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 ($\beta_0$).
time: The time effect on acquisition ($\beta_\mathrm{time}$).
mass: The mass action effect on acquisition ($\beta_\mathrm{mass}$).
freq: The frequency effect on acquisition ($\beta_\mathrm{freq}$).
col_abx: The effect for colonized individuals on antibiotics ($\beta_{\bullet℞}$).
suss_abx: The effect on susceptible individuals currently on antibiotics ($\beta_{\circ℞}$).
suss_ever: The effect on susceptible individuals ever being on antibiotics ($\beta_{\circ^*℞}$).

Value

A list of parameters for acquisition.

Details

Notation: States are represented by circles - susceptible ($\circ$), colonized ($\bullet$), latent ($\circ^*$). The symbol ℞ represents antibiotic effects.

The model for this acquisition model is given by

$$ P(\mathrm{Acq(t)}) = \left[e^{\beta_\mathrm{time}(t-t_0)}\right]\\ \left\{e^{\beta_0} \left[ \left( \frac{\beta_\mathrm{freq}}{P(t)}+(1 - e^{\beta_\mathrm{freq}}) \right) e^{\beta_\mathrm{mass}}\left( (N_{\bullet}(t) - N_{\bullet℞}(t)) + e^{\beta_{\bullet℞}}N_{\bullet℞}(t) \right) + 1 - e^{\beta_\mathrm{mass}} \right] \right\}\\ \left[ N_{\circ}(t) - N_{\circ^*℞}(t) + e^{\beta_{\circ^*℞}} \left( \left( N_{\circ^*℞}(t) - N_{\circ℞}(t) \right) + N_{\circ℞}(t)e^{\beta_{\circ℞}} \right) \right] $$ where P(Acq(t)) is the acquisition probability at time t, with effects from time ($\beta_\mathrm{time}$), mass action ($\beta_\mathrm{mass}$), frequency dependence ($\beta_\mathrm{freq}$), colonized individuals on antibiotics ($\beta_{\bullet℞}$), and susceptible individuals currently ($\beta_{\circ℞}$) or ever ($\beta_{\circ^*℞}$) 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"
#>