View source: R/map_optimize_reactivity.R
optimizeAgReactivity | R Documentation |
optimizeAgReactivity(
map,
optimization_number = 1,
reactivity_stress_weighting = 1,
fixed_ag_reactivities = rep(NA, numAntigens(map)),
start_pars = rep(0, numAntigens(map)),
reoptimize = FALSE,
number_of_optimizations = 100,
options = list()
)
map |
The acmap object |
optimization_number |
The optimization number for which to optimize antigen reactivity adjustments |
reactivity_stress_weighting |
The weighting to apply when calculating how much antigen reactivity changes should additionally contribute to stress in the optimization regime (see details). |
fixed_ag_reactivities |
A vector of fixed antigen reactivities, use NA values to distinguish the positions you would still like to be optimized. |
start_pars |
A vector of starting parameters to use for the optimizer,
you can still supply starting parameters for antigens listed in
|
reoptimize |
Should the map be reoptimized from scratch (slower but more likely to explore other optima) when testing each reactivity adjustment or simply relaxed from it's current coordinates (default) |
number_of_optimizations |
If reoptimizing from scratch, how many optimization runs should be performed each time. |
options |
A named list of additional options to pass to
|
The acmap object is returned with antigen reactivity adjustments
set to the value calculated in the optimizer. This can be queried with
agReactivityAdjustments()
.
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