Functions to get and set column bases specified for an optimization run, either through the minimum column basis or through a vector of specified column bases.

minColBasis(map, optimization_number = 1)
minColBasis(map, optimization_number = 1) <- value
fixedColBases(map, optimization_number = 1)
fixedColBases(map, optimization_number = 1) <- value
agReactivityAdjustments(map, optimization_number = 1)
agReactivityAdjustments(map, optimization_number = 1) <- value

Arguments

map

The acmap data object

optimization_number

The optimization run from which to get / set the data

value

New value to set

Value

Returns either the requested attribute when using a getter function or

the updated acmap object when using the setter function.

Details

In general a map can have column bases that are specified either through a minimum column basis or a vector of fixed column bases for each sera. When you call minColBasis(), it will return the minimum column basis if it has been set, or "fixed" if column bases have instead been fixed directly. The colBases() function will return the column bases as calculated for a given optimization run. Setting column bases through this function with colBases()<- will fix the column bases to the supplied vector of values.

Note that although the output from colBases() might be the same in a case where a minimum column basis was set or a case where column bases were set explcitely, when a minimum column basis is set, the column bases will still depend on the log titers recorded against a given sera, so changing the titers may therefore change the actual column bases calculated. For fixed column bases case, column bases will remain fixed at their values independently of measured titers.

See also

Other map optimization attribute functions: mapComment(), mapDimensions(), mapStress(), mapTransformation(), ptBaseCoords(), ptCoords()