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Calculate LR for a profile for sample-specific error probabilities integrated over the donor prior distribution using numerical integration

Source: R/LR-integrate.R
calc_LRs_wTwR_integrate_wT_num.Rd

NOTE: Unless you have a reason, please use calc_LRs_wTwR_integrate_wT() instead.

Usage

calc_LRs_wTwR_integrate_wT_num(
  xT,
  xR,
  shape1T_H1,
  shape2T_H1,
  shape1T_H2,
  shape2T_H2,
  wR,
  p,
  lower_int = 0,
  ...
)

Arguments

xT

profile from case (of 0, 1, 2)

xR

profile from suspect (of 0, 1, 2)

shape1T_H1

Under $H_1$ (in $LR$'s numerator), wT has beta prior on (0, 0.5) with parameters shape1T_H1 and shape2T_H1

shape2T_H1

see shape1T_Hp

shape1T_H2

Under $H_2$ (in $LR$'s denominator), wT has beta prior (on 0-0.5) with parameters shape1T_H2 and shape2T_H2

shape2T_H2

see shape1T_H2

wR

error probability for PoI sample

p

list of genotype probabilities (same length as xT/xR, or vector of length 3 for reuse)

lower_int

lowest value to integrate from; should be 0, but numerical instability can make this problematic

...

pass on to integrate(), e.g., rel.tol and abs.tol

Examples

calc_LRs_wTwR(xT = c(0, 0), xR = c(0, 1), wT = 1e-2, wR = 1e-5, p = c(0.25, 0.25, 0.5))
#> [1] 3.95916097 0.04006872

shpD <- get_beta_parameters(mu = 1e-2, sigmasq = 2*1e-3, a = 0, b = 0.5)
calc_LRs_wTwR_integrate_wT_mc(
  xT = c(0, 0), 
  xR = c(0, 1), 
  shape1D = shpD[1], shape2D = shpD[2], 
  wR = 1e-5, 
  p = c(0.25, 0.25, 0.5),
  n_samples = 100)
#> Error in calc_LRs_wTwR_integrate_wT_mc(xT = c(0, 0), xR = c(0, 1), shape1D = shpD[1],     shape2D = shpD[2], wR = 1e-05, p = c(0.25, 0.25, 0.5), n_samples = 100): unused arguments (shape1D = shpD[1], shape2D = shpD[2])
calc_LRs_wTwR_integrate_wT_num(
  xT = c(0, 0), 
  xR = c(0, 1), 
  shape1D = shpD[1], shape2D = shpD[2], 
  wR = 1e-5, 
  p = c(0.25, 0.25, 0.5))
#> Error in f(x, ...): unused arguments (shape1D = 0.029, shape2D = 1.421)
# curve(dbeta05(x, shpD[1], shpD[2]), from = 0, to = 0.5)

calc_LRs_wTwR_integrate_wT_mc(
  xT = c(0, 0), 
  xR = c(0, 1), 
  shape1D = 1, shape2D = 1, 
  wR = 1e-5, 
  p = c(0.25, 0.25, 0.5),
  n_samples = 100)
#> Error in calc_LRs_wTwR_integrate_wT_mc(xT = c(0, 0), xR = c(0, 1), shape1D = 1,     shape2D = 1, wR = 1e-05, p = c(0.25, 0.25, 0.5), n_samples = 100): unused arguments (shape1D = 1, shape2D = 1)
calc_LRs_wTwR_integrate_wT_num(
  xT = c(0, 0),
  xR = c(0, 1),
  shape1D = 1, shape2D = 1,
  wR = 1e-5,
  p = c(0.25, 0.25, 0.5),
  n_samples = 100)
#> Error in f(x, ...): unused arguments (shape1D = 1, shape2D = 1, n_samples = 100)
# curve(dbeta05(x, 1, 1), from = 0, to = 0.5)