Optimize algebraic systems which describe thermodynamic binding systems
opti.RdOptimize algebraic systems which describe thermodynamic binding systems
Usage
opti(
case,
lowerBounds,
upperBounds,
path,
additionalParameters,
npop = 40,
ngen = 200,
Topology = "random",
errorThreshold = -Inf,
runAsShiny = FALSE
)Arguments
- case
is a character describing which system should be investigated. Either: "hg", "ida" or "gda".
- lowerBounds
is a numeric vector defining the lower boundaries of the parameter. In case of hg the order of the parameters is: khd, I0, IHD and ID In case of ida and ga the order of the parameters is: kg, I0, IHD and ID.
- upperBounds
is a numeric vector defining the upper boundaries of the parameter. The order is the same as for the lower boundaries.
- path
is a filepath which contains tabular x-y data. The concentraion of dye or guest respectivly is assumed to be in the first column. Furthermore, should the corresponding signal be stored in the second column. As an alternative an already loaded data.frame can be passed to the function.
- additionalParameters
are required parameters which are specific for each case. In case of hg a numeric vector of length 1 is expected which contains the concentration of the host. In case of ida a numeric vector of length 3 is expected which contains the concentration of the host, dye and the khd parameter. In case of gda a numeric vector of length 3 is expected which contains the concentration of the host, guest and the khd parameter.
- npop
is an optional integer argument defining the number of particles during optimization. The default value is set to 40.
- ngen
is an optional integer argument defining the number of generations of the particle swarm optimization. The default value is set to 200.
- Topology
is an optional character argument defining which topology should be used by the particle swarm algorithm. The options are "star" and "random". The default topology is the "random" topology.
- errorThreshold
is an optional numeric argument defining a sufficient small error which acts as a stop signal for the particle swarm algorithm. The default value is set to -Inf.
- runAsShiny
is internally used when running the algorithm from shiny.
Value
either an instance of ErrorClass if something went wrong. Otherwise the optimized parameter and the insilico signal values are returned.
Examples
path <- paste0(system.file("examples", package = "tsf"), "/IDA.txt")
opti("ida", c(1, 0, 0, 0), c(10^9, 10^6, 10^6, 10^6), path, c(4.3, 6.0, 7079458))
#> [1] 2
#> [1] 28060975.29 465987.19 390031.39 20065.22
#> [1] 21178.86
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#> [1] 28060975.29 465987.19 390031.39 20065.22
#> [1] 21178.86
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#> [1] 5.736756e+08 0.000000e+00 1.000000e+06 6.101458e+03
#> [1] 8918.934
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#> [1] 1000000000.0 0.0 603439.2 0.0
#> [1] 4391.296
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#> [1] 1000000000.0 0.0 590145.5 0.0
#> [1] 4294.094
#> [1] 7
#> [1] 1000000000.0 0.0 348388.7 0.0
#> [1] 2526.388
#> [1] 8
#> [1] 789805326.7 0.0 172243.1 0.0
#> [1] 1299.917
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#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 170
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 171
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 172
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 173
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 174
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 175
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 176
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 177
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 178
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 179
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 180
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 181
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 182
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 183
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 184
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 185
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 186
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 187
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 188
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 189
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 190
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 191
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 192
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 193
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 194
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 195
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 196
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 197
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 198
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 199
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [1] 200
#> [1] 87732402.810 0.000 1305.587 0.000
#> [1] 0.5562147
#> [[1]]
#> guest signal signal_insilico d hd
#> 1 0.0000 5846.100 5614.0223 1.700000 4.2999996
#> 2 0.4975 5251.420 4993.0020 2.175664 3.8243359
#> 3 0.9901 4579.220 4398.0111 2.631391 3.3686091
#> 4 1.4778 3922.710 3834.4000 3.063083 2.9369172
#> 5 1.9608 3351.840 3308.4807 3.465905 2.5340950
#> 6 2.4390 2791.560 2827.7179 3.834140 2.1658599
#> 7 2.9126 2333.070 2399.0455 4.162477 1.8375230
#> 8 3.3816 1969.980 2027.6770 4.446923 1.5530772
#> 9 3.8462 1653.070 1714.9782 4.686431 1.3135690
#> 10 4.3062 1398.690 1458.1487 4.883147 1.1168532
#> 11 4.7619 1210.670 1250.5191 5.042178 0.9578216
#> 12 5.2133 1054.340 1083.9160 5.169786 0.8302137
#> 13 5.6604 936.536 950.1846 5.272216 0.7277836
#> 14 6.1033 827.836 842.1811 5.354941 0.6450595
#> 15 6.5421 757.271 754.1359 5.422378 0.5776222
#> 16 6.9767 687.888 681.6061 5.477931 0.5220688
#> 17 7.4074 628.260 621.1497 5.524237 0.4757629
#> 18 7.8341 582.921 570.2200 5.563246 0.4367538
#> 19 8.2569 541.771 526.8629 5.596455 0.4035449
#> 20 8.6758 505.525 489.5988 5.624997 0.3750029
#> 21 9.0909 478.098 457.2821 5.649750 0.3502503
#>
#> [[2]]
#> kguest I0 IHD ID
#> 1 87732403 0 1305.587 0
#>
#> [[3]]
#>
#> [[4]]
#> [[4]]$mse
#> [1] 8739.878
#>
#> [[4]]$rmse
#> [1] 93.48732
#>
#> [[4]]$mae
#> [1] 60.13659
#>
#> [[4]]$r2
#> [1] 0.9987043
#>
#> [[4]]$r2adjusted
#> [1] 0.9986361
#>
#>