generate_antigenic_map_flexible: Generate antigenic map, flexible

In seroanalytics/serosolver: Inference Framework for Serological Data

Generate antigenic map, flexible

Description

Fits a smoothing spline through a set of antigenic coordinates, and uses this to predict antigenic coordinates for all potential infection time points. This version is more flexible than generate_antigenic_map, and allows the user to specify "clusters" to assume that strains circulating in a given period are all identical, rather than on a continuous path through space as a function of time.

Usage

generate_antigenic_map_flexible(
  antigenic_distances,
  buckets = 1,
  clusters = NULL,
  use_clusters = FALSE,
  spar = 0.3,
  year_min = 1968,
  year_max = 2016
)

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" should be a single number giving the year of circulation of that strain. See example_antigenic_map
buckets	= 1 the number of epochs per year. 1 means that each year has 1 strain; 12 means that each year has 12 strains (monthly resolution)
clusters	= NULL a data frame of cluster labels, indicating which cluster each circulation year belongs to. Note that each row (year) gets repeated by the number of buckets. Column names "year" and "cluster_used"
use_clusters	= FALSE if TRUE, uses the clusters data frame above, otherwise just returns as normal
spar	= 0.3 to be passed to smooth.spline
year_min	= 1968 first year in the antigenic map (usually 1968)
year_max	= 2016 last year in the antigenic map

Value

a fitted antigenic map

See Also

generate_antigenic_map

Other antigenic_maps: create_start_level_data()

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_coords$Strain <- c(68,72,75,77,79,87,89,92,95,97,102,104,105,106) + 1900
antigenic_map <- generate_antigenic_map_flexible(antigenic_coords, buckets=1, year_min=1968, year_max=2015,spar=0.3)

times <- 1968:2010
n_times <- length(times)
clusters <- rep(1:5, each=10)
clusters <- clusters[1:n_times]
clusters <- data.frame(year=times, cluster_used=clusters)
antigenic_map <- generate_antigenic_map_flexible(antigenic_coords, buckets=1, 
                                                clusters=clusters,use_clusters=TRUE,
                                                year_min=1968, year_max=2010,spar=0.5)

## End(Not run)

seroanalytics/serosolver documentation built on Dec. 14, 2024, 5:33 a.m.