generate_antigenic_map: Generate antigenic map

In seroanalytics/serosolver: Inference Framework for Serological Data

Generate antigenic map

Description

Fits a smoothing spline through a set of antigenic coordinates, and uses this to predict antigenic coordinates for all potential infection time points

Usage

generate_antigenic_map(antigenic_distances, buckets = 1, spar = 0.3)

Arguments

antigenic_distances	a data frame of antigenic coordinates, with columns labelled X, Y and Strain for x coord, y coord and Strain label respectively. Strain labels should be in the virus_key vector which is at the top of this source code. See example_antigenic_map
buckets	the number of epochs per year. 1 means that each year has 1 strain; 12 means that each year has 12 strains (monthly resolution)
spar	to be passed to smooth.spline

Value

a fitted antigenic map

See Also

generate_antigenic_map_flexible

Other antigenic_maps: generate_antigenic_map_flexible()

Examples

## Not run: 
antigenic_coords_path <- system.file("extdata", "fonville_map_approx.csv", package = "serosolver")
antigenic_coords <- read.csv(antigenic_coords_path, stringsAsFactors=FALSE)
antigenic_map <- generate_antigenic_map(antigenic_coords, 1)

## End(Not run)

seroanalytics/serosolver documentation built on April 24, 2023, 9:52 a.m.