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 184.000 184.00 184 184.00 184.000
#> 2 eletriptan_0.069 175.91800 1.64929765 172.000 175.00 176 177.00 178.000
#> 3 eletriptan_0.14 163.75533 3.43046074 154.000 163.00 165 166.00 168.000
#> 4 eletriptan_0.21 151.49233 4.73413969 139.000 149.00 153 155.00 158.000
#> 5 eletriptan_0.28 138.53767 5.20028161 128.000 135.00 139 142.00 147.000
#> 6 eletriptan_0.34 128.55667 5.11939368 120.000 125.00 129 132.00 138.025
#> 7 eletriptan_0.41 117.98433 4.76364552 110.000 114.00 117 121.00 128.000
#> 8 eletriptan_0.48 107.74100 4.67809226 99.000 105.00 107 111.00 118.000
#> 9 eletriptan_0.55 97.74900 4.57518412 89.000 95.00 98 101.00 107.000
#> 10 eletriptan_0.62 89.21967 4.35067688 81.000 86.00 89 92.00 98.000
#> 11 eletriptan_0.69 81.27067 4.66297337 72.000 78.00 81 84.00 90.000
#> 12 eletriptan_0.76 73.51433 4.97762194 63.000 70.00 74 77.00 83.000
#> 13 eletriptan_0.83 66.14767 5.27602818 55.000 63.00 66 70.00 76.000
#> 14 eletriptan_0.9 58.84433 5.58520361 48.000 55.00 59 63.00 70.000
#> 15 eletriptan_0.97 51.90467 5.56032529 41.000 48.00 52 56.00 63.000
#> 16 eletriptan_1 48.57667 5.33662959 39.000 45.00 48 52.00 60.000
#> 17 eletriptan_1.1 41.76267 4.19605472 34.000 39.00 42 44.00 51.000
#> 18 eletriptan_1.2 37.63233 3.32046629 32.000 35.00 38 40.00 44.000
#> 19 eletriptan_1.3 34.76433 2.93126685 31.000 32.00 35 37.00 41.000
#> 20 eletriptan_1.4 32.32133 2.65965589 29.000 30.00 32 34.00 38.000
#> 21 eletriptan_1.5 30.06767 2.32871113 27.000 28.00 29 31.00 36.000
#> 22 eletriptan_1.6 28.04067 2.01371081 25.000 27.00 27 29.00 33.000
#> 23 eletriptan_1.7 26.15267 1.75110870 23.000 25.00 26 27.00 31.000
#> 24 eletriptan_1.8 24.34400 1.57601563 22.000 23.00 24 25.00 28.000
#> 25 eletriptan_1.9 22.63133 1.48598596 20.000 22.00 23 23.00 26.000
#> 26 eletriptan_2 20.95167 1.43132111 18.000 20.00 21 22.00 24.000
#> 27 sumatriptan_0.069 179.81933 1.12150739 178.000 179.00 180 181.00 181.000
#> 28 sumatriptan_0.14 172.37367 2.10543365 167.975 172.00 173 174.00 175.000
#> 29 sumatriptan_0.21 165.89100 3.19069154 157.000 165.00 167 168.00 170.000
#> 30 sumatriptan_0.28 158.51733 4.08957305 147.000 157.00 159 161.00 164.000
#> 31 sumatriptan_0.34 152.34267 4.69502509 140.000 150.00 153 156.00 159.000
#> 32 sumatriptan_0.41 144.84967 5.12872640 133.000 142.00 146 149.00 153.000
#> 33 sumatriptan_0.48 137.75400 5.19568562 128.000 134.75 138 142.00 147.000
#> 34 sumatriptan_0.55 131.39567 5.13451416 122.000 127.00 132 135.00 141.000
#> 35 sumatriptan_0.62 125.22067 4.87906152 117.000 121.00 125 129.00 135.000
#> 36 sumatriptan_0.69 119.77067 4.64046523 112.000 116.00 119 123.00 129.000
#> 37 sumatriptan_0.76 114.33433 4.45419291 107.000 111.00 114 117.00 124.000
#> 38 sumatriptan_0.83 109.09367 4.28443057 102.000 106.00 109 112.00 119.000
#> 39 sumatriptan_0.9 103.87900 4.13989596 97.000 101.00 103 106.00 113.000
#> 40 sumatriptan_0.97 99.05267 3.93967849 92.000 96.00 99 101.00 108.000
#> 41 sumatriptan_1 96.53667 3.89414651 89.000 94.00 96 99.00 105.000
#> 42 sumatriptan_1.1 90.75833 3.75543584 83.000 88.00 91 93.00 99.000
#> 43 sumatriptan_1.2 85.25700 3.83881881 78.000 83.00 85 88.00 93.000
#> 44 sumatriptan_1.3 79.89667 4.03601520 72.000 77.00 80 83.00 87.000
#> 45 sumatriptan_1.4 74.72300 4.14664554 66.000 72.00 75 78.00 83.000
#> 46 sumatriptan_1.5 69.74467 4.24548540 61.000 67.00 70 73.00 78.000
#> 47 sumatriptan_1.6 64.99533 4.37039415 56.000 62.00 65 68.00 73.000
#> 48 sumatriptan_1.7 60.30167 4.56774401 51.000 57.00 60 63.00 69.000
#> 49 sumatriptan_1.8 55.58733 4.74164535 46.000 52.00 56 59.00 65.000
#> 50 sumatriptan_1.9 51.09667 4.77181785 42.000 48.00 51 54.00 60.000
#> 51 sumatriptan_2 46.89233 4.64262058 38.000 44.00 47 50.00 56.000
#> 52 frovatriptan_0.069 177.69700 1.60272078 174.000 177.00 178 178.00 180.000
#> 53 frovatriptan_0.14 168.29633 3.58563878 159.000 167.00 169 171.00 173.000
#> 54 frovatriptan_0.21 158.68133 5.53118277 145.000 156.00 160 162.00 167.000
#> 55 frovatriptan_0.28 148.80200 7.11835793 133.000 144.00 150 154.00 161.000
#> 56 frovatriptan_0.34 140.22433 7.95171372 124.000 135.00 141 146.00 155.000
#> 57 frovatriptan_0.41 131.12700 8.47101669 116.000 125.00 131 137.00 148.000
#> 58 frovatriptan_0.48 122.72867 8.90225411 106.000 117.00 122 129.00 141.000
#> 59 frovatriptan_0.55 114.73833 9.45245895 97.000 109.00 115 121.00 134.000
#> 60 frovatriptan_0.62 107.13833 9.94663305 89.000 100.00 107 114.00 128.000
#> 61 frovatriptan_0.69 100.02800 10.27422678 81.000 93.00 100 107.00 121.000
#> 62 frovatriptan_0.76 93.41433 10.52566345 73.000 87.00 93 100.00 116.000
#> 63 frovatriptan_0.83 87.17300 10.90195802 66.000 80.00 87 94.00 110.000
#> 64 frovatriptan_0.9 81.23200 11.40415981 58.000 74.00 81 89.00 104.000
#> 65 frovatriptan_0.97 75.49433 11.91111215 51.000 68.00 76 84.00 99.000
#> 66 frovatriptan_1 72.50600 12.12230509 48.000 65.00 73 81.00 96.000
#> 67 frovatriptan_1.1 65.31500 12.52022472 43.000 56.00 66 74.00 89.000
#> 68 frovatriptan_1.2 58.81567 12.36527347 40.000 48.00 58 68.00 85.000
#> 69 frovatriptan_1.3 53.09533 11.76448239 38.000 43.00 51 61.00 79.000
#> 70 frovatriptan_1.4 48.18200 10.79514031 35.000 40.00 45 55.00 74.000
#> 71 frovatriptan_1.5 44.07500 9.70560532 32.000 38.00 41 49.00 69.025
#> 72 frovatriptan_1.6 40.56600 8.67164209 29.975 35.00 38 43.00 64.000
#> 73 frovatriptan_1.7 37.50067 7.75181891 27.000 33.00 36 39.00 60.000
#> 74 frovatriptan_1.8 34.77600 7.02407312 24.000 31.00 34 36.00 55.000
#> 75 frovatriptan_1.9 32.26400 6.48960777 22.000 29.00 32 34.00 50.025
#> 76 frovatriptan_2 29.96533 6.08411624 20.000 26.00 30 33.00 46.000
#> 77 almotriptan_0.069 179.82400 1.20145960 177.000 179.00 180 181.00 181.000
#> 78 almotriptan_0.14 172.37967 2.27491648 167.000 171.00 173 174.00 175.000
#> 79 almotriptan_0.21 165.69967 3.52594346 156.000 164.00 166 168.00 170.000
#> 80 almotriptan_0.28 158.41000 4.51996055 146.000 156.00 159 162.00 165.000
#> 81 almotriptan_0.34 152.15633 5.29923773 139.000 149.00 153 156.00 160.000
#> 82 almotriptan_0.41 144.77900 5.95980974 132.000 141.00 146 149.00 155.000
#> 83 almotriptan_0.48 137.71167 6.10903462 126.000 133.00 138 142.00 148.000
#> 84 almotriptan_0.55 131.30600 6.17114725 120.000 126.00 131 136.00 143.000
#> 85 almotriptan_0.62 125.27733 6.11180859 115.000 120.00 125 130.00 138.000
#> 86 almotriptan_0.69 119.67833 6.01206389 109.000 115.00 119 124.00 132.000
#> 87 almotriptan_0.76 114.30233 6.01240198 103.000 110.00 114 118.00 127.000
#> 88 almotriptan_0.83 108.99433 6.09004631 97.000 105.00 109 113.00 122.000
#> 89 almotriptan_0.9 103.88067 6.11235469 93.000 100.00 104 108.00 117.000
#> 90 almotriptan_0.97 99.04367 6.07201639 88.000 95.00 99 103.00 112.000
#> 91 almotriptan_1 96.45833 6.02791084 85.000 92.00 96 100.00 109.000
#> 92 almotriptan_1.1 90.62900 6.06203556 78.975 87.00 91 94.00 103.000
#> 93 almotriptan_1.2 85.11700 6.30734269 72.000 81.00 85 89.00 98.000
#> 94 almotriptan_1.3 79.79567 6.61224787 67.000 75.00 80 84.00 93.000
#> 95 almotriptan_1.4 74.62000 6.88772436 60.000 70.00 75 79.00 88.000
#> 96 almotriptan_1.5 69.61467 7.25017516 55.000 65.00 70 75.00 83.000
#> 97 almotriptan_1.6 64.74567 7.55367464 49.000 60.00 65 70.00 79.000
#> 98 almotriptan_1.7 59.98567 7.86622021 44.000 55.00 60 66.00 74.000
#> 99 almotriptan_1.8 55.41867 7.99783554 40.000 50.00 56 61.00 71.000
#> 100 almotriptan_1.9 51.08433 7.85763760 37.000 45.00 51 57.00 66.025
#> 101 almotriptan_2 47.11267 7.52548008 34.000 41.00 46 52.00 62.000
#> 102 zolmitriptan_0.34 144.60733 5.42914709 132.000 141.00 145 149.00 153.000
#> 103 zolmitriptan_0.69 106.95700 5.44870448 97.000 103.00 107 110.00 118.000
#> 104 zolmitriptan_1 81.62933 5.74592129 70.000 78.00 82 86.00 92.000
#> 105 zolmitriptan_1.4 55.25900 7.22061619 42.000 50.00 55 60.00 69.000
#> 106 zolmitriptan_1.7 41.39033 5.16360928 33.000 38.00 41 44.00 53.000
#> 107 zolmitriptan_2.1 33.67333 3.35107427 29.000 31.00 33 36.00 41.000
#> 108 zolmitriptan_2.4 29.70500 2.89080622 25.000 28.00 29 31.00 36.000
#> 109 zolmitriptan_2.8 25.65500 2.38925606 22.000 24.00 25 27.00 31.025
#> 110 zolmitriptan_3.1 22.98300 1.97146474 21.000 21.00 23 24.00 28.000
#> 111 zolmitriptan_3.4 20.89367 1.39774024 20.000 20.00 20 21.00 24.000
#> 112 zolmitriptan_3.8 19.24400 0.75098957 19.000 19.00 19 19.00 22.000
#> 113 zolmitriptan_4.1 18.08133 0.43218108 18.000 18.00 18 18.00 19.000
#> 114 zolmitriptan_4.5 17.01867 0.19747883 17.000 17.00 17 17.00 17.000
#> 115 zolmitriptan_4.8 16.00567 0.11092936 16.000 16.00 16 16.00 16.000
#> 116 zolmitriptan_5.2 15.00233 0.06051812 15.000 15.00 15 15.00 15.000
#> 117 zolmitriptan_5.5 14.00100 0.04081938 14.000 14.00 14 14.00 14.000
#> 118 zolmitriptan_5.9 13.00033 0.01825742 13.000 13.00 13 13.00 13.000
#> 119 zolmitriptan_6.2 12.00000 0.00000000 12.000 12.00 12 12.00 12.000
#> 120 zolmitriptan_6.6 11.00000 0.00000000 11.000 11.00 11 11.00 11.000
#> 121 zolmitriptan_6.9 10.00000 0.00000000 10.000 10.00 10 10.00 10.000
#> 122 zolmitriptan_7.2 9.00000 0.00000000 9.000 9.00 9 9.00 9.000
#> 123 zolmitriptan_7.6 8.00000 0.00000000 8.000 8.00 8 8.00 8.000
#> 124 zolmitriptan_7.9 7.00000 0.00000000 7.000 7.00 7 7.00 7.000
#> 125 zolmitriptan_8.3 6.00000 0.00000000 6.000 6.00 6 6.00 6.000
#> 126 zolmitriptan_8.6 5.00000 0.00000000 5.000 5.00 5 5.00 5.000
#> 127 zolmitriptan_9 4.00000 0.00000000 4.000 4.00 4 4.00 4.000
#> 128 zolmitriptan_9.3 3.00000 0.00000000 3.000 3.00 3 3.00 3.000
#> 129 zolmitriptan_9.7 2.00000 0.00000000 2.000 2.00 2 2.00 2.000
#> 130 zolmitriptan_10 1.00000 0.00000000 1.000 1.00 1 1.00 1.000
#> 131 naratriptan_0.069 182.98167 0.15057040 183.000 183.00 183 183.00 183.000
#> 132 naratriptan_0.14 179.90833 1.56057971 177.000 179.00 180 181.00 182.000
#> 133 naratriptan_0.21 176.50433 2.11395463 172.000 175.00 177 178.00 181.000
#> 134 naratriptan_0.28 173.26700 2.61036057 168.000 172.00 173 175.00 179.000
#> 135 naratriptan_0.34 170.47767 3.06800241 164.000 169.00 171 172.00 176.000
#> 136 naratriptan_0.41 167.45100 3.72543849 160.000 165.00 168 170.00 175.000
#> 137 naratriptan_0.48 164.42833 4.39802737 155.000 162.00 165 168.00 173.000
#> 138 naratriptan_0.55 161.39767 5.08863039 150.975 158.00 162 165.00 170.000
#> 139 naratriptan_0.62 158.42033 5.80030468 146.000 155.00 159 162.00 169.000
#> 140 naratriptan_0.69 155.41700 6.52001645 141.000 151.00 156 160.00 166.025
#> 141 naratriptan_0.76 152.45500 7.19740063 137.975 148.00 153 158.00 165.000
#> 142 naratriptan_0.83 149.52400 7.82448070 133.000 144.00 150 155.00 163.000
#> 143 naratriptan_0.9 146.61900 8.44746267 129.000 141.00 147 153.00 162.000
#> 144 naratriptan_0.97 143.76800 9.05381134 125.000 138.00 144 150.00 160.000
#> 145 naratriptan_1 142.00933 9.28529223 123.000 136.00 142 148.25 159.000
#> 146 naratriptan_1.1 138.48467 10.13485751 117.000 132.00 139 146.00 157.000
#> 147 naratriptan_1.2 135.04233 10.90248424 112.000 128.00 135 143.00 155.000
#> 148 naratriptan_1.3 131.62300 11.71784851 106.000 125.00 132 139.00 153.000
#> 149 naratriptan_1.4 128.32133 12.52172816 101.000 121.00 129 137.00 151.000
#> 150 naratriptan_1.5 125.04967 13.30374119 96.000 117.00 126 134.00 149.000
#> 151 naratriptan_1.6 121.84533 14.08065457 92.000 113.00 123 131.00 148.000
#> 152 naratriptan_1.7 118.67667 14.81850144 87.000 110.00 120 129.00 145.000
#> 153 naratriptan_1.8 115.60500 15.54188400 83.000 106.00 117 126.00 144.000
#> 154 naratriptan_1.9 112.53833 16.20773768 79.000 102.00 114 124.00 142.000
#> 155 naratriptan_2 109.56267 16.84432595 74.000 98.00 111 121.00 140.000
#> 156 rizatriptan_0.034 181.68900 0.76494491 180.000 182.00 182 182.00 182.000
#> 157 rizatriptan_0.069 174.80800 1.72900718 171.000 174.00 175 176.00 177.000
#> 158 rizatriptan_0.1 169.36000 2.55745580 163.000 169.00 170 171.00 172.000
#> 159 rizatriptan_0.14 161.90900 3.59291275 152.000 161.00 163 164.00 166.000
#> 160 rizatriptan_0.17 156.37767 4.24802501 144.000 155.00 157 159.00 162.000
#> 161 rizatriptan_0.21 148.54567 4.85012946 137.000 146.00 150 152.00 155.000
#> 162 rizatriptan_0.24 142.43467 5.11603259 131.000 140.00 143 146.00 151.000
#> 163 rizatriptan_0.28 134.89033 5.07394208 125.000 131.00 135 139.00 144.000
#> 164 rizatriptan_0.31 129.56100 5.03971678 121.000 126.00 130 133.00 139.000
#> 165 rizatriptan_0.34 124.26833 4.81124169 116.000 120.00 124 128.00 134.000
#> 166 rizatriptan_0.38 117.99333 4.59271015 110.000 115.00 117 121.00 128.000
#> 167 rizatriptan_0.41 113.03700 4.44141941 105.000 110.00 113 116.00 122.025
#> 168 rizatriptan_0.45 106.77467 4.39912972 99.000 104.00 107 109.00 116.000
#> 169 rizatriptan_0.48 101.87933 4.37666059 94.000 99.00 102 105.00 111.000
#> 170 rizatriptan_0.52 96.03300 4.19520889 88.000 93.00 96 99.00 104.000
#> 171 rizatriptan_0.55 91.82333 4.04873474 84.000 89.00 92 94.00 100.000
#> 172 rizatriptan_0.59 86.90267 4.10716640 78.000 84.00 87 90.00 95.000
#> 173 rizatriptan_0.62 83.03933 4.24615075 74.000 80.00 83 86.00 91.000
#> 174 rizatriptan_0.66 78.25167 4.41068573 69.000 75.00 78 81.00 87.000
#> 175 rizatriptan_0.69 74.49833 4.50571094 65.000 71.75 75 78.00 83.000
#> 176 rizatriptan_0.72 70.84533 4.59083545 61.000 68.00 71 74.00 80.000
#> 177 rizatriptan_0.76 66.36033 4.80501710 56.000 63.00 67 70.00 75.000
#> 178 rizatriptan_0.79 62.71467 4.98051404 52.000 59.00 63 66.00 72.000
#> 179 rizatriptan_0.83 58.21833 5.15863687 48.000 55.00 58 62.00 68.000
#> 180 rizatriptan_0.86 54.64067 5.21957478 44.000 51.00 55 58.00 65.000
#> 181 rizatriptan_0.9 50.40000 5.05996058 40.000 47.00 50 54.00 60.025
#> 182 rizatriptan_0.93 47.24600 4.78530219 38.000 44.00 47 50.00 57.000
#> 183 rizatriptan_0.97 43.82800 4.36487114 36.000 41.00 44 46.00 53.000
#> 184 rizatriptan_1 41.36067 4.07898667 34.000 39.00 41 44.00 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 1.999333 0.02581558 2 2 2 2 2
#> 3 rizatriptan_2 1.000667 0.02581558 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)
# }