R/dose_response.R
In albgarre/biorisk: What the Package Does (One Line, Title Case)
#' @title DoseResponse_Exponential Class
#'
#' @description
#' An element for the exponential dose-response model
#'
#'
#' @export
#'
DoseResponse_Exponential <- R6::R6Class(
classname = "DoseResponse_Exponential",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("r", "dose"),
input_types = list(r = "continuous",
dose = "discrete"),
units = units,
element_type = "dose_response",
output_var = "P_ill",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
r <- self$depends_on$r$point_estimate()
dose <- self$depends_on$dose$point_estimate()
1 - exp(-r*dose)
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(
P_ill = 1 - exp(-r*dose)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
P_ill = 1 - exp(-r*dose)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title DoseResponse_BetaPoisson Class
#'
#' @description
#' An element for the beta-Poisson dose-response model
#'
#'
#' @export
#'
DoseResponse_BetaPoisson <- R6::R6Class(
classname = "DoseResponse_BetaPoisson",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
super$initialize(name,
input_names = c("beta", "alpha", "dose"),
input_types = list(beta = "continuous",
alpha = "continuous",
dose = "discrete"),
units = units,
element_type = "dose_response",
output_var = "P_ill",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
dose <- self$depends_on$dose$point_estimate()
alpha <- self$depends_on$alpha$point_estimate()
beta <- self$depends_on$beta$point_estimate()
1 - (1 + dose/beta)^(-alpha)
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(
P_ill = 1 - (1 + dose/beta)^(-alpha)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
P_ill = 1 - (1 + dose/beta)^(-alpha)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Concentration2Dose Class
#'
#' @description
#' An element that acts as a helper to convert from concentration to dose
#'
#'
#' @export
#'
Concentration2Dose <- R6::R6Class(
classname = "Concentration2Dose",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("logN", "size"),
input_types = list(logN = "continuous",
size = "continuous"),
units = units,
element_type = "simple",
output_var = "dose",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
10^self$depends_on$logN$point_estimate() * self$depends_on$size$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
expected_dose = 10^logN * size,
dose = rpois(nrow(.), expected_dose)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
expected_dose = 10^logN * size,
dose = rpois(nrow(.), expected_dose)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Concentration2Dose_continuous Class
#'
#' @description
#' An element that acts as a helper to convert from concentration to dose
#'
#'
#' @export
#'
Concentration2Dose_continuous <- R6::R6Class(
classname = "Concentration2Dose_continuous",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("logN", "size"),
input_types = list(logN = "continuous",
size = "continuous"),
units = units,
element_type = "simple",
output_var = "dose",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
10^self$depends_on$logN$point_estimate() * self$depends_on$size$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
dose = 10^logN * size
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
dose = 10^logN * size
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Pill2Cases_1 Class
#'
#' @description
#' An element that acts as a helper to convert from probability of illness to number of cases
#'
#'
#' @export
#'
Pill2Cases_1 <- R6::R6Class(
classname = "Pill2Cases_1",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("Pill"),
input_types = list(Pill = "continuous"),
units = units,
element_type = "simple",
output_var = "case",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
self$depends_on$Pill$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
case = rbinom(nrow(.), 1, Pill)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(.,
case = rbinom(nrow(.), 1, Pill)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Pill2Cases_N Class
#'
#' @description
#' An element that acts as a helper to convert from probability of illness to number of cases
#'
#'
#' @export
#'
Pill2Cases_N <- R6::R6Class(
classname = "Pill2Cases_N",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("Pill", "servings"),
input_types = list(Pill = "continuous",
servings = "discrete"),
units = units,
element_type = "simple",
output_var = "case",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
self$depends_on$Pill$point_estimate() * self$depends_on$servings$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
case = rbinom(nrow(.), servings, Pill)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(.,
case = rbinom(nrow(.), servings, Pill)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
albgarre/biorisk documentation built on Feb. 23, 2025, 5:19 a.m.
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#' @title DoseResponse_Exponential Class
#'
#' @description
#' An element for the exponential dose-response model
#'
#'
#' @export
#'
DoseResponse_Exponential <- R6::R6Class(
classname = "DoseResponse_Exponential",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("r", "dose"),
input_types = list(r = "continuous",
dose = "discrete"),
units = units,
element_type = "dose_response",
output_var = "P_ill",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
r <- self$depends_on$r$point_estimate()
dose <- self$depends_on$dose$point_estimate()
1 - exp(-r*dose)
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(
P_ill = 1 - exp(-r*dose)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
P_ill = 1 - exp(-r*dose)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title DoseResponse_BetaPoisson Class
#'
#' @description
#' An element for the beta-Poisson dose-response model
#'
#'
#' @export
#'
DoseResponse_BetaPoisson <- R6::R6Class(
classname = "DoseResponse_BetaPoisson",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
super$initialize(name,
input_names = c("beta", "alpha", "dose"),
input_types = list(beta = "continuous",
alpha = "continuous",
dose = "discrete"),
units = units,
element_type = "dose_response",
output_var = "P_ill",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
dose <- self$depends_on$dose$point_estimate()
alpha <- self$depends_on$alpha$point_estimate()
beta <- self$depends_on$beta$point_estimate()
1 - (1 + dose/beta)^(-alpha)
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(
P_ill = 1 - (1 + dose/beta)^(-alpha)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
P_ill = 1 - (1 + dose/beta)^(-alpha)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Concentration2Dose Class
#'
#' @description
#' An element that acts as a helper to convert from concentration to dose
#'
#'
#' @export
#'
Concentration2Dose <- R6::R6Class(
classname = "Concentration2Dose",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("logN", "size"),
input_types = list(logN = "continuous",
size = "continuous"),
units = units,
element_type = "simple",
output_var = "dose",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
10^self$depends_on$logN$point_estimate() * self$depends_on$size$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
expected_dose = 10^logN * size,
dose = rpois(nrow(.), expected_dose)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
expected_dose = 10^logN * size,
dose = rpois(nrow(.), expected_dose)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Concentration2Dose_continuous Class
#'
#' @description
#' An element that acts as a helper to convert from concentration to dose
#'
#'
#' @export
#'
Concentration2Dose_continuous <- R6::R6Class(
classname = "Concentration2Dose_continuous",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("logN", "size"),
input_types = list(logN = "continuous",
size = "continuous"),
units = units,
element_type = "simple",
output_var = "dose",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
10^self$depends_on$logN$point_estimate() * self$depends_on$size$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
dose = 10^logN * size
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(
dose = 10^logN * size
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Pill2Cases_1 Class
#'
#' @description
#' An element that acts as a helper to convert from probability of illness to number of cases
#'
#'
#' @export
#'
Pill2Cases_1 <- R6::R6Class(
classname = "Pill2Cases_1",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("Pill"),
input_types = list(Pill = "continuous"),
units = units,
element_type = "simple",
output_var = "case",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
self$depends_on$Pill$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
case = rbinom(nrow(.), 1, Pill)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(.,
case = rbinom(nrow(.), 1, Pill)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
#' @title Pill2Cases_N Class
#'
#' @description
#' An element that acts as a helper to convert from probability of illness to number of cases
#'
#'
#' @export
#'
Pill2Cases_N <- R6::R6Class(
classname = "Pill2Cases_N",
inherit = ContinuousElement,
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param name A character defining the name for the element
#' @param units A character vector of units for each input
#' @param output_unit A character with the unit of the output
#'
#' @return A new instance of the element
#'
initialize = function(name,
units = NA,
output_unit = NA
) {
super$initialize(name,
input_names = c("Pill", "servings"),
input_types = list(Pill = "continuous",
servings = "discrete"),
units = units,
element_type = "simple",
output_var = "case",
output_unit = output_unit,
level = 0)
},
#' @description
#' Returns the expected value
#'
point_estimate = function() {
self$depends_on$Pill$point_estimate() * self$depends_on$servings$point_estimate()
}
),
private = list(
update_output = function(niter) {
sims <- self$simulations %>%
dplyr::mutate(.,
case = rbinom(nrow(.), servings, Pill)
)
self$simulations <- sims
},
update_output_level = function(niter0, iter1 = 1, level = 0) {
if (self$level > level) {
niter0 <- 1
}
sims <- self$simulations_multi[[iter1]] %>%
dplyr::mutate(.,
case = rbinom(nrow(.), servings, Pill)
)
## Save it
self$simulations_multi[[iter1]] <- sims
## Return the output
invisible(sims[[self$output]])
}
)
)
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