validadeW: Title Validate infector probability calculation

In thednainus/HIVepisimAnalysis: Functions to analyse results from network analysis

Title Validate infector probability calculation

Description

This function saves several values to compare W calculated on the true trees and the true transmission matrix. For the return values see below.

Usage

validadeW(
  sim,
  run,
  tm,
  W_true,
  W_estimated,
  seed_ID,
  MH,
  true_tree,
  prefix = NULL
)

Arguments

sim	Simulation number to know the parameter values that network was simulated
run	Run number
tm	Transmission matrix per seed
W_true	Infector probability calculated on the true trees
seed_ID	Seed ID name. Seed is the node ID that started the transmissions; it is the initial infected node in the simulations.
MH	maximum height in which infector probabilities were calculated
true_tree	object of class phylo
prefix	prefix to save results. If prefix = NULL, results will be saved on file W_stats.csv.

Value

a data frame of 1 row with the following values: 1. Code = code indicating if W was calculated on true trees 2. Maximum height = maximum height (MH) in which calculations were performed; 3. Total tips = total number of tips in the phylogenetic tree; 4. n_tips_region = total number of tips from region in the phylogenetic tree; 5. n_tips_global = total number of tips from global in the phylogenetic tree; 6. n_trans_W = total number of transmissions independent of infector probability values; 7. n_trans_tm = total number of transmissions based on transmission matrix subset by MH; 8. n_true_trans_W = total number of true transmission independent of infector probability (W) values. Here is the true transmission when compared to the transmission matrix; 9. n_W80_all = number of transmission in which W >= 80 10. n_W80_correctDonorRecipt = number of transmission in point 9 that is a true transmission (when comparing to the transmission matrix); 11. n_W80_swapDonorRecipt = number of transmission in point 9 that is a true transmission (when comparing to the transmission matrix), but there was a swap between donor and recipient; 12. expected_n_trans = expected number of transmission defined as the sum of all infector probability (W) values.

thednainus/HIVepisimAnalysis documentation built on Sept. 21, 2023, 7:32 a.m.