Linear Antibiotic Acquisition Parameters — LinearAbxAcquisitionParams • bayestransmission

Acquisition parameters for LinearAbxModel and LinearAbxModel2.

Usage

LinearAbxAcquisitionParams(
  base = Param(0.001),
  time = Param(1, 0),
  mass = Param(1, 1),
  freq = Param(1, 1),
  col_abx = Param(1, 0),
  suss_abx = Param(1, 0),
  suss_ever = Param(1, 0)
)

Arguments

base: The base rate of acquisition.
time: The time effect on acquisition.
mass: The mass action effect on acquisition.
freq: The frequency effect on acquisition.
col_abx: The effect for colonized on antibiotics.
suss_abx: The effect on susceptible being currently on antibiotics.
suss_ever: The effect on susceptible ever being on antibiotics.

Value

A list of parameters for acquisition.

Details

The model for this acquisition model is given by

$$ P(\mathrm{Acq(t)}) = \left[e^{\beta_\mathrm{time}(t-t_0)}\right]\\ \left\{e^{\beta_0} \left[ \left( \frac{\beta_\mathrm{freq}}{P(t)}+(1 - e^{\beta_\mathrm{freq}}) \right) e^{\beta_\mathrm{mass}}\left( (N_c(t) - N_{ca}(t)) + e^{\beta_\mathrm{col\_abx}}N_{ca}(t) \right) + 1 - e^{\beta_\mathrm{mass}} \right] \right\}\\ \left[ N_S(t) - N_E(t) + e^{\beta_\mathrm{suss\_ever}} \left( \left( E_i(t) - A_i(t) \right) + A_i(t)e^{\beta_\mathrm{suss\_abx}} \right) \right] $$ where P(Acq(t)) is the acquisition probability at time t, with effects from time (beta_time), mass action (beta_mass), frequency dependence (beta_freq), colonized individuals on antibiotics (beta_col_abx), and susceptible individuals currently (beta_suss_abx) or ever (beta_suss_ever) on antibiotics.

Examples

LinearAbxAcquisitionParams()
#> $base
#> $init
#> [1] 0.001
#> 
#> $update
#> [1] TRUE
#> 
#> $prior
#> [1] 0.001
#> 
#> $weight
#> [1] 1
#> 
#> attr(,"class")
#> [1] "Param"
#> 
#> $time
#> $init
#> [1] 1
#> 
#> $update
#> [1] FALSE
#> 
#> $prior
#> [1] 1
#> 
#> $weight
#> [1] 0
#> 
#> attr(,"class")
#> [1] "Param"
#> 
#> $mass
#> $init
#> [1] 1
#> 
#> $update
#> [1] TRUE
#> 
#> $prior
#> [1] 1
#> 
#> $weight
#> [1] 1
#> 
#> attr(,"class")
#> [1] "Param"
#> 
#> $freq
#> $init
#> [1] 1
#> 
#> $update
#> [1] TRUE
#> 
#> $prior
#> [1] 1
#> 
#> $weight
#> [1] 1
#> 
#> attr(,"class")
#> [1] "Param"
#> 
#> $col_abx
#> $init
#> [1] 1
#> 
#> $update
#> [1] FALSE
#> 
#> $prior
#> [1] 1
#> 
#> $weight
#> [1] 0
#> 
#> attr(,"class")
#> [1] "Param"
#> 
#> $suss_abx
#> $init
#> [1] 1
#> 
#> $update
#> [1] FALSE
#> 
#> $prior
#> [1] 1
#> 
#> $weight
#> [1] 0
#> 
#> attr(,"class")
#> [1] "Param"
#> 
#> $suss_ever
#> $init
#> [1] 1
#> 
#> $update
#> [1] FALSE
#> 
#> $prior
#> [1] 1
#> 
#> $weight
#> [1] 0
#> 
#> attr(,"class")
#> [1] "Param"
#>