Optimize algebraic systems which describe thermodynamic binding systems
sensitivity.RdOptimize algebraic systems which describe thermodynamic binding systems
Usage
sensitivity(
case,
parameters,
path,
additionalParameters,
percentage = NULL,
OffsetBoundaries = NULL,
runAsShiny = FALSE
)Arguments
- case
is a character describing which system should be investigated. Either: "hg", "ida" or "gda".
- parameters
is a numeric vector containing already optimized 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.
- 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.
- percentage
is the percentage +/- from parameters in which the sensitivity should be analysed.
- OffsetBoundaries
in case percentage is not suitable a numeric vector (equivalent to parameters) can be used which is added/substracted from parameters. It is only possible to set either percentage or OffsetBoundaries.
- runAsShiny
is internally used when running the algorithm from shiny.
Value
either an instance of ErrorClass if something went wrong. Otherwise plots showing the sensitivity are returned.
Examples
path <- paste0(system.file("examples", package = "tsf"), "/IDA.txt")
res <- 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] 7.897109e+08 4.886492e+05 6.211926e+05 1.071294e+03
#> [1] 14534.67
#> [1] 3
#> [1] 7.897109e+08 4.886492e+05 6.211926e+05 1.071294e+03
#> [1] 14534.67
#> [1] 4
#> [1] 1.0 183419.7 0.0 255286.7
#> [1] 12200.39
#> [1] 5
#> [1] 1.0 0.0 0.0 223541.2
#> [1] 7501.383
#> [1] 6
#> [1] 1.0 0.0 0.0 192949.6
#> [1] 6471.946
#> [1] 7
#> [1] 527866481.6 164225.8 283640.0 0.0
#> [1] 5625.277
#> [1] 8
#> [1] 618845592.5 0.0 330425.9 0.0
#> [1] 2659.152
#> [1] 9
#> [1] 472584306 0 0 0
#> [1] 21
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#> [1] 472584306 0 0 0
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#> [1] 11
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#> [1] 13
#> [1] 7.024793e+08 0.000000e+00 3.814083e+03 0.000000e+00
#> [1] 18.56668
#> [1] 14
#> [1] 6.091756e+08 0.000000e+00 2.361073e+03 0.000000e+00
#> [1] 11.84767
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#> [1] 10.91898
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#> [1] 5.002578
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#> [1] 2.385739
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#> [1] 98161663.706 0.000 1357.984 0.000
#> [1] 0.7825929
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#> [1] 0.7825929
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#> [1] 173
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 174
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 175
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 176
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 177
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 178
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 179
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 180
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 181
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 182
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 183
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 184
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 185
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 186
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 187
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 188
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 189
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 190
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 191
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 192
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 193
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 194
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 195
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 196
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 197
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 198
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 199
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
#> [1] 200
#> [1] 81757169.853 0.000 1272.561 0.000
#> [1] 0.613118
sensitivity("ida", res[[2]], path, c(4.3, 6.0, 7079458), 20)
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
