0.48 107.84833 4.53396620 99.000 105 108 111 117.000
#> 9 eletriptan_0.55 97.87167 4.42044990 89.000 95 98 101 107.000
#> 10 eletriptan_0.62 89.33533 4.19707319 81.000 87 89 92 98.000
#> 11 eletriptan_0.69 81.44567 4.54319213 72.000 78 82 85 90.000
#> 12 eletriptan_0.76 73.74333 4.82975821 64.000 71 74 77 83.000
#> 13 eletriptan_0.83 66.38600 5.12306086 56.000 63 67 70 76.000
#> 14 eletriptan_0.9 59.14200 5.42484829 48.000 56 59 63 70.000
#> 15 eletriptan_0.97 52.16900 5.42422773 42.000 48 52 56 63.000
#> 16 eletriptan_1 48.83167 5.23518223 39.000 45 49 52 60.000
#> 17 eletriptan_1.1 41.92267 4.10661754 34.000 39 42 44 51.000
#> 18 eletriptan_1.2 37.68533 3.26085816 33.000 35 38 40 44.000
#> 19 eletriptan_1.3 34.81133 2.85127717 31.000 32 35 37 41.000
#> 20 eletriptan_1.4 32.33600 2.58456908 29.000 30 32 34 38.000
#> 21 eletriptan_1.5 30.09767 2.25221788 27.000 28 29 31 36.000
#> 22 eletriptan_1.6 28.07600 1.95946519 25.000 27 28 29 33.000
#> 23 eletriptan_1.7 26.20333 1.68471609 24.000 25 26 27 31.000
#> 24 eletriptan_1.8 24.41867 1.52430073 22.000 23 24 25 28.025
#> 25 eletriptan_1.9 22.69067 1.43119845 20.000 22 23 23 26.000
#> 26 eletriptan_2 21.04500 1.37074237 18.000 20 21 22 24.000
#> 27 sumatriptan_0.069 179.81467 1.11418073 177.000 179 180 181 181.000
#> 28 sumatriptan_0.14 172.32300 2.16184231 167.000 172 173 174 175.000
#> 29 sumatriptan_0.21 165.77867 3.25482353 156.000 165 167 168 170.000
#> 30 sumatriptan_0.28 158.38667 4.14361502 146.000 157 159 161 163.000
#> 31 sumatriptan_0.34 152.16400 4.73271277 139.000 150 153 156 159.000
#> 32 sumatriptan_0.41 144.70600 5.08771648 133.000 142 146 149 152.000
#> 33 sumatriptan_0.48 137.50900 5.15060792 128.000 134 138 141 146.000
#> 34 sumatriptan_0.55 131.17333 5.05092000 122.000 127 132 135 140.000
#> 35 sumatriptan_0.62 124.98967 4.78705183 117.000 121 125 129 134.000
#> 36 sumatriptan_0.69 119.53767 4.52069981 112.000 116 119 123 129.000
#> 37 sumatriptan_0.76 114.11500 4.27401420 107.000 111 113 117 123.000
#> 38 sumatriptan_0.83 108.87133 4.14702835 101.000 106 108 111 118.000
#> 39 sumatriptan_0.9 103.67133 4.00674384 96.000 101 103 106 112.000
#> 40 sumatriptan_0.97 98.82833 3.79732412 92.000 96 99 101 107.000
#> 41 sumatriptan_1 96.31400 3.72371132 89.000 94 96 98 104.000
#> 42 sumatriptan_1.1 90.54700 3.61664915 83.000 88 91 93 98.000
#> 43 sumatriptan_1.2 85.08700 3.75297117 77.000 83 85 88 92.000
#> 44 sumatriptan_1.3 79.70900 3.95915108 72.000 77 80 82 87.000
#> 45 sumatriptan_1.4 74.54300 4.06033411 66.000 72 75 77 82.000
#> 46 sumatriptan_1.5 69.57367 4.13524767 61.000 67 70 72 77.000
#> 47 sumatriptan_1.6 64.82233 4.28760567 56.000 62 65 68 73.000
#> 48 sumatriptan_1.7 60.11267 4.48099684 51.000 57 60 63 69.000
#> 49 sumatriptan_1.8 55.43400 4.63006010 46.000 52 56 59 64.000
#> 50 sumatriptan_1.9 50.91567 4.63699491 42.000 48 51 54 60.000
#> 51 sumatriptan_2 46.71967 4.48431893 38.000 44 47 50 56.000
#> 52 frovatriptan_0.069 177.70100 1.59575932 174.000 177 178 178 180.000
#> 53 frovatriptan_0.14 168.31533 3.57894321 159.000 167 169 171 173.000
#> 54 frovatriptan_0.21 158.67233 5.51541245 144.000 156 159 162 168.000
#> 55 frovatriptan_0.28 148.79167 7.04675927 133.000 144 150 154 161.000
#> 56 frovatriptan_0.34 140.28500 7.86513796 125.000 135 141 146 155.000
#> 57 frovatriptan_0.41 131.13933 8.40083989 116.000 125 131 137 148.000
#> 58 frovatriptan_0.48 122.77567 8.76776097 107.000 117 122 129 141.000
#> 59 frovatriptan_0.55 114.86767 9.34130119 97.000 109 115 121 134.000
#> 60 frovatriptan_0.62 107.30133 9.81192928 89.000 100 107 114 127.000
#> 61 frovatriptan_0.69 100.23267 10.14817856 82.000 93 100 107 121.000
#> 62 frovatriptan_0.76 93.60267 10.39121995 74.000 87 93 100 115.000
#> 63 frovatriptan_0.83 87.42933 10.72557779 67.000 80 87 94 110.000
#> 64 frovatriptan_0.9 81.50667 11.14941218 59.000 74 82 88 104.000
#> 65 frovatriptan_0.97 75.80500 11.68402672 52.000 68 76 83 98.000
#> 66 frovatriptan_1 72.84867 11.87355993 49.000 65 73 81 96.000
#> 67 frovatriptan_1.1 65.66867 12.34283868 44.000 57 66 74 89.025
#> 68 frovatriptan_1.2 59.07933 12.29054075 41.000 49 59 68 84.000
#> 69 frovatriptan_1.3 53.30700 11.74271610 38.000 43 51 61 79.000
#> 70 frovatriptan_1.4 48.37467 10.78621369 35.000 40 45 55 74.000
#> 71 frovatriptan_1.5 44.23133 9.74112150 33.000 38 41 49 69.000
#> 72 frovatriptan_1.6 40.68233 8.69927087 30.000 35 38 43 65.000
#> 73 frovatriptan_1.7 37.64700 7.78566609 28.000 33 36 39 60.000
#> 74 frovatriptan_1.8 34.91500 7.06019762 25.000 31 34 37 56.000
#> 75 frovatriptan_1.9 32.40433 6.47555600 22.000 29 32 34 51.000
#> 76 frovatriptan_2 30.09900 6.07460555 20.000 27 30 33 46.000
#> 77 almotriptan_0.069 179.78633 1.25746052 177.000 179 180 181 181.000
#> 78 almotriptan_0.14 172.28067 2.35394844 166.975 171 173 174 175.000
#> 79 almotriptan_0.21 165.55467 3.62492183 156.000 164 166 168 170.000
#> 80 almotriptan_0.28 158.28500 4.57632559 145.000 156 159 161 164.000
#> 81 almotriptan_0.34 151.99800 5.29496694 139.000 149 153 156 160.000
#> 82 almotriptan_0.41 144.63800 5.87365212 132.000 141 145 149 154.000
#> 83 almotriptan_0.48 137.53300 6.06249362 126.000 133 138 142 148.000
#> 84 almotriptan_0.55 131.07433 6.10911191 120.000 126 131 136 142.000
#> 85 almotriptan_0.62 125.06400 6.03236000 115.000 120 125 129 137.000
#> 86 almotriptan_0.69 119.46867 5.93594390 109.000 115 119 124 131.000
#> 87 almotriptan_0.76 114.08367 5.97315322 103.000 110 114 118 126.000
#> 88 almotriptan_0.83 108.82267 6.07729633 98.000 105 108 113 121.000
#> 89 almotriptan_0.9 103.72500 6.11237777 93.000 100 103 107 116.000
#> 90 almotriptan_0.97 98.86733 6.09032815 88.000 95 99 103 111.000
#> 91 almotriptan_1 96.31800 6.05726337 85.000 92 96 100 109.000
#> 92 almotriptan_1.1 90.46733 6.06551974 78.000 87 90 94 103.000
#> 93 almotriptan_1.2 84.97500 6.32579747 72.000 81 85 89 97.000
#> 94 almotriptan_1.3 79.65300 6.62645413 66.000 75 80 84 92.000
#> 95 almotriptan_1.4 74.50833 6.95169326 60.000 70 75 79 87.000
#> 96 almotriptan_1.5 69.52333 7.27757583 54.975 65 70 74 83.000
#> 97 almotriptan_1.6 64.65667 7.63895107 49.000 60 65 70 79.000
#> 98 almotriptan_1.7 59.87600 7.93067394 44.000 54 60 65 75.000
#> 99 almotriptan_1.8 55.30867 8.05069331 40.000 49 56 61 70.000
#> 100 almotriptan_1.9 50.97700 7.93524587 37.000 45 51 57 67.000
#> 101 almotriptan_2 47.03467 7.57574609 34.000 41 46 52 63.000
#> 102 zolmitriptan_0.34 144.28033 5.54490714 132.000 141 145 148 153.000
#> 103 zolmitriptan_0.69 106.58367 5.51529444 96.000 103 106 110 118.000
#> 104 zolmitriptan_1 81.27967 5.76858262 70.000 77 82 85 92.000
#> 105 zolmitriptan_1.4 54.77367 7.15016187 41.000 50 55 60 69.000
#> 106 zolmitriptan_1.7 41.06467 4.99841438 33.000 38 41 44 53.000
#> 107 zolmitriptan_2.1 33.43967 3.27647244 28.000 31 33 36 40.000
#> 108 zolmitriptan_2.4 29.48367 2.81360481 25.000 28 29 31 36.000
#> 109 zolmitriptan_2.8 25.44800 2.27472067 22.000 24 25 27 31.000
#> 110 zolmitriptan_3.1 22.79600 1.80225786 21.000 21 22 24 27.000
#> 111 zolmitriptan_3.4 20.76133 1.23701858 20.000 20 20 21 24.000
#> 112 zolmitriptan_3.8 19.17767 0.60406086 19.000 19 19 19 21.000
#> 113 zolmitriptan_4.1 18.05300 0.33500509 18.000 18 18 18 19.000
#> 114 zolmitriptan_4.5 17.01000 0.15024710 17.000 17 17 17 17.000
#> 115 zolmitriptan_4.8 16.00400 0.12106012 16.000 16 16 16 16.000
#> 116 zolmitriptan_5.2 15.00200 0.08163877 15.000 15 15 15 15.000
#> 117 zolmitriptan_5.5 14.00167 0.06581793 14.000 14 14 14 14.000
#> 118 zolmitriptan_5.9 13.00100 0.04081938 13.000 13 13 13 13.000
#> 119 zolmitriptan_6.2 12.00033 0.01825742 12.000 12 12 12 12.000
#> 120 zolmitriptan_6.6 11.00033 0.01825742 11.000 11 11 11 11.000
#> 121 zolmitriptan_6.9 10.00000 0.00000000 10.000 10 10 10 10.000
#> 122 zolmitriptan_7.2 9.00000 0.00000000 9.000 9 9 9 9.000
#> 123 zolmitriptan_7.6 8.00000 0.00000000 8.000 8 8 8 8.000
#> 124 zolmitriptan_7.9 7.00000 0.00000000 7.000 7 7 7 7.000
#> 125 zolmitriptan_8.3 6.00000 0.00000000 6.000 6 6 6 6.000
#> 126 zolmitriptan_8.6 5.00000 0.00000000 5.000 5 5 5 5.000
#> 127 zolmitriptan_9 4.00000 0.00000000 4.000 4 4 4 4.000
#> 128 zolmitriptan_9.3 3.00000 0.00000000 3.000 3 3 3 3.000
#> 129 zolmitriptan_9.7 2.00000 0.00000000 2.000 2 2 2 2.000
#> 130 zolmitriptan_10 1.00000 0.00000000 1.000 1 1 1 1.000
#> 131 naratriptan_0.069 182.98433 0.14408843 183.000 183 183 183 183.000
#> 132 naratriptan_0.14 179.95167 1.56166903 178.000 179 180 181 182.000
#> 133 naratriptan_0.21 176.56167 2.06775783 173.000 175 177 178 181.000
#> 134 naratriptan_0.28 173.36067 2.56634271 168.000 172 173 175 179.000
#> 135 naratriptan_0.34 170.59300 3.00328002 164.000 169 171 173 176.000
#> 136 naratriptan_0.41 167.57833 3.64201666 160.000 165 168 170 175.000
#> 137 naratriptan_0.48 164.58633 4.32104583 155.975 162 165 168 173.000
#> 138 naratriptan_0.55 161.59033 5.00494986 151.000 158 162 165 171.000
#> 139 naratriptan_0.62 158.62367 5.67657007 146.000 155 159 162 169.000
#> 140 naratriptan_0.69 155.63733 6.40386415 142.000 152 156 160 167.000
#> 141 naratriptan_0.76 152.71267 7.04674808 138.000 148 153 158 165.000
#> 142 naratriptan_0.83 149.79200 7.67700342 134.000 145 150 155 164.000
#> 143 naratriptan_0.9 146.94233 8.26384323 130.000 141 147 153 162.000
#> 144 naratriptan_0.97 144.10900 8.86957395 126.000 138 144 151 160.000
#> 145 naratriptan_1 142.35100 9.10648716 123.000 137 142 149 159.000
#> 146 naratriptan_1.1 138.85400 9.92032366 118.000 133 139 146 158.000
#> 147 naratriptan_1.2 135.44000 10.68792827 113.000 129 135 143 155.000
#> 148 naratriptan_1.3 132.07367 11.46289838 108.000 125 132 140 153.000
#> 149 naratriptan_1.4 128.79867 12.26954137 102.000 122 129 137 151.000
#> 150 naratriptan_1.5 125.55700 13.01895728 97.000 118 126 134 150.000
#> 151 naratriptan_1.6 122.37233 13.76377547 93.000 114 123 132 148.000
#> 152 naratriptan_1.7 119.26967 14.51715752 89.000 111 120 129 146.000
#> 153 naratriptan_1.8 116.15033 15.21217287 84.000 107 117 127 144.000
#> 154 naratriptan_1.9 113.13967 15.89298657 80.000 103 114 124 143.000
#> 155 naratriptan_2 110.17967 16.52001887 76.000 99 111 122 141.000
#> 156 rizatriptan_0.034 181.66633 0.75929270 180.000 181 182 182 182.000
#> 157 rizatriptan_0.069 174.76333 1.77097930 170.000 174 175 176 177.000
#> 158 rizatriptan_0.1 169.28733 2.62457661 162.000 168 170 171 172.000
#> 159 rizatriptan_0.14 161.79900 3.66001788 151.000 161 163 164 166.000
#> 160 rizatriptan_0.17 156.23633 4.32389237 144.000 155 157 159 162.000
#> 161 rizatriptan_0.21 148.38867 4.88353231 136.000 146 149 152 155.000
#> 162 rizatriptan_0.24 142.26933 5.14304805 131.000 139 143 146 151.000
#> 163 rizatriptan_0.28 134.73433 5.10572659 125.000 131 135 138 144.000
#> 164 rizatriptan_0.31 129.32033 5.02760501 121.000 125 130 133 139.000
#> 165 rizatriptan_0.34 124.10567 4.79285841 116.000 120 124 128 133.000
#> 166 rizatriptan_0.38 117.82567 4.58267842 110.000 115 117 121 127.000
#> 167 rizatriptan_0.41 112.90867 4.38688270 105.000 110 112 116 122.000
#> 168 rizatriptan_0.45 106.62667 4.41706453 98.000 104 106 109 116.000
#> 169 rizatriptan_0.48 101.74333 4.38480684 94.000 99 102 105 111.000
#> 170 rizatriptan_0.52 95.90600 4.21407366 88.000 93 96 99 105.000
#> 171 rizatriptan_0.55 91.69933 4.09339120 83.000 89 92 94 100.000
#> 172 rizatriptan_0.59 86.82200 4.12674117 78.000 84 87 90 94.025
#> 173 rizatriptan_0.62 82.93967 4.31866996 74.000 80 83 86 91.000
#> 174 rizatriptan_0.66 78.18300 4.45362653 69.000 75 78 81 86.000
#> 175 rizatriptan_0.69 74.44833 4.57773406 65.000 71 74 78 83.000
#> 176 rizatriptan_0.72 70.77033 4.67135174 61.000 68 71 74 80.000
#> 177 rizatriptan_0.76 66.26000 4.89248186 56.000 63 66 70 75.000
#> 178 rizatriptan_0.79 62.65000 5.05582375 52.000 59 63 66 72.000
#> 179 rizatriptan_0.83 58.13833 5.27925065 47.975 55 58 62 68.000
#> 180 rizatriptan_0.86 54.56233 5.30567287 44.000 51 54 58 65.000
#> 181 rizatriptan_0.9 50.34067 5.15009262 41.000 47 50 54 60.000
#> 182 rizatriptan_0.93 47.19500 4.88940457 38.000 44 47 50 57.000
#> 183 rizatriptan_0.97 43.76933 4.46804738 36.000 41 44 47 53.000
#> 184 rizatriptan_1 41.29300 4.16600563 34.000 38 41 44 50.000
#>
# Rank selected predictions from an Emax dose-response MBNMA
emax <- mbnma.run(network, fun=demax(), method="random")
#> `likelihood` not given by user - set to `binomial` based on data provided
#> `link` not given by user - set to `logit` based on assigned value for `likelihood`
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 182
#> Unobserved stochastic nodes: 197
#> Total graph size: 4115
#>
#> Initializing model
#>
doses <- list("eletriptan"=c(0,1,2,3), "rizatriptan"=c(0.5,1,2))
pred <- predict(emax, E0 = "rbeta(n, shape1=1, shape2=5)",
exact.doses=doses)
rank <- rank(pred,
rank.doses=list("eletriptan"=c(0,2), "rizatriptan"=2))
# Print and generate summary data frame for `mbnma.rank` object
summary(rank)
#> $Predictions
#> rank.param mean sd 2.5% 25% 50% 75% 97.5%
#> 1 eletriptan_0 3.000000 0.00000000 3 3 3 3 3
#> 2 eletriptan_2 1.998667 0.03649657 2 2 2 2 2
#> 3 rizatriptan_2 1.001333 0.03649657 1 1 1 1 1
#>
print(rank)
#>
#> ================================
#> Ranking of dose-response MBNMA
#> ================================
#>
#> Includes ranking of predictions from dose-response MBNMA
#>
#> 3 predictions ranked with negative responses being `worse`
#>
#> Predictions ranking (from best to worst)
#>
#> |Treatment | Mean| Median| 2.5%| 97.5%|
#> |:-------------|----:|------:|----:|-----:|
#> |rizatriptan_2 | 1| 1| 1| 1|
#> |eletriptan_2 | 2| 2| 2| 2|
#> |eletriptan_0 | 3| 3| 3| 3|
#>
#>
# Plot `mbnma.rank` object
plot(rank)
# }