unstableMaps: Notes on unstable maps

In Racmacs: Antigenic Cartography Macros

Notes on unstable maps

Description

Tips for exploring maps that are difficult to find a consistent optimal solution for.

Details

Maps may be difficult to optimize or unstable for a variety of reasons, a common one with larger maps being simply that it is difficult to find a global optima and so many different local optima are found each time.

One approach that can sometimes help is to consider running the optimizer with options = list(dim_annealing = TRUE) (see see vignette("intro-to-antigenic-cartography") for an explanation of the dimensional annealing approach). However be wary that in our experience, while applying dimensional annealing can sometimes significantly speed up finding a better minima, it can also sometimes be more prone to getting stuck in worse local optima.

If there are many missing or non-detectable titers it is also possible that points in map are too poorly connected to find a robust solution, to check this see mapCohesion().

See Also

Other map diagnostic functions: agCohesion(), bootstrapBlobs(), bootstrapMap(), checkHemisphering(), dimensionTestMap(), logtiterTable(), map-table-distances, mapBootstrapCoords, mapDistances(), mapRelaxed(), mapResiduals(), pointStress, ptBootstrapBlob, ptBootstrapCoords(), ptLeverage, ptTriangulationBlob, recalculateStress(), stressTable(), tableColbases(), tableDistances(), triangulationBlobs()

Racmacs documentation built on June 22, 2024, 11:33 a.m.