README.md

acsimdata

The goal of acsimdata is to create simulated data to allow reproducible testing of antigenic cartography methods and quality measures.

Installation

You can install the released version of acsimdata from Github with:

devtools::install_github("drserajames/acsimdata")

Example

This is the basic usage:

library(acsimdata)

# Create random map and distances
rand_map <- map_maker_random(5,5,10, seed=327458)
plot(rand_map$coord, asp=1)

# Add random noise to the distances
noisy_dist <- add_noise(rand_map$dist)

# Convert the distances into titres like HI data
noisy_titres <- dist_to_hi_titre(noisy_dist$noise_dist_table)

# Remove titres to create missing data
miss_noisy_titres <- miss_titres_random(noisy_titres$lessthan_titre, proportion = 0.2)

# Output which can be used with the Racmacs package
miss_noisy_titres$rm_titre
#>     SR1     SR2    SR3    SR4    SR5    
#> AG1 "10240" "320"  "160"  "40"   "*"    
#> AG2 "80"    "5120" "5120" "2560" "320"  
#> AG3 "<10"   "1280" "1280" "320"  "320"  
#> AG4 "<10"   "*"    "*"    "5120" "20"   
#> AG5 "20"    "1280" "*"    "*"    "10240"